WorldWideScience

Sample records for investigating molecular interactions

  1. Investigation of the molecular level interactions between mucins and food proteins: Spectroscopic, tribological and rheological studies

    DEFF Research Database (Denmark)

    Celebioglu, Hilal Yilmaz

    The thesis investigated the structure and molecular-level interaction of β-lactoglobulin (BLG) and mucins, representing major components of the dairy products and saliva/digestion systems, respectively. Mucins are long glycoprotein molecules responsible for the gel nature of the mucous layer covers...... submaxillary mucin (BSM), a major salivary protein, were studied using high and low field Nuclear Magnetic Resonance (NMR), Dynamic Light Scattering (DLS), and Circular Dichroism (CD) spectroscopy. The zeta potentials of the proteins were also measured to provide information on the role of electrostatic forces...

  2. The interaction between 4-aminoantipyrine and bovine serum albumin: Multiple spectroscopic and molecular docking investigations

    International Nuclear Information System (INIS)

    Teng Yue; Liu Rutao; Li Chao; Xia Qing; Zhang Pengjun

    2011-01-01

    4-Aminoantipyrine (AAP) is widely used in the pharmaceutical industry, in biochemical experiments and in environmental monitoring. AAP as an aromatic pollutant in the environment poses a great threat to human health. To evaluate the toxicity of AAP at the protein level, the effects of AAP on bovine serum albumin (BSA) were investigated by multiple spectroscopic techniques and molecular modeling. After the inner filter effect was eliminated, the experimental results showed that AAP effectively quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites, the binding constant, the thermodynamic parameters and binding subdomain were measured, and indicated that AAP could spontaneously bind with BSA on subdomain IIIA through electrostatic forces. Molecular docking results revealed that AAP interacted with the Glu 488 and Glu 502 residues of BSA. Furthermore, the conformation of BSA was demonstrably changed in the presence of AAP. The skeletal structure of BSA loosened, exposing internal hydrophobic aromatic ring amino acids and peptide strands to the solution.

  3. Polyphilic Interactions as Structural Driving Force Investigated by Molecular Dynamics Simulation (Project 7

    Directory of Open Access Journals (Sweden)

    Christopher Peschel

    2017-09-01

    Full Text Available We investigated the effect of fluorinated molecules on dipalmitoylphosphatidylcholine (DPPC bilayers by force-field molecular dynamics simulations. In the first step, we developed all-atom force-field parameters for additive molecules in membranes to enable an accurate description of those systems. On the basis of this force field, we performed extensive simulations of various bilayer systems containing different additives. The additive molecules were chosen to be of different size and shape, and they included small molecules such as perfluorinated alcohols, but also more complex molecules. From these simulations, we investigated the structural and dynamic effects of the additives on the membrane properties, as well as the behavior of the additive molecules themselves. Our results are in good agreement with other theoretical and experimental studies, and they contribute to a microscopic understanding of interactions, which might be used to specifically tune membrane properties by additives in the future.

  4. Investigation of the interaction of naringin palmitate with bovine serum albumin: spectroscopic analysis and molecular docking.

    Directory of Open Access Journals (Sweden)

    Xia Zhang

    Full Text Available BACKGROUND: Bovine serum albumin (BSA contains high affinity binding sites for several endogenous and exogenous compounds and has been used to replace human serum albumin (HSA, as these two compounds share a similar structure. Naringin palmitate is a modified product of naringin that is produced by an acylation reaction with palmitic acid, which is considered to be an effective substance for enhancing naringin lipophilicity. In this study, the interaction of naringin palmitate with BSA was characterised by spectroscopic and molecular docking techniques. METHODOLOGY/PRINCIPAL FINDINGS: The goal of this study was to investigate the interactions between naringin palmitate and BSA under physiological conditions, and differences in naringin and naringin palmitate affinities for BSA were further compared and analysed. The formation of naringin palmitate-BSA was revealed by fluorescence quenching, and the Stern-Volmer quenching constant (KSV was found to decrease with increasing temperature, suggesting that a static quenching mechanism was involved. The changes in enthalpy (ΔH and entropy (ΔS for the interaction were detected at -4.11 ± 0.18 kJ·mol(-1 and -76.59 ± 0.32 J·mol(-1·K(-1, respectively, which indicated that the naringin palmitate-BSA interaction occurred mainly through van der Waals forces and hydrogen bond formation. The negative free energy change (ΔG values of naringin palmitate at different temperatures suggested a spontaneous interaction. Circular dichroism studies revealed that the α-helical content of BSA decreased after interacting with naringin palmitate. Displacement studies suggested that naringin palmitate was partially bound to site I (subdomain IIA of the BSA, which was also substantiated by the molecular docking studies. CONCLUSIONS/SIGNIFICANCE: In conclusion, naringin palmitate was transported by BSA and was easily removed afterwards. As a consequence, an extension of naringin applications for use in food, cosmetic

  5. Molecular dynamics investigation of nanoscale substrate topography and its interaction with liquids

    Science.gov (United States)

    Cordeiro Rodrigues, Jhonatam

    Nanotechnology has been presenting successful applications in several areas. However, experimentation with nanoscale materials is costly and limited in analysis capability. This research investigates the use of molecular dynamics (MD) simulations to model and study nanomaterials and manufacturing processes. MD simulations are employed to reduce cost, optimize design, increase productivity and allow for the investigation of material interactions not yet observable through experimentation. This work investigates the interaction of water with substrates at the nanoscale. The effect of temperature, droplet impingement velocities and size, as well as substrate material, are investigated at the nanoscale. Several substrate topography designs were modeled to reveal their influence on the wettability of the substrate. Nanoscale gold and silicon substrates are more hydrophilic at higher temperatures than at room temperature. The reduction in droplet diameter increases its wettability. High impingement velocity of droplets does not influence final wettability of substrates but induces higher diffusion rates of droplets in a heated environment. Droplets deposited over a gradient of surface exposure presents spontaneous movement. The Leidenfrost effect was investigated at the nanoscale. Droplets of 4 and 10nm in diameter presented behaviors pertinent to the Leidenfrost effect at 373K, significantly lower than at micro scale and of potential impact to the field. Topographical features were manipulated using superhydrophobic coating resulting in micro whiskers. Nanoimprint lithography (NIL) was used to manufacture substrate topographies at the nanoscale. Water droplets were deposited on the substrates and their wettability was measured using droplet contact angles. Lower surface area exposure resulted in higher contact angles. The experimental relationships between surface topography and substrate wettability were used to validate the insights gained from MD simulations for

  6. Investigation of the Josephin Domain protein-protein interaction by molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Marco A Deriu

    Full Text Available Spinocerebellar ataxia (SCA 3, the most common form of SCA, is a neurodegenerative rare disease characterized by polyglutamine tract expansion and self-assembly of Ataxin3 (At3 misfolded proteins into highly organized fibrillar aggregates. The At3 N-terminal Josephin Domain (JD has been suggested as being responsible for mediating the initial phase of the At3 double-step fibrillogenesis. Several issues concerning the residues involved in the JD's aggregation and, more generally, the JD clumping mechanism have not been clarified yet. In this paper we present an investigation focusing on the JD protein-protein interaction by means of molecular modeling. Our results suggest possible aminoacids involved in JD contact together with local and non-local effects following JD dimerization. Surprisingly, JD conformational changes following the binding may involve ubiquitin binding sites and hairpin region even though they do not pertain to the JD interaction surfaces. Moreover, the JD binding event has been found to alter the hairpin open-like conformation toward a closed-like arrangement over the simulated timescale. Finally, our results suggest that the JD aggregation might be a multi-step process, with an initial fast JD-JD binding mainly driven by Arg101, followed by slower structural global rearrangements involving the exposure to the solvent of Leu84-Trp87, which might play a role in a second step of JD aggregation.

  7. Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiyong, E-mail: wangry@zzu.edu.cn; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun, E-mail: chjsong@zzu.edu.cn; Chang, Junbiao, E-mail: changjunbiao@zzu.edu.cn

    2014-10-15

    In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking.

  8. MDM2-MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance.

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2-MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2-MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD ) in the micromolar range for the MDM2-MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2-MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2-MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation.

  9. Investigating the Interaction of Fe Nanoparticles with Lysozyme by Biophysical and Molecular Docking Studies.

    Directory of Open Access Journals (Sweden)

    Zahra Aghili

    Full Text Available Herein, the interaction of hen egg white lysozyme (HEWL with iron nanoparticle (Fe NP was investigated by spectroscopic and docking studies. The zeta potential analysis revealed that addition of Fe NP (6.45±1.03 mV to HEWL (8.57±0.54 mV can cause to greater charge distribution of nanoparticle-protein system (17.33±1.84 mV. In addition, dynamic light scattering (DLS study revealed that addition of Fe NP (92.95±6.11 nm to HEWL (2.68±0.37 nm increases suspension potential of protein/nanoparticle system (51.17±3.19 nm. Fluorescence quenching studies reveled that both static and dynamic quenching mechanism occur and hydrogen bond and van der Waals interaction give rise to protein-NP system. Synchronous fluorescence spectroscopy of HEWL in the presence of Fe NP showed that the emission maximum wavelength of tryptophan (Trp residues undergoes a red-shift. ANS fluorescence data indicated a dramatic exposure of hydrophobic residues to the solvent. The considerable reduction in melting temperature (T(m of HEWL after addition of Fe NP determines an unfavorable interaction system. Furthermore circular dichoroism (CD experiments demonstrated that, the secondary structure of HEWL has not changed with increasing Fe NP concentrations; however, some conformational changes occur in tertiary structure of HEWL. Moreover, protein-ligand docking study confirmed that the Fe NP forms hydrogen bond contacts with HEWL.

  10. Investigation on the interactions of clenbuterol to bovine serum albumin and lysozyme by molecular fluorescence technique.

    Science.gov (United States)

    Bi, Shuyun; Pang, Bo; Wang, Tianjiao; Zhao, Tingting; Yu, Wang

    2014-01-01

    Clenbuterol interacting with bovine serum albumin (BSA) or lysozyme (LYS) in physiological buffer (pH 7.4) was investigated by the fluorescence spectroscopy and UV-vis absorption spectroscopy. The results indicated that clenbuterol quenched the intrinsic fluorescence of BSA and LYS via a static quenching procedure. The binding constants of clenbuterol with BSA and LYS were 1.16×10(3) and 1.49×10(3) L mol(-1) at 291 K. The values of ΔH and ΔS implied that hydrophobic and electrostatic interaction played a major role in stabilizing the complex (clenbuterol-BSA or clenbuterol-LYS). In the presence of Fe2+, Fe3+, Cu2+, Mg2+, Ca2+, or Zn2+, the binding constants of clenbuterol to BSA or LYS had no significant differences. The distances between the donor (BSA or LYS) and acceptor (clenbuterol) were 2.61 and 2.19 nm for clenbuterol-BSA and clenbuterol-LYS respectively. Furthermore, synchronous fluorescence spectrometry was used to analyze the conformational changes of BSA and LYS. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Investigating the Interaction Pattern and Structural Elements of a Drug-Polymer Complex at the Molecular Level.

    Science.gov (United States)

    Nie, Haichen; Mo, Huaping; Zhang, Mingtao; Song, Yang; Fang, Ke; Taylor, Lynne S; Li, Tonglei; Byrn, Stephen R

    2015-07-06

    Strong associations between drug and polymeric carriers are expected to contribute to higher drug loading capacities and better physical stability of amorphous solid dispersions. However, molecular details of the interaction patterns and underlying mechanisms are still unclear. In the present study, a series of amorphous solid dispersions of clofazimine (CLF), an antileprosy drug, were prepared with different polymers by applying the solvent evaporation method. When using hypromellose phthalate (HPMCP) as the carrier, the amorphous solid dispersion system exhibits not only superior drug loading capacity (63% w/w) but also color change due to strong drug-polymer association. In order to further explain these experimental observations, the interaction between CLF and HPMCP was investigated in a nonpolar volatile solvent system (chloroform) prior to forming the solid dispersion. We observed significant UV/vis and (1)H NMR spectral changes suggesting the protonation of CLF and formation of ion pairs between CLF and HPMCP in chloroform. Furthermore, nuclear Overhauser effect spectroscopy (NOESY) and diffusion order spectroscopy (DOSY) were employed to evaluate the strength of associations between drug and polymers, as well as the molecular mobility of CLF. Finally, by correlating the experimental values with quantum chemistry calculations, we demonstrate that the protonated CLF is binding to the carboxylate group of HPMCP as an ion pair and propose a possible structural model of the drug-polymer complex. Understanding the drug and carrier interaction patterns from a molecular perspective is critical for the rational design of new amorphous solid dispersions.

  12. Investigation of the Interaction between Patulin and Human Serum Albumin by a Spectroscopic Method, Atomic Force Microscopy, and Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Li Yuqin

    2014-01-01

    Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.

  13. Atomic and Molecular Interactions

    International Nuclear Information System (INIS)

    2002-01-01

    The Gordon Research Conference (GRC) on Atomic and Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field

  14. DFT/CCSD(T) investigation of the interaction of molecular hydrogen with carbon nanostructures

    Czech Academy of Sciences Publication Activity Database

    Rubeš, Miroslav; Bludský, Ota

    2009-01-01

    Roč. 10, č. 11 (2009), s. 1868-1873 ISSN 1439-4235 R&D Projects: GA AV ČR IAA400550613; GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular hydrogen * physisorption * graphene * nanotubes Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.453, year: 2009

  15. Investigation of the interaction of aurantio-obtusin with human serum albumin by spectroscopic and molecular docking methods.

    Science.gov (United States)

    Liu, Jianming; Yan, Xuyang; Yue, Yuanyuan; Zhao, Shufang

    2018-02-01

    The interaction between human serum albumin (HSA) and aurantio-obtusin was investigated by spectroscopic techniques combined with molecular docking. The Stern-Volmer quenching constants (K SV ) decreased from 8.56 × 10 5  M -1 to 5.13 × 10 5  M -1 with a rise in temperatures from 289 to 310 K, indicating that aurantio-obtusin produced a static quenching of the intrinsic fluorescence of HSA. Time-resolved fluorescence studies proved again that the static quenching mechanism was involved in the interaction. The sign and magnitude of the enthalpy change as well as the entropy change suggested involvement of hydrogen bonding and hydrophobic interaction in aurantio-obtusin-HSA complex formation. Aurantio-obtusin binding to HSA produced significant alterations in secondary structures of HSA, as revealed from the time-resolved fluorescence, Fourier transform infrared (FT-IR) spectroscopy, three-dimensional (3D) fluorescence and circular dichroism (CD) spectral results. Molecular docking study and site marker competitive experiment confirmed aurantio-obtusin bound to HSA at site I (subdomain IIA). Copyright © 2017 John Wiley & Sons, Ltd.

  16. Molecular interaction of 2,4-diacetylphloroglucinol (DAPG) with human serum albumin (HSA): The spectroscopic, calorimetric and computational investigation

    Science.gov (United States)

    Pragna Lakshmi, T.; Mondal, Moumita; Ramadas, Krishna; Natarajan, Sakthivel

    2017-08-01

    Drug molecule interaction with human serum albumin (HSA) affects the distribution and elimination of the drug. The compound, 2,4-diacetylphloroglucinol (DAPG) has been known for its antimicrobial, antiviral, antihelminthic and anticancer properties. However, its interaction with HSA is not yet reported. In this study, the interaction between HSA and DAPG was investigated through steady-state fluorescence, time-resolved fluorescence (TRF), circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetry (ITC), molecular docking and molecular dynamics simulation (MDS). Fluorescence spectroscopy results showed the strong quenching of intrinsic fluorescence of HSA due to interaction with DAPG, through dynamic quenching mechanism. The compound bound to HSA with reversible and moderate affinity which explained its easy diffusion from circulatory system to target tissue. The thermodynamic parameters from fluorescence spectroscopic data clearly revealed the contribution of hydrophobic forces but, the role of hydrogen bonds was not negligible according to the ITC studies. The interaction was exothermic and spontaneous in nature. Binding with DAPG reduced the helical content of protein suggesting the unfolding of HSA. Site marker fluorescence experiments revealed the change in binding constant of DAPG in the presence of site I (warfarin) but not site II marker (ibuprofen) which confirmed that the DAPG bound to site I. ITC experiments also supported this as site I marker could not bind to HSA-DAPG complex while site II marker was accommodated in the complex. In silico studies further showed the lowest binding affinity and more stability of DAPG in site I than in site II. Thus the data presented in this study confirms the binding of DAPG to the site I of HSA which may help in further understanding of pharmacokinetic properties of DAPG.

  17. Investigation on molecular interactions of antibiotics in alcohols using volumetric and acoustic studies at different temperatures

    International Nuclear Information System (INIS)

    Naseem, Bushra; Iftikhar, Madeeha

    2017-01-01

    Highlights: • Antibiotics in different alcohols are used to study their interactions in solutions. • Density and sound velocity for antibiotic solutions are measured at different temperatures. • Apparent molar volume and isentropic compressibility are used to calculate partial molar quantities. • Acoustical parameters are calculated and discussed in terms of solute–solute and solute–solvent interactions. - Abstract: The density and sound velocity for pure alcohols (methanol, ethanol, iso-propanol and n-butanol) and molal solutions of nitroimidazoles (metronidazole (MNZ) and dimetridazole (DMZ) have been measured at different temperatures (293.15–313.15 K). Different volumetric and acoustical parameters like apparent molar volume (V ϕ ), partial molar volume (VЛљ ϕ ), apparent molar isentropic compressibility (K ϕ ), partial molar isentropic compressibility (KЛљ ϕ ), hydration number (n H ), acoustic impedance (Z) and intermolecular free length (L f ) of antibiotic solutions were calculated from the experimental values of density and sound velocity. The derived values have been used to explore the solute–solute and solute–solvent interactions. The V ϕ values are positive and K ϕ values are negative in both antibiotics, indicative of strong solute–solvent interactions and closely packed structure of antibiotics in alcohols. The decreasing trend of L f with increasing antibiotic concentration shows the presence of strong intermolecular interactions in solutions.

  18. Interaction of human chymase with ginkgolides, terpene trilactones of Ginkgo biloba investigated by molecular docking simulations.

    Science.gov (United States)

    Dubey, Amit; Marabotti, Anna; Ramteke, Pramod W; Facchiano, Angelo

    2016-04-29

    The search for natural chymase inhibitors has a good potential to provide a novel therapeutic approach against the cardiovascular diseases and other heart ailments. We selected from literature 20 promising Ginkgo biloba compounds, and tested them for their potential ability to bind chymase enzyme using docking and a deep analysis of surface pocket features. Docking results indicated that the compounds may interact with the active site of human chymase, with favorable distinct interactions with important residues Lys40, His57, Lys192, Phe191, Val146, Ser218, Gly216, and Ser195. In particular, proanthocyanidin is the one with the best-predicted binding energy, with seven hydrogen bonds. Interestingly, all active G. biloba compounds have formed the hydrogen bond interactions with the positively charged Lys192 residue at the active site, involved in the mechanism of pH enhancement for the cleavage of angiotensin I site. Ginkgolic acid and proanthocyanidin have better predicted binding energy towards chymase than other serine proteases, i.e kallikrein, tryptase and elastase, suggesting specificity for chymase inhibition. Our study suggests these G. biloba compounds are a promising starting point for developing chymase inhibitors for the potential development of future drugs. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Multispectroscopic and molecular modeling approach to investigate the interaction of diclofop-methyl enantiomers with human serum albumin

    International Nuclear Information System (INIS)

    Zhang, Ping; Liu, Donghui; Li, Zhe; Shen, Zhigang; Wang, Peng; Zhou, Meng; Zhou, Zhiqiang; Zhu, Wentao

    2014-01-01

    Pesticides and related environmental contaminants have always been threated to human health due to their intrinsic toxicity. In the context of this contribution, the interaction between diclofop-methyl (DM) enantiomers and human serum albumin (HSA) has been characterized by steady state and three-dimensional fluorescence, molecular modeling, circular dichroism (CD) and ultraviolet–visible (UV–vis) spectroscopy. The binding constants significantly showed the binding was enantioselective and HSA had higher affinity for S-DM. The thermodynamic parameters of the binding reaction (ΔG, ΔH and ΔS) clearly signified that hydrophobic effects and H-bonds contribute to the formation of DM-HSA complex. The alterations of protein secondary structure in the presence of DM enantiomers were confirmed by CD spectroscopy, UV–vis and three-dimensional fluorescence spectroscopy. In addition, both fluorescence probe study and molecular modeling simulation evidenced the binding of DM enantiomers to HSA primarily took place in subdomain IIIA (Sudlow's site II). This investigation highlights the binding mechanism, specific binding sites and binding region of DM enantiomers on human serum albumin at the first time. Besides, such task can provide important insight to the interaction of the physiological protein HSA with chiral aryloxyphenoxypropionate herbicides and give support to the human health risk assessment. - Highlights: • The binding of DM enantiomers to HSA was enantioselective. • HSA had higher affinity for S-DM than R-DM. • Hydrophobic effects and hydrogen bonds were involved in the DM-HSA interaction. • The binding of DM enantiomers to HSA primarily took place in Sudlow's site II. • DM enantiomers could alter the second structure of HSA

  20. Multispectroscopic and molecular modeling approach to investigate the interaction of diclofop-methyl enantiomers with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ping; Liu, Donghui; Li, Zhe; Shen, Zhigang; Wang, Peng [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Zhou, Meng [Business School, University of Bedfordshire, Luton LU1 3JU (United Kingdom); Zhou, Zhiqiang [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Zhu, Wentao, E-mail: wentaozhu@cau.edu.cn [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China)

    2014-11-15

    Pesticides and related environmental contaminants have always been threated to human health due to their intrinsic toxicity. In the context of this contribution, the interaction between diclofop-methyl (DM) enantiomers and human serum albumin (HSA) has been characterized by steady state and three-dimensional fluorescence, molecular modeling, circular dichroism (CD) and ultraviolet–visible (UV–vis) spectroscopy. The binding constants significantly showed the binding was enantioselective and HSA had higher affinity for S-DM. The thermodynamic parameters of the binding reaction (ΔG, ΔH and ΔS) clearly signified that hydrophobic effects and H-bonds contribute to the formation of DM-HSA complex. The alterations of protein secondary structure in the presence of DM enantiomers were confirmed by CD spectroscopy, UV–vis and three-dimensional fluorescence spectroscopy. In addition, both fluorescence probe study and molecular modeling simulation evidenced the binding of DM enantiomers to HSA primarily took place in subdomain IIIA (Sudlow's site II). This investigation highlights the binding mechanism, specific binding sites and binding region of DM enantiomers on human serum albumin at the first time. Besides, such task can provide important insight to the interaction of the physiological protein HSA with chiral aryloxyphenoxypropionate herbicides and give support to the human health risk assessment. - Highlights: • The binding of DM enantiomers to HSA was enantioselective. • HSA had higher affinity for S-DM than R-DM. • Hydrophobic effects and hydrogen bonds were involved in the DM-HSA interaction. • The binding of DM enantiomers to HSA primarily took place in Sudlow's site II. • DM enantiomers could alter the second structure of HSA.

  1. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    International Nuclear Information System (INIS)

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo; Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong; Pratontep, Sirapat; Puttipipatkhachorn, Satit

    2010-01-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ( 1 H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1 H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1 H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  2. Investigating Molecular Interactions

    DEFF Research Database (Denmark)

    Clausen, Henrik Fanø

    2010-01-01

    of the experimentally determined charge density distribution of a cobalt coordination polymer at 15K is presented in Chapter 4. The study exemplifies the immense advances in experimental charge density analysis made possible by utilization of intense third generation synchrotrons, as even the single crystal structural......This thesis is the result of four years work at the Laboratory of Inorganic Chemistry, Department of Chemistry, Aarhus University. I have decided to divide the thesis into seven chapters, where the two first chapters introduce the theory and compound classes of this dissertation. The next two...... chapters concern transition metal coordination polymers and the last three describe hydroquinone co-crystals and clathrate structures. Even though, the goal of the thesis has been to give account of all the work that I have performed, I have chosen to leave out results of certain projects, and confine...

  3. Interactive molecular dynamics

    Science.gov (United States)

    Schroeder, Daniel V.

    2015-03-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.

  4. Investigation on the Molecular Interactions Stabilizing the Structure of α-synuclein Fibril: An In silico Study.

    Science.gov (United States)

    Sanjeev, Airy; Mattaparthi, Venkata S K

    2017-01-01

    Amyloid fibrils represent stable form of many misfolded proteins associated with numerous diseases like Parkinson's Disease (PD), Type II diabetes and Alzheimer's disease (AD). α-synuclein protein is the principal constituent of Lewy bodies that are considered to be pathological hallmark of PD. Recently, a high resolution structure of α-synuclein protein that stacks together forming fibrils in brains of PD patients were identified. What structural features drive pathology of PD can now be possibly answered from the fibril structure of protein. To understand the molecular interactions those are responsible for the stability of the α- synuclein fibril structure. To study the molecular interactions stabilizing the α-synuclein fibril, we have used a high resolution amyloid fibril structure (PDB ID 2N0A). The molecular interactions in fibril structure were studied using PDBSum server. We then looked into the destabilization of α-synuclein fibril by disrupting the salt-bridge holding the strands and probable methods to decompose fibril into structurally distinct units using Top-domain web-server. The effect of salt-bridges on the stability of the fibril structure was studied by mutating one of the residues involved in the formation of salt-bridge using molecular dynamics simulation. Our results indicate a finite salt-bridge (E46-K80) is crucial for stability of protofibril. Besides, we observed hydrogen bonds and non-bonded contacts involved in fibril stabilization. We noticed α-synuclein dimer predominantly exists in conformations distinct from fibril. We characterized the salient molecular interactions in α-synuclein fibril and these findings may be useful to design potential inhibitors for the treatment of PD. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  5. Investigations on the interactions of diclofenac sodium with HSA and ctDNA using molecular modeling and multispectroscopic methods

    Science.gov (United States)

    Cui, Yanrui; Hao, Erjun; Hui, Guangquan; Guo, Wei; Cui, Fengling

    2013-06-01

    A tentative study on interaction of diclofenac sodium (DF-Na) with human serum albumin (HSA) and calf thymus DNA (ctDNA) was conducted by using multi-spectroscopic and molecular modeling techniques under simulative physiological conditions. The results of spectroscopic measurements suggested that the quenching mechanisms were static quenching. Three-dimensional fluorescence spectroscopy clearly demonstrated the occurrence of conformational changes of HSA with addition of DF-Na. In addition, competitive studies with ethidium bromide (EB) have shown that DF-Na can bind to ctDNA relatively strong via groove binding. Based on the values of thermodynamic parameters and the results of molecular modeling, it was confirmed that hydrophobic forces and hydrogen bond were the mainly binding forces in DF-Na-HSA and DF-Na-DNA systems. The binding distance between DF-Na and HSA was also determined using the theory of the Förster energy transference.

  6. Probing the interaction of a therapeutic flavonoid, pinostrobin with human serum albumin: multiple spectroscopic and molecular modeling investigations.

    Directory of Open Access Journals (Sweden)

    Shevin R Feroz

    Full Text Available Interaction of a pharmacologically important flavonoid, pinostrobin (PS with the major transport protein of human blood circulation, human serum albumin (HSA has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 10(5 M(-1 at 25°C between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol(-1 K(-1 and ΔH = -15.48 kJ mol(-1 and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow's site I, located at subdomain IIA, and was well supported by the molecular modelling data.

  7. A multispectroscopic and molecular docking investigation of the binding interaction between serum albumins and acid orange dye

    Science.gov (United States)

    Naveenraj, Selvaraj; Solomon, Rajadurai Vijay; Mangalaraja, Ramalinga Viswanathan; Venuvanalingam, Ponnambalam; Asiri, Abdullah M.; Anandan, Sambandam

    2018-03-01

    The interaction of Acid Orange 10 (AO10) with bovine serum albumin (BSA) was investigated comparatively with that of human serum albumin (HSA) using multispectroscopic techniques for understanding their toxic mechanism. Further, density functional theory calculations and docking studies have been carried out to gain more insights into the nature of interactions existing between AO10 and serum albumins. The fluorescence results suggest that AO10 quenched the fluorescence of BSA through the combination of static and dynamic quenching mechanism. The same trend was followed in the interaction of AO10 with HSA. In addition to the type of quenching mechanism, the fluorescence spectroscopic results suggest that the binding occurs near the tryptophan moiety of serum albumins and the binding. AO10 has more binding affinity towards BSA than HSA. An AO10-Trp model has been created to explicitly understand the Csbnd Htbnd π interactions from Bader's quantum theory of atoms in molecules analysis which confirmed that AO10 bind more strongly with BSA than that of HSA due to the formation of three hydrogen bonds with BSA whereas it forms two hydrogen bonds in the case of HSA. These obtained results provide an in-depth understanding of the interaction of the acid azo dye AO10 with serum albumins. This interaction study provides insights into the underlying reasons for toxicity of AO10 relevant to understand its effect on bovids and humans during the blood transportation process.

  8. An Investigation of Bacterial Protein Interactions as a Primary Research Project in a Sophomore-Level Molecular Biology Course

    Directory of Open Access Journals (Sweden)

    Jean A. Cardinale

    2011-09-01

    Full Text Available Longer term research activities that may be incorporated in undergraduate courses are a powerful tool for promoting student interest and learning, developing cognitive process skills, and allowing undergraduates to experience real research activities in which they may not otherwise have the opportunity to participate. The challenge to doing so in lower-level courses is that students may have not fully grasped the scientific concepts needed to undertake such research endeavors, and that they may be discouraged if activities are perceived to be too challenging. The paper describes how a bacterial protein:protein interaction detection system was adapted and incorporated into the laboratory component of a sophomore-level Molecular Cell Biology course. The project was designed to address multiple learning objectives connecting course content to the laboratory activities, as well as teach basic molecular biology laboratory skills and procedures in the context of a primary research activity. Pre- and posttesting and student surveys both suggest that the laboratory curriculum resulted in significant learning gains, as well as being well received and valued by the students.

  9. An investigation of bacterial protein interactions as a primary research project in a sophomore-level molecular biology course.

    Science.gov (United States)

    Cardinale, Jean A

    2011-01-01

    Longer term research activities that may be incorporated in undergraduate courses are a powerful tool for promoting student interest and learning, developing cognitive process skills, and allowing undergraduates to experience real research activities in which they may not otherwise have the opportunity to participate. The challenge to doing so in lower-level courses is that students may have not fully grasped the scientific concepts needed to undertake such research endeavors, and that they may be discouraged if activities are perceived to be too challenging. The paper describes how a bacterial protein:protein interaction detection system was adapted and incorporated into the laboratory component of a sophomore-level Molecular Cell Biology course. The project was designed to address multiple learning objectives connecting course content to the laboratory activities, as well as teach basic molecular biology laboratory skills and procedures in the context of a primary research activity. Pre- and posttesting and student surveys both suggest that the laboratory curriculum resulted in significant learning gains, as well as being well received and valued by the students.

  10. Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation.

    Directory of Open Access Journals (Sweden)

    Matteo eLambrughi

    2012-11-01

    Full Text Available Cyclin-dependent kinase inhibitors (CKIs are key regulatory proteins of the eukaryotic cell cycle, which modulate cyclin-dependent kinase (Cdk activity. CKIs perform their inhibitory effect by the formation of ternary complexes with a target kinase and its cognate cyclin. These regulators generally belong to the class of intrinsically disordered proteins (IDPs, which lack a well-defined and organized three-dimensional structure in their free state, undergoing folding upon binding to specific partners. Unbound IDPs are not merely random-coil structures, but can present intrinsically folded structural units (IFSUs and collapsed conformations. These structural features can be relevant to protein function in vivo.The yeast CKI Sic1 is a 284-amino acid IDP that binds to Cdk1 in complex with the Clb5,6 cyclins, preventing phosphorylation of G1 substrates and, therefore, entrance to the S phase. Sic1 degradation, triggered by multiple phosphorylation events, promotes cell-cycle progression. Previous experimental studies pointed out a propensity of Sic1 and its isolated domains to populate both extended and compact conformations. The present contribution provides models of the compact conformations of the Sic1 kinase-inhibitory domain (KID by all-atom molecular-dynamics simulations in explicit solvent and in the absence of interactors. The results are integrated by spectroscopic and spectrometric data. Helical IFSUs are identified, along with networks of intramolecular interactions. The results identify a group of hub residues and electrostatic interactions which are likely to be involved in the stabilization of globular states.

  11. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    2016-01-01

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD) in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. PMID:27621617

  12. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Directory of Open Access Journals (Sweden)

    Moscetti I

    2016-08-01

    Full Text Available Ilaria Moscetti,1 Emanuela Teveroni,2,3 Fabiola Moretti,3 Anna Rita Bizzarri,1 Salvatore Cannistraro1 1Biophysics and Nanoscience Centre, Department DEB, Università della Tuscia, Viterbo, Italy; 2Department of Endocrinology and Metabolism, Università Cattolica di Roma, Roma, Italy; 3Institute of Cell Biology and Neurobiology, Consiglio Nazionale delle Ricerche (CNR, Roma, Italy Abstract: Murine double minute 2 (MDM2 and 4 (MDM4 are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. Keywords: MDM2, MDM4, atomic force spectroscopy, surface plasmon resonance

  13. Detection of molecular interactions

    Science.gov (United States)

    Groves, John T [Berkeley, CA; Baksh, Michael M [Fremont, CA; Jaros, Michal [Brno, CH

    2012-02-14

    A method and assay are described for measuring the interaction between a ligand and an analyte. The assay can include a suspension of colloidal particles that are associated with a ligand of interest. The colloidal particles are maintained in the suspension at or near a phase transition state from a condensed phase to a dispersed phase. An analyte to be tested is then added to the suspension. If the analyte binds to the ligand, a phase change occurs to indicate that the binding was successful.

  14. Molecular Interactions at Membranes

    DEFF Research Database (Denmark)

    Jagalski, Vivien

    Biological membranes are essential and complex structures in every living cell consisting of a fluid lipid bilayer sheet and membrane proteins. Its significance makes biological membranes not only interesting for medical research, but also has made it a target for toxins in the course of evolution....... Today, we know more than ever before about the properties of biological membranes. Advanced biophysical techniques and sophisticated membrane models allow us to answer specific questions about the structure of the components within membranes and their interactions. However, many detailed structural...... mechanisms of membrane compounds, including compounds associated with membranes, are still unknown due to the challenges that arise when probing the hydrophobic nature of the membrane's interior. For integral membrane proteins that span through the entire membrane, the amphiphilic environment is essential...

  15. Investigating the molecular pathway through which L-Lactate interacts with synaptic NMDAR to modulate neuronal plasticity

    KAUST Repository

    Ibrahim, Engy

    2016-12-01

    In the brain, glycogen, the storage form of glucose, is exclusively localized in astrocytes (Magistretti and Allaman, 2015). Glycogenolysis leads to the production of L-lactate, which is shuttled to neurons for ATP production. Interestingly, L-lactate was recently shown to be not only a source of energy, but also a signaling molecule to neurons. This was demonstrated through the inhibition of L-lactate production or transport in an inhibitory avoidance paradigm, where the rodents developed amnesia. This inhibition of memory consolidation was rescued by L-lactate and not by equicaloric glucose emphasizing that L-lactate acts as a signaling molecule as well (Suzuki et al., 2011). A recent study in our laboratory suggests that the action of L-lactate takes place through a cascade of molecular events via the modulation of N-methyl-D-aspartate receptor (NMDAR) activity (Yang et al., 2014). Since NADH produced similar results to those seen with L-lactate, it was hypothesized that the action of the latter is based on altering the redox state of the cell, in particular in view of the fact that redox-sensitive sites are present on the NMDAR. However, the precise molecular mechanism underlying the apparent change in the NMDAR activity is not fully elucidated. The objective of this study is to explore those mechanisms.

  16. Topology of molecular interaction networks

    NARCIS (Netherlands)

    Winterbach, W.; Van Mieghem, P.; Reinders, M.; Wang, H.; De Ridder, D.

    2013-01-01

    Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over

  17. Using Affinity Chromatography to Investigate Novel Protein-Protein Interactions in an Undergraduate Cell and Molecular Biology Lab Course

    Science.gov (United States)

    Belanger, Kenneth D.

    2009-01-01

    Inquiry-driven lab exercises require students to think carefully about a question, carry out an investigation of that question, and critically analyze the results of their investigation. Here, we describe the implementation and assessment of an inquiry-based laboratory exercise in which students obtain and analyze novel data that contribute to our…

  18. Molecular dynamics simulation on the interaction mechanism ...

    Indian Academy of Sciences (India)

    Investigation on the microscopic interaction between polymer inhibitors and calcium phosphate contributes to the understanding of their scale inhibition mechanism. The results obtained may provide a theoretical guidance to developing new scale inhibitors. In this study, molecular dynamics simulations have been ...

  19. Investigation on the Interaction between Cyclophosphamide and Lysozyme in the Presence of Three Different Kind of Cyclodextrins: Determination of the Binding Mechanism by Spectroscopic and Molecular Modeling Techniques

    Directory of Open Access Journals (Sweden)

    Jamshidkhan Chamani

    2013-01-01

    Full Text Available The interactions between cyclophosphamide (CYC and lysozyme (LYZ in the presence of different cyclodextrins (CDs were investigated by UV absorption, fluorescence spectroscopy, circular dichroism (CD, and molecular modeling techniques under imitated physiological conditions. The UV absorption results showed the formation of complexes between CYC and LYZ in the presence of different CDs. Fluorescence data show that CYC has a stronger quenching effect on LYZ, and the red shifts suggested that the microenvironment of Trp residues was changed and became more hydrophilic. The interaction of CYC with LYZ and quenching properties of the complexes caused strong static fluorescence quenching in binary and ternary systems. The binding affinities as well as the number of binding sites were obtained from interaction between CYC and LYZ in the presence of different CDs as binary and ternary systems by modified Stern-Volmer plots. The Resonance Light Scattering (RLS technique was utilized to investigate the effect of drug and CDs on conformational changes of LYZ as separate and simultaneous. The results suggested that the enhancement of RLS intensity was attributed to the formation of a complex between drug and protein in absence and presence of CDs. The effect of CYC and cyclodextrins on the conformation of LYZ was analyzed using synchronous fluorescence spectroscopy. Our results revealed that the fluorescence quenching of LYZ originated from the Trp and Tyr residues, and demonstrated conformational changes of LYZ with the addition of CYC and CDs. The molecular distances between the donor (LYZ and acceptor (CYC and CDs in binary and ternary systems were estimated according to Forster’s theory and showed static quenching for protein with CYC in the presence of CDs. The CD spectra indicated that the binding of the CYC induced secondary structural changes in LYZ in binary and ternary systems. Molecular modeling suggested the binding sites of CYC in the ternary

  20. Atomic-scale investigation of the interactions between tetrabromobisphenol A, tetrabromobisphenol S and bovine trypsin by spectroscopies and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Ding, Keke; Zhang, Huanxin; Wang, Haifei; Lv, Xuan; Pan, Liumeng; Zhang, Wenjing; Zhuang, Shulin

    2015-01-01

    Highlights: • The interaction of TBBPA/TBBPS with bovine trypsin was deciphered for the first time. • The fluorescence of bovine trypsin was quenched in a concentration-dependent mode. • TBBPA and TBBPS bind at the ANS binding site with distinct binding modes. • TBBPS has a higher binding affinity toward bovine trypsin than TBBPA. • Our in vitro and in silico approach is helpful to assess risk of TBBPA-related BFRs. - Abstract: Tetrabromobisphenol A (TBBPA) and its replacement alternative tetrabromobisphenol S (TBBPS) are used widely as brominated flame retardants (BFRs). However, the potential risk of their effects on bovine trypsin remains largely unknown. We investigated the effects of TBBPA and TBBPS to bovine trypsin by the fluorescence spectroscopy, circular dichroism and molecular dynamics (MD) simulations. They statically quenched the intrinsic fluorescence of bovine trypsin in a concentration-dependent mode and caused slight red-shifted fluorescence. The short and long fluorescence lifetime decay components of bovine trypsin were both affected, partly due to the disturbed microenvironmental changes of Trp215. The β-sheet content of bovine trypsin was significantly reduced from 82.4% to 75.7% and 76.6% by TBBPA and TBBPS, respectively, possibly impairing the physiological function of bovine trypsin. TBBPA and TBBPS bind at the 8-anilinonaphthalene-1-sulfonate (ANS) binding site with an association constant of 1.09 × 10 4 M −1 and 2.41 × 10 4 M −1 at 298 K, respectively. MD simulations revealed that van der Waals interactions and hydrogen bond interactions are dominant for TBBPA, whereas electrostatic interactions are critical for TBBPS. Our in vitro and in silico studies are beneficial to the understanding of risk assessment and future design of environmental benign BFRs.

  1. Molecular Soybean-Pathogen Interactions.

    Science.gov (United States)

    Whitham, Steven A; Qi, Mingsheng; Innes, Roger W; Ma, Wenbo; Lopes-Caitar, Valéria; Hewezi, Tarek

    2016-08-04

    Soybean hosts a wide variety of pathogens that cause significant yield losses. The importance of soybean as a major oilseed crop has led to research focused on its interactions with pathogens, such as Soybean mosaic virus, Pseudomonas syringae, Phytophthora sojae, Phakopsora pachyrhizi, and Heterodera glycines. Pioneering work on soybean's interactions with these organisms, which represent the five major pathogen groups (viruses, bacteria, oomycetes, fungi, and nematodes), has contributed to our understanding of the molecular mechanisms underlying virulence and immunity. These mechanisms involve conserved and unique features that validate the need for research in both soybean and homologous model systems. In this review, we discuss identification of effectors and their functions as well as resistance gene-mediated recognition and signaling. We also point out areas in which model systems and recent advances in resources and tools have provided opportunities to gain deeper insights into soybean-pathogen interactions.

  2. Molecular interactions in nanocellulose assembly

    Science.gov (United States)

    Nishiyama, Yoshiharu

    2017-12-01

    The contribution of hydrogen bonds and the London dispersion force in the cohesion of cellulose is discussed in the light of the structure, spectroscopic data, empirical molecular-modelling parameters and thermodynamics data of analogue molecules. The hydrogen bond of cellulose is mainly electrostatic, and the stabilization energy in cellulose for each hydrogen bond is estimated to be between 17 and 30 kJ mol-1. On average, hydroxyl groups of cellulose form hydrogen bonds comparable to those of other simple alcohols. The London dispersion interaction may be estimated from empirical attraction terms in molecular modelling by simple integration over all components. Although this interaction extends to relatively large distances in colloidal systems, the short-range interaction is dominant for the cohesion of cellulose and is equivalent to a compression of 3 GPa. Trends of heat of vaporization of alkyl alcohols and alkanes suggests a stabilization by such hydroxyl group hydrogen bonding to be of the order of 24 kJ mol-1, whereas the London dispersion force contributes about 0.41 kJ mol-1 Da-1. The simple arithmetic sum of the energy is consistent with the experimental enthalpy of sublimation of small sugars, where the main part of the cohesive energy comes from hydrogen bonds. For cellulose, because of the reduced number of hydroxyl groups, the London dispersion force provides the main contribution to intermolecular cohesion. This article is part of a discussion meeting issue `New horizons for cellulose nanotechnology'.

  3. Molecular mechanisms of membrane interaction at implantation.

    Science.gov (United States)

    Davidson, Lien M; Coward, Kevin

    2016-03-01

    Successful pregnancy is dependent upon the implantation of a competent embryo into a receptive endometrium. Despite major advancement in our understanding of reproductive medicine over the last few decades, implantation failure still occurs in both normal pregnancies and those created artificially by assisted reproductive technology (ART). Consequently, there is significant interest in elucidating the etiology of implantation failure. The complex multistep process of implantation begins when the developing embryo first makes contact with the plasma membrane of epithelial cells within the uterine environment. However, although this biological interaction marks the beginning of a fundamental developmental process, our knowledge of the intricate physiological and molecular processes involved remains sparse. In this synopsis, we aim to provide an overview of our current understanding of the morphological changes which occur to the plasma membrane of the uterine endothelium, and the molecular mechanisms that control communication between the early embryo and the endometrium during implantation. A multitude of molecular factors have been implicated in this complex process, including endometrial integrins, extracellular matrix molecules, adhesion molecules, growth factors, and ion channels. We also explore the development of in vitro models for embryo implantation to help researchers investigate mechanisms which may underlie implantation failure. Understanding the precise molecular pathways associated with implantation failure could help us to generate new prognostic/diagnostic biomarkers, and may identify novel therapeutic targets. © 2016 Wiley Periodicals, Inc.

  4. Investigation into the interaction of losartan with human serum albumin and glycated human serum albumin by spectroscopic and molecular dynamics simulation techniques: A comparison study.

    Science.gov (United States)

    Moeinpour, Farid; Mohseni-Shahri, Fatemeh S; Malaekeh-Nikouei, Bizhan; Nassirli, Hooriyeh

    2016-09-25

    The interaction between losartan and human serum albumin (HSA), as well as its glycated form (gHSA) was studied by multiple spectroscopic techniques and molecular dynamics simulation under physiological conditions. The binding information, including the binding constants, effective quenching constant and number of binding sites showed that the binding partiality of losartan to HSA was higher than to gHSA. The findings of three-dimensional fluorescence spectra demonstrated that the binding of losartan to HSA and gHSA would alter the protein conformation. The distances between Trp residue and the binding sites of the drug were evaluated on the basis of the Förster theory, and it was indicated that non-radiative energy transfer from HSA and gHSA to the losartan happened with a high possibility. According to molecular dynamics simulation, the protein secondary and tertiary structure changes were compared in HSA and gHSA for clarifying the obtained results. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  5. Theoretical studies of molecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Lester, W.A. Jr. [Univ. of California, Berkeley (United States)

    1993-12-01

    This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

  6. Interactions between epinastine and human serum albumin: Investigation by fluorescence, UV-vis, FT-IR, CD, lifetime measurement and molecular docking

    Science.gov (United States)

    Ariga, Girish G.; Naik, Praveen N.; Chimatadar, Shivamurti A.; Nandibewoor, Sharanappa T.

    2017-06-01

    The fluorescence quenching of human serum albumin (HSA) by epinastine hydrochloride (EPN) at pH 7.4 buffer was studied using absorption, fluorescence quenching, time-resolved, circular-dichroism, synchronous and molecular docking studies have been employed in the system. The fluorescence quenching study revealed that the static quenching mechanism was involved in the interaction of EPN with human serum albumin. The value number of binding sites, n, is close to unity, EPN-HSA, indicated the presence of a single class of binding site for the drug in protein. The binding constant value of EPN_HSA was observed to be 2.72 × 104 M-1 at 298 K. The spectral results attest that the binding of EPN-HSA induced conformational changes in the HSA. The metal ions viz., Ca2+, Co2+, Cu2+, Ni2+ and Zn2+ were found to influence the binding of the EPN to HSA. Based on the Forster's theory of non-radiation energy transfer, the binding average distance, r, between the donor (HSA) and acceptor (EPN) was found to be 4.33 nm. The circular dichroism data revealed that the presence of EPN decreased the α-helix content of serum albumin, which indicated conformation changes in HSA upon interaction with EPN.

  7. Defining Elastic Fiber Interactions by Molecular Fishing

    Science.gov (United States)

    Cain, Stuart A.; McGovern, Amanda; Small, Elaine; Ward, Lyle J.; Baldock, Clair; Shuttleworth, Adrian; Kielty, Cay M.

    2009-01-01

    Deciphering interacting networks of the extracellular matrix is a major challenge. We describe an affinity purification and mass spectrometry strategy that has provided new insights into the molecular interactions of elastic fibers, essential extracellular assemblies that provide elastic recoil in dynamic tissues. Using cell culture models, we defined primary and secondary elastic fiber interaction networks by identifying molecular interactions with the elastic fiber molecules fibrillin-1, MAGP-1, fibulin-5, and lysyl oxidase. The sensitivity and validity of our method was confirmed by identification of known interactions with the bait proteins. Our study revealed novel extracellular protein interactions with elastic fiber molecules and delineated secondary interacting networks with fibronectin and heparan sulfate-associated molecules. This strategy is a novel approach to define the macromolecular interactions that sustain complex extracellular matrix assemblies and to gain insights into how they are integrated into their surrounding matrix. PMID:19755719

  8. determination of morphological features and molecular interactions

    African Journals Online (AJOL)

    User

    ABSTRACT. This research focused on identifying the morphological features and molecular interactions of the. Nigerian Bentonitic clays using Scanning Electron Microscope (SEM) characterisation technique. The SEM microstructure images indicated that the bentonite samples are generally moderately dispersive to ...

  9. Equilibrium Molecular Interactions in Pure Gases

    Directory of Open Access Journals (Sweden)

    Boris I. Sedunov

    2012-01-01

    Full Text Available The equilibrium molecular interactions in pure real gases are investigated based on the chemical thermodynamics principles. The parallels between clusters in real gases and chemical compounds in equilibrium media have been used to improve understanding of the real gas structure. A new approach to the equilibrium constants for the cluster fractions and new methods to compute them and their significant parameters from the experimental thermophysical data are developed. These methods have been applied to some real gases, such as Argon and Water vapors and gaseous Alkanes. It is shown that the four-particle clusters make a noticeable contribution in the thermophysical properties of the equilibrium Water vapor. It is shown also that the effective bond energy for dimers in Alkanes linearly grows with the number of carbon atoms in the molecule.

  10. MINT, the molecular interaction database: 2009 update.

    Science.gov (United States)

    Ceol, Arnaud; Chatr Aryamontri, Andrew; Licata, Luana; Peluso, Daniele; Briganti, Leonardo; Perfetto, Livia; Castagnoli, Luisa; Cesareni, Gianni

    2010-01-01

    MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals. Since its last report, MINT has grown considerably in size and evolved in scope to meet the requirements of its users. The main changes include a more precise definition of the curation policy and the development of an enhanced and user-friendly interface to facilitate the analysis of the ever-growing interaction dataset. MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium.

  11. Molecular analysis and antibiotic resistance investigation of ...

    African Journals Online (AJOL)

    Molecular analysis and antibiotic resistance investigation of Staphylococcus aureus isolates associated with staphylococcal food poisoning and nosocomial infections. Y Zhang, S Cheng, G Ding, M Zhu, X Pan, L Zhang ...

  12. Interactive association between biopolymers and biofunctions in carinata seeds as energy feedstock and their coproducts (carinata meal) from biofuel and bio-oil processing before and after biodegradation: current advanced molecular spectroscopic investigations.

    Science.gov (United States)

    Yu, Peiqiang; Xin, Hangshu; Ban, Yajing; Zhang, Xuewei

    2014-05-07

    Recent advances in biofuel and bio-oil processing technology require huge supplies of energy feedstocks for processing. Very recently, new carinata seeds have been developed as energy feedstocks for biofuel and bio-oil production. The processing results in a large amount of coproducts, which are carinata meal. To date, there is no systematic study on interactive association between biopolymers and biofunctions in carinata seed as energy feedstocks for biofuel and bioethanol processing and their processing coproducts (carinata meal). Molecular spectroscopy with synchrotron and globar sources is a rapid and noninvasive analytical technique and is able to investigate molecular structure conformation in relation to biopolymer functions and bioavailability. However, to date, these techniques are seldom used in biofuel and bioethanol processing in other research laboratories. This paper aims to provide research progress and updates with molecular spectroscopy on the energy feedstock (carinata seed) and coproducts (carinata meal) from biofuel and bioethanol processing and show how to use these molecular techniques to study the interactive association between biopolymers and biofunctions in the energy feedstocks and their coproducts (carinata meal) from biofuel and bio-oil processing before and after biodegradation.

  13. Técnicas de caracterização para investigar interações no nível molecular em filmes de Langmuir e Langmuir-Blodgett (LB Characterization techniques to investigate molecular-level interactions in Langmuir and Langmuir-Blodgett (LB films

    Directory of Open Access Journals (Sweden)

    Marystela Ferreira

    2005-06-01

    Full Text Available This paper discusses fundamental concepts for the characterization of Langmuir monolayers and Langmuir-Blodgett (LB films, with emphasis on investigations of material properties at the molecular level. By way of illustration, results for phospholipid monolayers interacting with the drug dipyridamole are highlighted. These results were obtained with several techniques, including in situ grazing incidence X-ray diffraction, Fourier transform infrared (FTIR spectroscopy, fluorescence microscopy, in addition to surface pressure and surface potential isotherms. Also mentioned are the difficulties in producing Langmuir and LB films from macromolecules, and how molecular-level interactions in mixed polymer LB films can be exploited in sensors.

  14. Atomic and Molecular Manipulation of Chemical Interactions

    National Research Council Canada - National Science Library

    Ho, Wilson

    2007-01-01

    .... In effect, the goal is to carry out chemical changes by manipulating individual atoms and molecules to induce different bonding geometry and to create new interactions with their environment. These studies provide the scientific basis for the advancement of technology in catalysis, molecular electronics, optics, chemical and biological sensing, and magnetic storage.

  15. Determination of morphological features and molecular interactions ...

    African Journals Online (AJOL)

    This research focused on identifying the morphological features and molecular interactions of the Nigerian Bentonitic clays using Scanning Electron Microscope (SEM) characterisation technique. The SEM microstructure images indicated that the bentonite samples are generally moderately dispersive to dispersive with ...

  16. Quantitative investigation of intermolecular interactions in dimorphs ...

    Indian Academy of Sciences (India)

    RAHUL SHUKLA

    2018-03-23

    Mar 23, 2018 ... molecular interactions in derivatives of 1,2,4-triazoles. CrystEngComm 16 1702. 48. Shukla R, Mohan T P, Vishalakshi B and Chopra D. 2017 Synthesis, crystal structure and theoretical analysis of intermolecular interactions in two biologically active derivatives of 1,2,4-triazoles J. Mol. Struct. 1134 426. 49.

  17. Microbial interactions: ecology in a molecular perspective.

    Science.gov (United States)

    Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

    2016-12-01

    The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  18. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  19. Molecular interactions of graphene oxide with human blood plasma proteins

    Science.gov (United States)

    Kenry, Affa Affb Affc; Loh, Kian Ping; Lim, Chwee Teck

    2016-04-01

    We investigate the molecular interactions between graphene oxide (GO) and human blood plasma proteins. To gain an insight into the bio-physico-chemical activity of GO in biological and biomedical applications, we performed a series of biophysical assays to quantify the molecular interactions between GO with different lateral size distributions and the three essential human blood plasma proteins. We elucidate the various aspects of the GO-protein interactions, particularly, the adsorption, binding kinetics and equilibrium, and conformational stability, through determination of quantitative parameters, such as GO-protein association constants, binding cooperativity, and the binding-driven protein structural changes. We demonstrate that the molecular interactions between GO and plasma proteins are significantly dependent on the lateral size distribution and mean lateral sizes of the GO nanosheets and their subtle variations may markedly influence the GO-protein interactions. Consequently, we propose the existence of size-dependent molecular interactions between GO nanosheets and plasma proteins, and importantly, the presence of specific critical mean lateral sizes of GO nanosheets in achieving very high association and fluorescence quenching efficiency of the plasma proteins. We anticipate that this work will provide a basis for the design of graphene-based and other related nanomaterials for a plethora of biological and biomedical applications.

  20. Investigating Ebola virus pathogenicity using molecular dynamics.

    Science.gov (United States)

    Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

    2017-08-11

    Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

  1. Interactive investigations into planetary interiors

    Science.gov (United States)

    Rose, I.

    2015-12-01

    Many processes in Earth science are difficult to observe or visualize due to the large timescales and lengthscales over which they operate. The dynamics of planetary mantles are particularly challenging as we cannot even look at the rocks involved. As a result, much teaching material on mantle dynamics relies on static images and cartoons, many of which are decades old. Recent improvements in computing power and technology (largely driven by game and web development) have allowed for advances in real-time physics simulations and visualizations, but these have been slow to affect Earth science education.Here I demonstrate a teaching tool for mantle convection and seismology which solves the equations for conservation of mass, momentum, and energy in real time, allowing users make changes to the simulation and immediately see the effects. The user can ask and answer questions about what happens when they add heat in one place, or take it away from another place, or increase the temperature at the base of the mantle. They can also pause the simulation, and while it is paused, create and visualize seismic waves traveling through the mantle. These allow for investigations into and discussions about plate tectonics, earthquakes, hot spot volcanism, and planetary cooling.The simulation is rendered to the screen using OpenGL, and is cross-platform. It can be run as a native application for maximum performance, but it can also be embedded in a web browser for easy deployment and portability.

  2. Investigation of Galactosylated Low Molecular Weight Chitosan ...

    African Journals Online (AJOL)

    the stability towards drug release and for targeting purposes. Chitosan coated liposomes have been formed via ionic interaction between the positively charged chitosan and negatively charged lipid on the surface of the liposomes [9]. The aim of the present investigation was to develop and characterize DOX-bearing, ligand.

  3. Neuroendocrine and Molecular Interactions in Eating Disorders

    Directory of Open Access Journals (Sweden)

    Selma Bozkurt Zincir

    2014-08-01

    Full Text Available There are three basic pillars for the development of eating disorders: genetic predisposition, neuro-endocrine-molecular changes in the brain and metabolic response to it. As a result of neuroendocrine research, a close relationship has been found between neuroendocrine functions and symptom domains of psychiatric disorders such as eating disorders and mood disorders. Certain hormones, neurotransmitters and other molecules which might have effect on the basis of eating disorders can be listed as estrogen, serotonin, leptin, ghreline, alpha-melanocyte stimulating hormone, cholecystokinin, dopamine, noradrenaline, brain-derived neurotropic factor, agouti-related protein, neuropeptide-Y, opioids and their receptors, thiamine, zinc, omega-3 acids. In this review, main neuroendocrine-molecular changes and interactions that occur in the eating disorders have been discussed. [Psikiyatride Guncel Yaklasimlar - Current Approaches in Psychiatry 2014; 6(4.000: 389-400

  4. Controlling single-molecule junction conductance by molecular interactions

    Science.gov (United States)

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  5. Interacting With Robots to Investigate the Bases of Social Interaction.

    Science.gov (United States)

    Sciutti, Alessandra; Sandini, Giulio

    2017-12-01

    Humans show a great natural ability at interacting with each other. Such efficiency in joint actions depends on a synergy between planned collaboration and emergent coordination, a subconscious mechanism based on a tight link between action execution and perception. This link supports phenomena as mutual adaptation, synchronization, and anticipation, which cut drastically the delays in the interaction and the need of complex verbal instructions and result in the establishment of joint intentions, the backbone of social interaction. From a neurophysiological perspective, this is possible, because the same neural system supporting action execution is responsible of the understanding and the anticipation of the observed action of others. Defining which human motion features allow for such emergent coordination with another agent would be crucial to establish more natural and efficient interaction paradigms with artificial devices, ranging from assistive and rehabilitative technology to companion robots. However, investigating the behavioral and neural mechanisms supporting natural interaction poses substantial problems. In particular, the unconscious processes at the basis of emergent coordination (e.g., unintentional movements or gazing) are very difficult-if not impossible-to restrain or control in a quantitative way for a human agent. Moreover, during an interaction, participants influence each other continuously in a complex way, resulting in behaviors that go beyond experimental control. In this paper, we propose robotics technology as a potential solution to this methodological problem. Robots indeed can establish an interaction with a human partner, contingently reacting to his actions without losing the controllability of the experiment or the naturalness of the interactive scenario. A robot could represent an "interactive probe" to assess the sensory and motor mechanisms underlying human-human interaction. We discuss this proposal with examples from our

  6. Fanconi Anemia Proteins and Their Interacting Partners: A Molecular Puzzle

    Science.gov (United States)

    Kaddar, Tagrid; Carreau, Madeleine

    2012-01-01

    In recent years, Fanconi anemia (FA) has been the subject of intense investigations, primarily in the DNA repair research field. Many discoveries have led to the notion of a canonical pathway, termed the FA pathway, where all FA proteins function sequentially in different protein complexes to repair DNA cross-link damages. Although a detailed architecture of this DNA cross-link repair pathway is emerging, the question of how a defective DNA cross-link repair process translates into the disease phenotype is unresolved. Other areas of research including oxidative metabolism, cell cycle progression, apoptosis, and transcriptional regulation have been studied in the context of FA, and some of these areas were investigated before the fervent enthusiasm in the DNA repair field. These other molecular mechanisms may also play an important role in the pathogenesis of this disease. In addition, several FA-interacting proteins have been identified with roles in these “other” nonrepair molecular functions. Thus, the goal of this paper is to revisit old ideas and to discuss protein-protein interactions related to other FA-related molecular functions to try to give the reader a wider perspective of the FA molecular puzzle. PMID:22737580

  7. Molecular effects: interactions with chemicals and viruses

    International Nuclear Information System (INIS)

    Hanawalt, P.C.

    1980-01-01

    Research focused upon an understanding of the cellular responses to the molecular effects of ionizing radiation should be an essential program component in the Federal Strategy for Research into the Biological Effects of Ionizing Radiation. Although we know that DNA is a principal target molecule for some highly significant biological effects of ionizing radiation, we need to learn which other target substances such as membrane components may also be important. Most of the emphasis should continue to be on DNA effects and highest priority should be assigned to the identification of the complete spectrum of products produced in DNA. Once the lesions are known we can proceed to determine how these behave as blocks to replication and transcription or as modulators on the fidelity of these crucial processes. Considerable work should be done on the repair of these lesions. High priority should be given to the search for mutants in mammalian cell systems with evident defects in the processing of specific lesions. Viruses should provide important tools for the research in this area, as probes for host cell repair responses and also for the isolation of mutants. Furthermore, it is important to consider the interaction of viruses and ionizing radiation with regard to possible modulating effects on repair processes and tumorigenesis. Finally we must consider the important problem of the modification of repair responses by environmental factors

  8. Molecular Recognition and Specific Interactions for Biosensing Applications

    Directory of Open Access Journals (Sweden)

    Dae Joon Kang

    2008-10-01

    Full Text Available Molecular recognition and specific interactions are reliable and versatile routes for site-specific and well-oriented immobilization of functional biomolecules on surfaces. The control of surface properties via the molecular recognition and specific interactions at the nanoscale is a key element for the nanofabrication of biosensors with high sensitivity and specificity. This review intends to provide a comprehensive understanding of the molecular recognition- and specific interaction-mediated biosensor fabrication routes that leads to biosensors with well-ordered and controlled structures on both nanopatterned surfaces and nanomaterials. Herein self-assembly of the biomolecules via the molecular recognition and specific interactions on nanoscaled surfaces as well as nanofabrication techniques of the biomolecules for biosensor architecture are discussed. We also describe the detection of molecular recognition- and specific interaction-mediated molecular binding as well as advantages of nanoscale detection.

  9. Characterization of molecular interactions between E. coli RNA polymerase and topoisomerase I by molecular simulations

    Science.gov (United States)

    Tiwari, Purushottam Babu; Chapagain, Prem P.; Banda, Srikanth; Darici, Yesim; Üren, Aykut; Tse-Dinh, Yuk-Ching

    2016-01-01

    Escherichia coli topoisomerase I (EctopoI), a type IA DNA topoisomerase, relaxes the negative DNA supercoiling generated by RNA polymerase (RNAP) during transcription elongation. Due to the lack of structural information on the complex, the exact nature of the RNAP-EctopoI interactions remains unresolved. Herein, we report for the first time, the structure-based modeling of the RNAP-EctopoI interactions using computational methods. Our results predict that the salt-bridge as well as hydrogen bond interactions are responsible for the formation and stabilization of the RNAP-EctopoI complex. Our investigations provide molecular insights for understanding how EctopoI interacts with RNAP, a critical step for preventing hypernegative DNA supercoiling during transcription. PMID:27448274

  10. Experimental investigation on particle-wall interactions

    International Nuclear Information System (INIS)

    Zeisel, H.; Dorfner, V.

    1988-01-01

    There is still a lack in the knowledge about many physical processes in two-phase flows and therefore their mathematical description for the modelling of two-phase flows by computer simulations still needs some improvement. One required information is the physical procedure of the momentum transfer between the phases themselves, such as particle-particle or particle-fluid interactions, and between the phases and the flow boundaries, such as particle-wall or fluid-wall interactions. The interaction between the two phases can be either a 'long-range' interference or a direct contact between both. For the particle-fluid two-phase flow system the interaction can be devided in particle-fluid, particle-particle and particle-boundary interactions. In this investigation the attention is drawn to the special case of a particle-wall interaction and its 'long-range' interference effect between the wall and a small particle which approaches the wall in normal direction. (orig./GL)

  11. Molecular interactions with reference to manifestation of solvation ...

    African Journals Online (AJOL)

    The density and viscosity data were analyzed by some semi-empirical viscosity models, and the results have been discussed in terms of molecular interactions and structural effects. The excess properties were found to be either negative or positive depending on the molecular interactions and the nature of liquid mixtures.

  12. Molecular Indicators of Soil Humification and Interaction with Heavy Metals

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Teresa W.-M.; Higashi, Richard M.; Cassel, Teresa; Green, Peter; Lane, Andrew N.

    2003-03-26

    For stabilization of heavy metals at contaminated sites, interaction of soil organic matter (SOM) with heavy metal ions is critically important for long-term sustainability, a factor that is poorly understood at the molecular level. Using 13C- and 15N-labeled soil humates (HS), we investigated the turnover of five organic amendments (celluose, wheat straw, pine shavings, chitin and bone meal) in relation to heavy metal ion leaching in soil column experiments. The labeled molecular substructures in HS were examined by multinuclear 2-D NMR and pyrolysis GC-MS while the element profile in the leachates was analyzed by ICP-MS. Preliminary analysis revealed that peptidic and polysaccharidic structures were highly enriched, which suggests their microbial origin. Cd(II) leaching was significantly attenuated with humification of lignocellulosic materials. Correlation of 13C and 15N turnovers of HS substructures to metal leaching is underway.

  13. Dispersion Interactions in Molecular Assemblies from First-Principles Calculations

    Science.gov (United States)

    Li, Yan; Lu, Deyu; Viet Nguyen, Huy; Galli, Giulia

    2010-03-01

    We have investigated inter-molecular interactions in weakly bonded molecular assemblies from first principles, by combining exact exchange energies (EXX) with correlation energies defined by the adiabatic connection fluctuation-dissipation theorem, within the random phase approximation (RPA)[1,2]. We present results for three different types of molecular systems: the benzene crystal, the methane crystal and self-assembled monolayers of phenylenediisocyanide. We describe in detail how computed equilibrium lattice constants and cohesive energies may be affected by input ground state wave functions and orbital energies, by the geometries of the molecular monomers in the assemblies, and by the inclusion of zero point energy contribution to the total energy. We find that the EXX/RPA perturbative approach provides an overall satisfactory, first principle description of dispersion forces, in good agreement with experiments and advanced quantum chemistry results. However, binding energies tend to be underestimated and possible reasons for this discrepancy are discussed. This work was funded by DOE/BES DE-FG02-06ER46262 and DOE/SciDAC DE-FC02-06ER25794.[1] Y. Li, D. Lu, H-V. Nguyen and G. Galli, J. Phys. Chem.(submitted). [2]D. Lu, Y. Li, D. Rocca and G. Galli, Phys. Rev. Lett. 102, 206411(2009).

  14. Molecular Contamination Investigation Facility (MCIF) Capabilities

    Science.gov (United States)

    Soules, David M.

    2013-01-01

    This facility was used to guide the development of ASTM E 1559 center dot Multiple Quartz Crystal Microbalances (QCMs), large sample and spectral effects capability center dot Several instrumented, high vacuum chamber systems are used to evaluate the molecular outgassing characteristics of materials, flight components and other sensitive surfaces. Test materials for spacecraft/instrument selection center.Test flight components for acceptable molecular outgas levels center dot Determine time/temperature vacuum bake-out requirements center. Data used to set limits for use of materials and specific components center. Provide Input Data to Contamination Transport Models -Applied to numerous flight projects over the past 20 years.

  15. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    cates an easy outlook of the makeup of the molec- ular orbitals in a certain energy range. The energy split between the HOMOs and LUMOs are the crit- ical parameters in special molecular electrical trans- port properties which help in the measure of elec- tron conductivity.42 The HOMO represents the ability to donate an ...

  16. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    The spectroscopic properties of the title compound have beeninvestigated by using IR, UV–Vis and ¹H NMR techniques. The molecular geometry and spectroscopic data of the title compound have been calculated by using the density functional method (B3LYP) invoking 6-311G(d,p) basis set. UV-Vis spectra of the two ...

  17. Molecular investigations of flaxseed mucilage polysaccharides.

    Science.gov (United States)

    Roulard, Romain; Petit, Emmanuel; Mesnard, François; Rhazi, Larbi

    2016-05-01

    The molecular properties of flaxseed mucilage were determined using a multi-angle laser light scattering (MALLS) detector coupled on-line to size exclusion chromatography (SEC) and asymmetric flow field-flow fractionation (AF4). Water and salt solution were tested as mobile phases. The SEC-MALLS method gave partial information and enabled molecular characterization of disaggregated mucilage molecules. Regardless of the eluent used, the observed Mw ranged from about 1.6 × 10(6) to more than 10 × 10(6) g/mol for mucilage polysaccharides. The AF4-MALLS system enabled a complete analysis of mucilage carbohydrate aggregates in water, in which two populations were satisfactorily separated. The molecular weight distribution (MWD) of molecules ranged from 1.5 × 10(6) to more than 4 × 10(8) g/mol. Experiments showed that the conformational structure of mucilage molecules was strongly influenced by ionic strength. Mucilage carbohydrates exhibited a spherical and compact structure in NaCl solution while they displayed a random-coil conformation in water. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    Science.gov (United States)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  19. Molecular and biological interactions in colorectal cancer

    NARCIS (Netherlands)

    Heer, Pieter de

    2007-01-01

    The current thesis discusses the use of molecular and biological tumor markers to predict clinical outcome. By studying several key processes in the develepment of cancer as regulation of cell motility (non-receptor protein tyrosin adesion kinases, FAK, Src and paxillin, Apoptosis (caspase-3

  20. Molecular infection biology : interactions between microorganisms and cells

    National Research Council Canada - National Science Library

    Hacker, Jörg (Jörg Hinrich); Heesemann, Jurgen

    2002-01-01

    ... and epidemiology of infectious diseases. Investigators, specialists, clinicians, and graduate students in biology, pharmacy, and medicine will find Molecular Infection Biology an invaluable addition to their professional libraries...

  1. Tick-Pathogen Ensembles: Do Molecular Interactions Lead Ecological Innovation?

    Czech Academy of Sciences Publication Activity Database

    Cabezas Cruz, Alejandro; Estrada-Peňa, A.; Rego, Ryan O. M.; de la Fuente, J.

    2017-01-01

    Roč. 7, 13 March (2017), č. článku 74. ISSN 2235-2988 Institutional support: RVO:60077344 Keywords : tick-pathogen interactions * transcriptional reprogramming * epigenetics * ecological adaptation * Anaplasma phagocytophilum Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 4.300, year: 2016

  2. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  3. Maximum power operation of interacting molecular motors

    DEFF Research Database (Denmark)

    Golubeva, Natalia; Imparato, Alberto

    2013-01-01

    We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the thermodynamic efficiency at maximum power of the motors, as compa......We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the thermodynamic efficiency at maximum power of the motors...

  4. Interactive Multimodal Molecular Set – Designing Ludic Engaging Science Learning Content

    DEFF Research Database (Denmark)

    Thorsen, Tine Pinholt; Christiansen, Kasper Holm Bonde; Jakobsen Sillesen, Kristian

    2014-01-01

    This paper reports on an exploratory study investigating 10 primary school students’ interaction with an interactive multimodal molecular set fostering ludic engaging science learning content in primary schools (8th and 9th grade). The concept of the prototype design was to bridge the physical an...

  5. Detailed Investigations of Interactions between Ionizing Radiation and Neutral Gases

    Energy Technology Data Exchange (ETDEWEB)

    Landers, Allen L

    2014-03-31

    We are investigating phenomena that stem from the many body dynamics associated with ionization of an atom or molecule by photon or charged particle. Our program is funded through the Department of Energy EPSCoR Laboratory Partnership Award in collaboration with Lawrence Berkeley National Laboratory. We are using variations on the well established COLTRIMS technique to measure ions and electrons ejected during these interactions. Photoionization measurements take place at the Advanced Light Source at LBNL as part of the ALS-COLTRIMS collaboration with the groups of Reinhard Dörner at Frankfurt and Ali Belkacem at LBNL. Additional experiments on charged particle impact are conducted locally at Auburn University where we are studying the dissociative molecular dynamics following interactions with either ions or electrons over a velocity range of 1 to 12 atomic units.

  6. Developing a Molecular Roadmap of Drug-Food Interactions

    DEFF Research Database (Denmark)

    Jensen, Kasper; Ni, Yueqiong; Panagiotou, Gianni

    2015-01-01

    in ∼ 1800 plant-based foods with the pharmacokinetics and pharmacodynamics processes of medicine, with the purpose of elucidating the molecular mechanisms involved. By employing a systems chemical biology approach that integrates data from the scientific literature and online databases, we gained a global...... view of the associations between diet and dietary molecules with drug targets, metabolic enzymes, drug transporters and carriers currently deposited in Drug-Bank. Moreover, we identified disease areas and drug targets that are most prone to the negative effects of drug-food interactions, showcasing...... a platform for making recommendations in relation to foods that should be avoided under certain medications. Lastly, by investigating the correlation of gene expression signatures of foods and drugs we were able to generate a completely novel drug-diet interactome map....

  7. Molecular basis and regulation of OTULIN-LUBAC interaction

    DEFF Research Database (Denmark)

    Elliott, Paul R.; Al-Saoudi, Sofie Vincents; Marco-Casanova, Paola

    2014-01-01

    Ub. Now, we show that OTULIN binds via a conserved PUB-interacting motif (PIM) to the PUB domain of the LUBAC component HOIP. Crystal structures and nuclear magnetic resonance experiments reveal the molecular basis for the high-affinity interaction and explain why OTULIN binds the HOIP PUB domain...

  8. DockingShop: A Tool for Interactive Molecular Docking

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  9. Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer

    Science.gov (United States)

    2015-09-01

    compelling evidence linking obesity to aggressive prostate cancer, but the underlying causes of this relationship are unclear. In this study we used whole...1 AWARD NUMBER: W81XWH-14-1-0250 TITLE: Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer PRINCIPAL INVESTIGATOR: Ericka...TITLE AND SUBTITLE Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-14-1-0250

  10. Interaction Between New Anti-cancer Drug Syndros and CNT(6,6-6) Nanotube for Medical Applications: Geometry Optimization, Molecular Structure, Spectroscopic (NMR, UV/Vis, Excited state), FMO, MEP and HOMO-LUMO Investigation

    Science.gov (United States)

    Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Kumar, Rakesh

    2018-03-01

    In the present work, Density Functional Theory (DFT) was first time employed to investigate the interaction between new drug (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydrobenzo[c]chromen-1-ol (Syndros) and the CNT(6,6-6) Nanotube in the gaseous phase. The interaction effects of compounds Syndros and CNT (6,6-6) nanotube on the electronic properties, chemical shift tensors and natural charge was also determined and discussed. The electronic spectra of the Syndros and the complex CNT(6,6-6)/Syndros in the gas phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for the formation of adsorption effect on maximum wavelength of the Syndros. Nucleus-Independent Chemical Shifts (NICS) calculations have also been carried out for the compound Syndors and the complex CNT(6,6-6)/Syndros and the aromaticity of the compound Syndors before and after interaction with the CNT(6,6-6) Nanotube was investigated.

  11. Investigation of nanodiamonds interactions in canine blood

    Science.gov (United States)

    WÄ sowicz, Michał; Marek, Kulka; Cićkiewicz, Maciej; Cymerman, Magdalena

    2017-02-01

    The whole blood contains red cells, white cells, and platelets suspended in plasma. In the following study we investigated an impact of nanodiamond particles on blood elements over various periods of time.The material used in the study consisted of samples taken from ten healthy canines (Canis lupus f. domestica) of various age, different blood types and both sexes. The markings were conducted by adding to the blood unmodified diamonds (SND), modified O2 (SO2) suspended in 0,9% NaCl. The blood was put under an impact of two diamond concentrations: 20μl and 100μl. The amount of abnormal cells increased with time. The percentage of echinocytes as a result of interaction with nanodiamonds in various time periods for individual specimens was scarce. In the examined microscopic image a summary was made for 100 white blood cells. Following cells were included in said group: band neutrophils, segmented neutrophils, eosinophils, basophils, lymphocytes, monocytes, lymphocytes with granulates, stimulated lymphocytes, lymphocytes with vacuoles, metamielocytes and smudge cells. The impact of the three diamond types had no clinical importance on red blood cells. After the diamonds mixed with white blood cells, atypical cells came into being, in the range of agranulocytes in stimulated form or with granulates and/or vacuoles. It is supposed that as a result of longlasting exposure a stimulation and vacuolisation takes place, because of the function of the cells.

  12. Experimental investigation of shock wave - bubble interaction

    Energy Technology Data Exchange (ETDEWEB)

    Alizadeh, Mohsen

    2010-04-09

    In this work, the dynamics of laser-generated single cavitation bubbles exposed to lithotripter shock waves has been investigated experimentally. The energy of the impinging shock wave is varied in several steps. High-speed photography and pressure field measurements simultaneously with image acquisition provide the possibility of capturing the fast bubble dynamics under the effect of the shock wave impact. The pressure measurement is performed using a fiber optic probe hydrophone (FOPH) which operates based on optical diagnostics of the shock wave propagating medium. After a short introduction in chapter 1 an overview of the previous studies in chapter 2 is presented. The reported literatures include theoretical and experimental investigations of several configurations of physical problems in the field of bubble dynamics. In chapter 3 a theoretical description of propagation of a shock wave in a liquid like water has been discussed. Different kinds of reflection of a shock wave at an interface are taken into account. Undisturbed bubble dynamics as well as interaction between a planar shock wave and an initially spherical bubble are explored theoretically. Some physical parameters which are important in this issue such as the velocity of the shock-induced liquid jet, Kelvin impulse and kinetic energy are explained. The shock waves are generated in a water filled container by a focusing piezoelectric generator. The shock wave profile has a positive part with pulse duration of ∼1 μs followed by a longer tension tail (i.e. ∼3 μs). In chapter 4 high-speed images depict the propagation of a shock wave in the water filled tank. The maximum pressure is also derived for different intensity levels of the shock wave generator. The measurement is performed in the free field (i.e. in the absence of laser-generated single bubbles). In chapter 5 the interaction between lithotripter shock waves and laserinduced single cavitation bubbles is investigated experimentally. An

  13. Studying Interactions by Molecular Dynamics Simulations at High Concentration

    Directory of Open Access Journals (Sweden)

    Federico Fogolari

    2012-01-01

    Full Text Available Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.

  14. Interactive analysis of systems biology molecular expression data

    OpenAIRE

    Prabhakar Sunil; Salt David E; Kane Michael D; Stephenson Alan; Ouyang Qi; Zhang Mingwu; Burgner John; Buck Charles; Zhang Xiang

    2008-01-01

    Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferr...

  15. Plant-aphid interactions: molecular and ecological perspectives.

    Science.gov (United States)

    Goggin, Fiona L

    2007-08-01

    Many aphids are major agricultural pests because of their unparalleled reproductive capacity and their ability to manipulate host plant physiology. Aphid population growth and its impact on plant fitness are strongly influenced by interactions with other organisms, including plant pathogens, endophytes, aphid endosymbionts, predators, parasitoids, ants, and other herbivores. Numerous molecular and genomic resources have recently been developed to identify sources of aphid resistance in plants, as well as potentially novel targets for control in aphids. Moreover, the same model systems that are used to explore direct molecular interactions between plants and aphids can be utilized to study the ecological context in which they occur.

  16. Investigation on particle-solid interactions

    International Nuclear Information System (INIS)

    Yano, Syukuro

    1988-08-01

    Basic processes in plasma-material interactions have been surveyed and reviewed. Problems concerned with carbon materials, which have been progressively used for the first wall and limiters in Tokamaks, are mainly discussed. Recent usage of carbon materials, basic properties and characteristics of carbon/graphite materials, desorption of gasses are described. As to the interactions of incident hydrogen isotope particles with graphite surface, data of trapping, depth profile, reemission, isotope exchange, and diffusion are reviewed and discussed. (author)

  17. 2004 Atomic and Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  18. 2004 Atomic and Molecular Interactions Gordon Research Conference

    International Nuclear Information System (INIS)

    Dr. Paul J. Dagdigian

    2004-01-01

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference

  19. Molecular interaction maps as information organizers and simulation guides.

    Science.gov (United States)

    Kohn, Kurt W.

    2001-03-01

    A graphical method for mapping bioregulatory networks is presented that is suited for the representation of multimolecular complexes, protein modifications, as well as actions at cell membranes and between protein domains. The symbol conventions defined for these molecular interaction maps are designed to accommodate multiprotein assemblies and protein modifications that can generate combinatorially large numbers of molecular species. Diagrams can either be "heuristic," meaning that detailed knowledge of all possible reaction paths is not required, or "explicit," meaning that the diagrams are totally unambiguous and suitable for simulation. Interaction maps are linked to annotation lists and indexes that provide ready access to pertinent data and references, and that allow any molecular species to be easily located. Illustrative interaction maps are included on the domain interactions of Src, transcription control of E2F-regulated genes, and signaling from receptor tyrosine kinase through phosphoinositides to Akt/PKB. A simple method of going from an explicit interaction diagram to an input file for a simulation program is outlined, in which the differential equations need not be written out. The role of interaction maps in selecting and defining systems for modeling is discussed. (c) 2001 American Institute of Physics.

  20. MIMO: an efficient tool for molecular interaction maps overlap

    Science.gov (United States)

    2013-01-01

    Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

  1. Fluid structure and molecular interaction of acetophenone derivatives

    Indian Academy of Sciences (India)

    pp. 1129-1137. Fluid structure and molecular interaction of acetophenone derivatives. K K GUPTA and P J sINGH. Department of Physics, Government MSJ (PG) College, Bharatpur 321 001, India. E-mail: kkguptakkg@indiatimes.com. MS received 4 June 2003; revised 2 January 2004; accepted 2 January 2004. Abstract.

  2. Modeling molecular boiling points using computed interaction energies.

    Science.gov (United States)

    Peterangelo, Stephen C; Seybold, Paul G

    2017-12-20

    The noncovalent van der Waals interactions between molecules in liquids are typically described in textbooks as occurring between the total molecular dipoles (permanent, induced, or transient) of the molecules. This notion was tested by examining the boiling points of 67 halogenated hydrocarbon liquids using quantum chemically calculated molecular dipole moments, ionization potentials, and polarizabilities obtained from semi-empirical (AM1 and PM3) and ab initio Hartree-Fock [HF 6-31G(d), HF 6-311G(d,p)], and density functional theory [B3LYP/6-311G(d,p)] methods. The calculated interaction energies and an empirical measure of hydrogen bonding were employed to model the boiling points of the halocarbons. It was found that only terms related to London dispersion energies and hydrogen bonding proved significant in the regression analyses, and the performances of the models generally improved at higher levels of quantum chemical computation. An empirical estimate for the molecular polarizabilities was also tested, and the best models for the boiling points were obtained using either this empirical polarizability itself or the polarizabilities calculated at the B3LYP/6-311G(d,p) level, along with the hydrogen-bonding parameter. The results suggest that the cohesive forces are more appropriately described as resulting from highly localized interactions rather than interactions between the global molecular dipoles.

  3. Volumetric and Viscometric Studies of Molecular Interactions in ...

    African Journals Online (AJOL)

    NJD

    In previous work we have presented a systematic study of the thermodynamic, acoustic and transport properties of binary mixtures of amides with alcohols.1–6 The objective underlying such studies is to improve our understanding of molecular interactions for characterizing the physico-chemical behaviour of mixtures at the ...

  4. Ultrasonic study of molecular interaction in binary liquid mixtures at ...

    Indian Academy of Sciences (India)

    physics pp. 695–701. Ultrasonic study of molecular interaction in binary liquid mixtures at 30 о. C. A ALI and A K NAIN. Department of Chemistry, Jamia Millia ... The variation of these parameters with composition of the mixture helps ... AR grade, 99.5 and 99.0%, respectively) were purified by standard procedure [11]. The.

  5. NGLview-interactive molecular graphics for Jupyter notebooks.

    Science.gov (United States)

    Nguyen, Hai; Case, David A; Rose, Alexander S

    2018-04-01

    NGLview is a Jupyter/IPython widget to interactively view molecular structures as well as trajectories from molecular dynamics simulations. Fast and scalable molecular graphics are provided through the NGL Viewer. The widget supports showing data from the file-system, online data bases and from objects of many popular analysis libraries including mdanalysis, mdtraj, pytraj, rdkit and more. The source code is freely available under the MIT license at https://github.com/arose/nglview. Python packages are available from PyPI and bioconda. NGLview uses Python on the server-side and JavaScript on the client. The integration with Jupyter is done through the ipywidgets package. The NGL Viewer is embedded client-side to provide WebGL accelerated molecular graphics. asr.moin@gmail.com.

  6. Molecular and Cellular Quantitative Microscopy: theoretical investigations, technological developments and applications to neurobiology

    NARCIS (Netherlands)

    Esposito, Alessandro

    2006-01-01

    This PhD project aims at the development and evaluation of microscopy techniques for the quantitative detection of molecular interactions and cellular features. The primarily investigated techniques are Fαrster Resonance Energy Transfer imaging and Fluorescence Lifetime Imaging Microscopy. These

  7. Investigations of interactions mediated by neutral currents

    International Nuclear Information System (INIS)

    Witek, M.

    2007-03-01

    The report is devoted to four-fermion interactions mediated by the neutral currents. The results from the second phase of LEP are presented, when the production of two massive bosons was possible with the increased energy of the e + e - collisions. It enabled for a direct test of nonabelian structure of the electroweak theory. The results concern the four-fermion production of the pairs of the ZZ bosons, single Z and Zγ * production as well as search for anomalous gauge bosons couplings. The large part of the report is devoted to experimental techniques, physics analyses and discussion of results. (author)

  8. Hadronic molecular states from the K anti K* interaction

    Energy Technology Data Exchange (ETDEWEB)

    Lue, Pei-Liang; He, Jun [Chinese Academy of Sciences, Theoretical Physics Division, Institute of Modern Physics, Lanzhou (China); Institute of Modern Physics of CAS and Lanzhou University, Research Center for Hadron and CSR Physics, Lanzhou (China)

    2016-12-15

    In this work, the K anti K* interaction is studied in a quasipotential Bethe-Salpeter equation approach combined with the one-boson-exchange model. With the help of the hidden-gauge Lagrangian, the exchanges of pseudoscalar mesons (π and η) and vector mesons (ρ, ω and φ) are considered to describe the K anti K* interaction. Besides the direct vector-meson exchange which can be related to the Weinberg-Tomozawa term, pseudoscalar-meson exchanges also play important roles in the mechanism of the K anti K* interaction. The poles of scattering amplitude are searched to find the molecular states produced from the K anti K* interaction. In the case of quantum number I{sup G}(J{sup PC}) = 0{sup +}(1{sup ++}), a pole is found with a reasonable cutoff, which can be related to the f{sub 1}(1285) in experiment. Another bound state with 0{sup -}(1{sup +-}) is also produced from the K anti K* interaction, which can be related to the h{sub 1}(1380). In the isovector sector, the interaction is much weaker and a bound state with 1{sup +}(1{sup +}) relevant to the b{sub 1}(1235) is produced but at a larger cutoff. Our results suggest that in the hadronic molecular state picture the f{sub 1}(1285) and b{sub 1}(1235) are the strange partners of the X(3872) and Z{sub c}(3900), respectively. (orig.)

  9. Molecular interactions of Leucoagaricus naucinus with uranium(VI) and europium(III)

    Energy Technology Data Exchange (ETDEWEB)

    Wollenberg, Anne; Raff, Johannes [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Biogeochemistry; Guenther, A. [Helmholtz Institute Freiberg for Resource Technology, Freiberg (Germany)

    2017-06-01

    With regard to a molecular understanding of the interaction of fungal mycelium with radionuclides and its possible application for precautionary radiation protection and bio-remediation, the binding mechanism of the radionuclide uranium and the metal europium, as surrogate for trivalent actinides, where investigated with different starting conditions by the living fungal cells of Leucoagaricus naucinus.

  10. Effect of molecular interactions on retention and selectivity in reversed-phase liquid chromatography.

    Science.gov (United States)

    Szepesy, László

    2002-06-25

    The linear solvation energy relationships (LSERs) have been applied in the last years for description and prediction of retention and selectivity in reversed-phase liquid chromatography with good results. Widely different stationary phases have been compared and characterized by LSERs. In recent publications the influence of the type of the organic moderator and the composition of the mobile phase have also been described. However, the influence of the molecular properties of the solutes to be separated has never been discussed. According to the LSER model variation in retention factors (log k) with solute structure can be related to their potential for various intermolecular interactions. The retention factor is given as the sum of the terms of the LSER equation representing various types of molecular interactions. For this reason the influence of the structure and molecular properties of the solutes to be separated can also be investigated using the LSER equation. In this study we shall demonstrate how the specific molecular interactions influence chromatographic retention and selectivity. We intend to show that retention and selectivity depend on all participants of the system. In addition to the structure and properties of the stationary phase and the type and composition of the mobile phase the molecular properties of the solutes, characterized by the solvation parameters, will also influence the type and extent of the various molecular interactions governing retention and selectivity.

  11. Investigation of beryllium/steam interaction

    Energy Technology Data Exchange (ETDEWEB)

    Chekhonadskikh, A.M.; Vurim, A.D.; Vasilyev, Yu.S.; Pivovarov, O.S. [Inst. of Atomic Energy National Nuclear Center of the Republic of Kazakstan Semipalatinsk (Kazakhstan); Shestakov, V.P.; Tazhibayeva, I.L.

    1998-01-01

    In this report program on investigations of beryllium emissivity and transient processes on overheated beryllium surface attacked by water steam to be carried out in IAE NNC RK within Task S81 TT 2096-07-16 FR. The experimental facility design is elaborated in this Report. (author)

  12. Investigation of molybdenum pentachloride interaction with chlorine

    International Nuclear Information System (INIS)

    Salyulev, A.B.; Vovkotrub, Eh.G.; Strekalovskij, V.N.

    1993-01-01

    In Raman spectra of molybdenum pentachloride solutions in liquid chlorine lines were recorded in case of 397, 312, 410, 217 and 180 cm - 1 vibrations of ν 1 (A 1 '), ν 2 (A 1 '), ν 5 (E'), ν 6 (E') and ν 8 (E'') monomer (symmetry D 3h ) molecules of MoCl 5 . Interaction of molten molybdenum pentachloride with chlorine at increased (up to 6 MPa) pressures of Cl 2 was studied. In Raman spectra of its vapour distillation in liquid chlorine alongside with MoCl 5 lines appearance of new lines at 363 and 272 cm -1 , similar in their frequency to the ones calculated for the vibrations ν 1 (A 1g ) and ν 2 (E g ) of MoCl 6 molecules (symmetry O h ), was observed

  13. Numerical Investigation of Ultrafast interaction between THz Fields and Crystalline Materials

    DEFF Research Database (Denmark)

    Pedersen, Pernille Klarskov; Clark, Stewart J.; Jepsen, Peter Uhd

    2014-01-01

    We present a quantum - mechanical molecular dynamics investigation of the interaction between strong single - cyc le THz pulses and ionic crystals . We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm.......We present a quantum - mechanical molecular dynamics investigation of the interaction between strong single - cyc le THz pulses and ionic crystals . We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm....

  14. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    Sci. Vol. 127, No. 12, December 2015, pp. 2137–2149. c Indian Academy of Sciences. DOI 10.1007/s12039-015-0976-x. Molecular structure and DFT investigations on new cobalt(II) chloride complex with superbase guanidine type ligand. SAIED M SOLIMANa,b,∗, MORSY A M ABU-YOUSSEFb,∗. , JΦRG ALBERINGc and.

  15. Molecular investigations on grain filling rate under terminal heat ...

    African Journals Online (AJOL)

    Ezedom Theresa

    2013-07-10

    Jul 10, 2013 ... Grain yield under post anthesis high temperature stress is largely influenced by grain filling rate (GFR). To investigate molecular basis of this trait, a set of 111 recombinant inbred lines (RILs) derived from Raj. 4014, a heat sensitive genotype and WH 730, heat tolerant cultivar was phenotyped during 2009- ...

  16. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    Science.gov (United States)

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  17. Molecular investigations on grain filling rate under terminal heat ...

    African Journals Online (AJOL)

    Grain yield under post anthesis high temperature stress is largely influenced by grain filling rate (GFR). To investigate molecular basis of this trait, a set of 111 recombinant inbred lines (RILs) derived from Raj 4014, a heat sensitive genotype and WH 730, heat tolerant cultivar was phenotyped during 2009-2010 and ...

  18. Perturbation approach to a molecular orbital theory of interaction energies

    International Nuclear Information System (INIS)

    Chipman, D.M.

    1982-01-01

    In order to provide a framework for better understanding of phenomena such as reaction mechanisms and photoelectron spectra that can be semiquantitatively described by molecular orbital theory, a formalism is developed to express the orbitals of a molecule in terms of orbitals of various fragments that make up the molecule. The total energy and individual orbital energies of the interacting fragments are obtained through second order in perturbation theory. Electrostatic interactions, orbital overlap effects, and self-consistency refinements are all considered explicitly and simultaneously to obtain the final results

  19. Immobilized enzymes: understanding enzyme - surface interactions at the molecular level.

    Science.gov (United States)

    Hoarau, Marie; Badieyan, Somayesadat; Marsh, E Neil G

    2017-11-22

    Enzymes immobilized on solid supports have important and industrial and medical applications. However, their uses are limited by the significant reductions in activity and stability that often accompany the immobilization process. Here we review recent advances in our understanding of the molecular level interactions between proteins and supporting surfaces that contribute to changes in stability and activity. This understanding has been facilitated by the application of various surface-sensitive spectroscopic techniques that allow the structure and orientation of enzymes at the solid/liquid interface to be probed, often with monolayer sensitivity. An appreciation of the molecular interactions between enzyme and surface support has allowed the surface chemistry and method of enzyme attachement to be fine-tuned such that activity and stability can be greatly enhanced. These advances suggest that a much wider variety of enzymes may eventually be amenable to immobilization as green catalysts.

  20. Investigation of pollutant gases with molecular absorption spectroscopy

    International Nuclear Information System (INIS)

    Izairi, N; Ajredini, F.; Shehabi, M.

    2011-01-01

    This paper contains the molecular absorption spectroscopic investigation on environmental pollution by many pollutants. For this purpose a laser absorption spectroscopy at 630 nm wavelength has been applied to excite the molecular spectra in order to identify the presence of main gas pollutants. The following was the experimental procedure. Preliminary the presence of pollutants was identified. The gas champions were taken in live environment, in Tetovo streets where cars moved, and in some points in Tetovo suburbia, during different periods of the day. A special civet, part of the apparatus, has been filled by environmental air, and latter, put into the apparatus. A laser beam pulse passes throughout absorbing gas medium in the civet to excite the gas, and the absorbing spectra were automatically registered. The molecular band spectra registration has been performed by an FT-IR Spectrometer (Spectrum BX FT-IR Perkin Elmer). For this purpose the measurements were focused in spectral region of 2075 cm -1 to 2384 cm -1 for CO 2 and CO bands investigation. The importance of such measurements is to investigate the spectral properties of absorption spectra and molecular structure, and for monitoring the environmental pollution. (Author)

  1. Specific interactions and binding energies between thermolysin and potent inhibitors: molecular simulations based on ab initio molecular orbital method.

    Science.gov (United States)

    Hirakawa, Tatsuya; Fujita, Seiya; Ohyama, Tatsuya; Dedachi, Kenichi; Khan, Mahmud Tareq Hassan; Sylte, Ingebrigt; Kurita, Noriyuki

    2012-03-01

    Biochemical functions of the metalloprotease thermolysin (TLN) are controlled by various inhibitors. In a recent study we identified 12 compounds as TLN inhibitors by virtual screening and in vitro competitive binding assays. However, the specific interactions between TLN and these inhibitors have not been clarified. We here investigate stable structures of the solvated TLN-inhibitor complexes by classical molecular mechanics simulations and elucidate the specific interactions between TLN and these inhibitors at an electronic level by using ab initio fragment molecular orbital (FMO) calculations. The calculated binding energies between TLN and the inhibitors are qualitatively consistent with the experimental results, and the FMO results elucidate important amino acid residues of TLN for inhibitor binding. Based on the calculated results, we propose a novel potent inhibitor having a large binding affinity to TLN. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Efficiency at Maximum Power of Interacting Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia; Imparato, Alberto

    2012-01-01

    We investigate the efficiency of systems of molecular motors operating at maximum power. We consider two models of kinesin motors on a microtubule: for both the simplified and the detailed model, we find that the many-body exclusion effect enhances the efficiency at maximum power of the many- motor...

  3. Molecular electrostatics for probing lone pair-π interactions.

    Science.gov (United States)

    Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

    2013-11-14

    An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

  4. Comparison of biomolecules on the basis of Molecular Interaction Potentials

    Directory of Open Access Journals (Sweden)

    Rodrigo Jordi

    2002-01-01

    Full Text Available Molecular Interaction Potentials (MIP are frequently used for the comparison of series of compounds displaying related biological behaviors. These potentials are interaction energies between the considered compounds and relevant probes. The interaction energies are computed in the nodes of grids defined around the compounds. There is a need of detailed and objective comparative analyses of MIP distributions in the framework of structure-activity studies. On the other hand, MIP-based studies do not have to be restricted to series of small ligands, since such studies present also interesting possibilities for the analysis and comparison of biological macromolecules. Such analyses can benefit from the application of new methods and computational approaches. The new software MIPSim (Molecular Interaction Potentials Similarity analysis has recently been introduced with the purpose of analyzing and comparing MIP distributions of series of biomolecules. This program is transparently integrated with other programs, like GAMESS or GRID, which can be used for the computation of the potentials to be analyzed or compared. MIPSim incorporates several definitions of similarity coefficients, and is capable of combining several similarity measures into a single one. On the other hand, MIPSim can perform automatic explorations of the maximum similarity alignments between pairs of molecules.

  5. Molecular metals with ferromagnetic interaction between localized magnetic moments

    Science.gov (United States)

    Nishijo, J.; Ogura, E.; Yamaura, J.; Miyazaki, A.; Enoki, T.; Takano, T.; Kuwatani, Y.; Iyoda, M.

    2000-11-01

    New charge-transfer salts (EDO-TTFI 2) 2M(mnt) 2 (M=Ni,Pt) are the first organic metals with strong ferromagnetic interactions. These salts consist of one-dimensional chains of EDO-TTFI 2 donors and M(mnt) 2 acceptors aligned in parallel to each other. The metallic conductivity is due to the one dimensional chain of EDO-TTFI 2, and a metal-insulator transition occurs at about 90 K. Localized spins of M(mnt) 2 behave as a one-dimensional ferromagnet, which interact with conduction electrons. The origin of the ferromagnetic interactions are orthogonality of the molecular orbitals of M(mnt) 2 and spin polarization effect which is explained by McConnell's first model.

  6. Intercalative interaction of asymmetric copper(II) complex with DNA: experimental, molecular docking, molecular dynamics and TDDFT studies.

    Science.gov (United States)

    Hu, Wei; Deng, Suwen; Huang, Jianyin; Lu, Yanmei; Le, Xueyi; Zheng, Wenxu

    2013-10-01

    The intercalative interactions of small molecules with DNA are important in a variety of biological processes including mutagenesis, carcinogenesis, and chemotherapy. A comprehensive research protocol including experiments and calculations was employed to investigate the intercalative interaction between metallointercalator copper(II) complex and DNA. The intercalative binding mode has been validated by UV spectra, fluorescence spectra, CD spectra and viscosity measurements. The classical molecular dynamics simulation was carried out to investigate the intercalative interaction between asymmetric copper(II) complex and DNA. An analytical method was proposed to simulate the dynamically changing absorption spectra of intercalator/DNA system. According to the established model, the changing process of the electronic absorption spectra for intercalator/DNA system can be predicted accurately. A rational explanation for the change law of absorption spectra has been proposed. Moreover, the analyses of the frontier orbital reveal that the red shift of the absorption spectra is due to the increase of π orbital energy caused by the coupling of the π orbital of the intercalated ligand with the π orbital of DNA. This cause of red shift of spectra is completely different from the previous inference. All these insights are of crucial importance for correctly analyzing the absorption spectra of intercalative interaction, as well as for explaining the macroscopic phenomena observed in experiments at the molecular level. © 2013.

  7. Comprehensive characterization of molecular interactions based on nanomechanics.

    Directory of Open Access Journals (Sweden)

    Murali Krishna Ghatkesar

    Full Text Available Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (approximately 748*10(6 Da adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions.

  8. Investigation of uranium molecular species using laser ablation

    Energy Technology Data Exchange (ETDEWEB)

    Curreli, Davide [Univ. of Illinois, Urbana, IL (United States). Dept. of Nuclear, Plasma, and Radiological Engineering

    2017-07-12

    The goal of this project is to investigate the dynamic evolution of uranium oxide (UOx) molecular species in a rapidly cooling low-temperature plasma using a coupled experimental and modeling approach. Our purpose is to develop quantitative constraints on the UOx phase chemistry under physical conditions similar to that of a nuclear fireball at the time of debris condensation. This work is motivated by a need to better understand the factors controlling uranium chemical fractionation in post-detonation nuclear debris.

  9. Experimental investigation of interactions between proteins and carbon nanomaterials

    Science.gov (United States)

    Sengupta, Bishwambhar

    The global market for nanomaterials based products is forecasted to reach $1 trillion per annum per annum for 2015. Engineered nanomaterials (ENMs) exhibit unique physicochemical properties with potential to impact diverse aspects of society through applications in electronics, renewable energy, and medicine. While the research and proposed applications of ENMs continue to grow rapidly, the health and safety of ENMs still remains a major concern to the public as well as to policy makers and funding agencies. It is now widely accepted that focused efforts are needed for identifying the list of physicochemical descriptors of ENM before they can be evaluated for nanotoxicity and biological response. This task is surprisingly challenging, as many physicochemical properties of ENMs are closely inter related and cannot be varied independently (e.g. increasing the size of an ENM can introduce additional defects). For example, varying toxic response may ensue due to different methods of nanomaterial preparation, dissimilar impurities and defects. Furthermore, the inadvertent coating of proteins on ENM surface in any biological milieu results in the formation of the so-called "protein/bio-corona" which can in turn alter the fate of ENMs and their biological response. Carbon nanomaterials (CNMs) such as carbon nanotubes, graphene, and graphene oxide are widely used ENMs. It is now known that defects in CNMs play an important role not only in materials properties but also in the determination of how materials interact at the nano-bio interface. In this regard, this work investigates the influence of defect-induced hydrophilicity on the bio-corona formation using micro Raman, photoluminescence, infrared spectroscopy, electrochemistry, and molecular dynamics simulations. Our results show that the interaction of proteins (albumin and fibrinogen) with CNMs is strongly influenced by charge transfer between them, inducing protein unfolding which enhances conformational entropy and

  10. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    International Nuclear Information System (INIS)

    De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.

    2002-01-01

    Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

  11. Ultrasonic Studies of Molecular Interactions in Organic Binary Liquid Mixtures

    Directory of Open Access Journals (Sweden)

    S. Thirumaran

    2010-01-01

    Full Text Available The ultrasonic velocity, density and viscosity have been measured for the mixtures of 1-alkanols such as 1-propanol and 1-butanol with N-N dimethylformamide (DMF at 303 K. The experimental data have been used to calculate the acoustical parameters namely adiabatic compressibility (β, free length (Lf, free volume (Vf and internal pressure (πi. The excess values of the above parameters are also evaluated and discussed in the light of molecular interaction existing in the mixtures. It is obvious that there is a formation of hydrogen bonding between DMF and 1-alkanols. Further, the addition of DMF causes dissociation of hydrogen bonded structure of 1-alkanols. The evaluated excess values confirm that the molecular association is more pronounced in system-II comparing to the system-I.

  12. Molecular structure investigation and tautomerism aspects of (E)-3 ...

    Indian Academy of Sciences (India)

    calculations. The effect of the intermolecular N-H—. O H-bonding interactions on the calculated geometric parameters has been tested. The electronic spectra were assigned with the aid of the TD-DFT calculations. 2. Experimental. 2.1 Synthesis and spectral investigations. A mixture of indolin-2-one 1 (1.5 mmol, 200 mg), ...

  13. VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins.

    Science.gov (United States)

    Couvineau, Alain; Laburthe, Marc

    2012-05-01

    The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

  14. Configuration interaction: molecular orbitals for accurate calculations on diatomics

    International Nuclear Information System (INIS)

    Ornellas, F.R.; Hagstrom, S.

    1981-06-01

    A procedure is developed to construct an optimum set of molecular orbitals (MO's) to be used in large scale configuration interaction expansion for diatomics. The set is optimum in the sense that a significant energy improvement can be obtained for a relatively short wavefunction expansion. Aplication of this methodology to the ground state of the LiH molecule gives an energy of -8.06347 a.u. for an expansion with 1852 obtained from a set with 16σ-, 12π-, and 6δ-type MO's. (Author) [pt

  15. Coulomb interactions via local dynamics: a molecular-dynamics algorithm

    International Nuclear Information System (INIS)

    Pasichnyk, Igor; Duenweg, Burkhard

    2004-01-01

    We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

  16. Characterization of the Interaction between Eupatorin and Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods

    Science.gov (United States)

    Xu, Hongliang; Yao, Nannan; Xu, Haoran; Wang, Tianshi; Li, Guiying; Li, Zhengqiang

    2013-01-01

    This study investigated the interaction between eupatorin and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular modeling at pH 7.4. Results of UV-vis and fluorescence spectroscopies illustrated that BSA fluorescence was quenched by eupatorin via a static quenching mechanism. Thermodynamic parameters revealed that hydrophobic and electrostatic interactions played major roles in the interaction. Moreover, the efficiency of energy transfer, and the distance between BSA and acceptor eupatorin, were calculated. The effects of eupatorin on the BSA conformation were analyzed using UV-vis, CD, and synchronous fluorescence. Finally, the binding of eupatorin to BSA was modeled using the molecular docking method. PMID:23839090

  17. Investigation of glassy state molecular motions in thermoset polymers

    Science.gov (United States)

    Tu, Jianwei

    This dissertation presents the investigation of the glassy state molecular motions in isomeric thermoset epoxies by means of solid-state deuterium (2H) NMR spectroscopy technique. The network structure of crosslinked epoxies was altered through monomer isomerism; specifically, diglycidyl ether of bisphenol A (DGEBA) was cured with isomeric amine curatives, i.e., the meta-substituted diaminodiphenylsulfone (33DDS) and para-substituted diaminodiphenylsulfone (44DDS). The use of structural isomerism provided a path way for altering macroscopic material properties while maintaining identical chemical composition within the crosslinked networks. The effects of structural isomerism on the glassy state molecular motions were studied using solid-state 2H NMR spectroscopy, which offers unrivaled power to monitor site-specific molecular motions. Three distinctive molecular groups on each isomeric network, i.e., the phenylene rings in the bisphenol A structure (BPA), the phenylene rings in the diaminodiphenylsulfone structure (DDS), and the hydroxypropoyl ether group (HPE) have been selectively deuterated for a comprehensive study of the structure-dynamics- property relationships in thermoset epoxies. Quadrupolar echo experiments and line shape simulations were employed as the main research approach to gain both qualitative and quantitative motional information of the epoxy networks in the glassy state. Quantitative information on the geometry and rate of the molecular motions allows the elucidation of the relationship between molecular motions and macro physical properties and the role of these motions in the mechanical relaxation. Specifically, it is revealed that both the BPA and HPE moieties in the isomeric networks have almost identical behaviors in the deep glassy state, which indicates that the molecular motions in the glassy state are localized, and the correlation length of the motions does not exceed the length of the DGEBA repeat unit. BPA ring motions contribute

  18. DP 71 AND BETA DYSTROGLYCAN INTERACTION: A MOLECULAR MODELING APPROACH TO UNDERSTAND DUCHENNE MUSCULAR DYSTROPHY

    Directory of Open Access Journals (Sweden)

    Simanti Bhattacharya,

    2013-12-01

    Full Text Available Dp 71 is the most prevalent and widely expressed non muscle isoform of dystrophin (Dp and its mutations are associated with Duchenne muscular dystrophy, a severe form of muscular disorder. Dp 71 deviates from the canonical Dp by means of its truncated N terminal which also has abolished certain amino acids that comprise WW domain in the canonical form. This WW domain is very crucial for Dp’s interaction with partner proteins to establish a bridge between extra cellular matrices and cellular cytoskeleton. In our current study we have employed molecular modeling technique to understand the structural architecture of the N terminal region of Dp 71 and its deviation from the canonical form. We have further extended our studies to analyze the interaction probabilities between Dp 71 and β-DG applying molecular docking. Our studies for the first time have revealed that in spite of the underlying differences in terms of amino acids and structural organization, Dp 71 can interact with β-DG with its N terminal region which shares the similar molecular surface with the canonical form of Dp. These findings have opened up a platform to investigate the molecular interactions, spatio temporal orientations of the amino acids of Dp 71 and β-DG to understand the onset of DMD in much more greater detail

  19. Exploring the Impact of and Perceptions about Interactive, Self-Explaining Environments in Molecular-Level Animations

    Science.gov (United States)

    Falvo, David A.; Urban, Michael J.; Suits, Jerry P.

    2011-01-01

    This mixed-method study investigates the effects of interactivity in animations of a molecular-level process and explores perceptions about the animated learning tool used. Treatments were based on principles of cognitive psychology designed to study the main effects of treatment and spatial ability and their interaction. Results with students (n…

  20. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

  1. Molecular dynamics simulations of interfacial interactions between small nanoparticles during diffusion-limited aggregation

    International Nuclear Information System (INIS)

    Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi

    2015-01-01

    Graphical abstract: - Highlights: • Diffusion-limited aggregation is analyzed using molecular dynamic simulations. • The aggregation processand aggregate structure vary with particle size. • Particle-particle interaction and surface diffusion result in direct bonding. • Water-mediated interaction is responsible for the separation betweennanoparticles. - Abstract: Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle–particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle–particle interaction and high surface diffusion result in the formation of particle–particle bonds of 2 nm TiO 2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO 2 nanoparticles.

  2. Dynamics of relaxation to a stationary state for interacting molecular motors

    Science.gov (United States)

    Gomes, Luiza V. F.; Kolomeisky, Anatoly B.

    2018-01-01

    Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscle contraction. It is known that these biological molecular motors usually perform their cellular tasks by acting collectively, and there are interactions between individual motors that specify the overall collective behavior. One of the fundamental issues related to the collective dynamics of motor proteins is the question if they function at stationary-state conditions. To investigate this problem, we analyze a relaxation to the stationary state for the system of interacting molecular motors. Our approach utilizes a recently developed theoretical framework, which views the collective dynamics of motor proteins as a totally asymmetric simple exclusion process of interacting particles, where interactions are taken into account via a thermodynamically consistent approach. The dynamics of relaxation to the stationary state is analyzed using a domain-wall method that relies on a mean-field description, which takes into account some correlations. It is found that the system quickly relaxes for repulsive interactions, while attractive interactions always slow down reaching the stationary state. It is also predicted that for some range of parameters the fastest relaxation might be achieved for a weak repulsive interaction. Our theoretical predictions are tested with Monte Carlo computer simulations. The implications of our findings for biological systems are briefly discussed.

  3. Investigation on molecular interactions of binary mixtures of isobutanol with 1-alkanols (C1 - C6) at different temperatures. Application of the Peng-Robinson-Stryjek-Vera (PSRV) equation of state (EOS)

    Science.gov (United States)

    Khanlarzadeh, K.; Iloukhani, H.; Soleimani, M.

    2017-07-01

    Densities were measured for binary mixtures of isobutanol with 1-alkanols, namely: methanol, ethanol, 1-propanol, 1-butanol, 1-pentanol and 1-hexanol at the temperatures of (288.15, 298.15 and 308.15) K and ambient pressure. Excess molar volumes, VmE , thermal expansion coefficients α, excess thermal expansion coefficients αE, and isothermal coefficients of pressure excess molar enthalpy, (∂HmE / ∂ P) T , x , were derived from the experimental data and the computed results were fitted to the Redlich-Kister equation. The Peng-Robinson-Stryjek-Vera (PRSV) equation of state was applied, in combination with simple mixing rules to predict the excess molar volume. The VmE results were positive for the mixtures of isobutanol with methanol, ethanol, 1-propanol, 1-butanol, and negative for isobutanol with 1-pentanol and 1-hexanol over the whole composition range. The results showed very small deviations from the behavior of ideal solutions in these mixtures and were analyzed to discuss the nature and strength of intermolecular interactions.

  4. Investigation of groundwater-seawater interactions: a review

    Science.gov (United States)

    Purwoarminta, A.; Moosdorf, N.; Delinom, R. M.

    2018-02-01

    This paper is to review how to investigate the interactions between groundwater and seawater. Those interactions divide into two, which are submarine groundwater discharge and seawater intrusion. This investigation is important because the interactions can give impact to coastal aquifer and marine ecosystem. On land, fresh groundwater is vulnerable to seawater disturbance. Coastal aquifer is under pressure from abstraction caused by population, industry, and agriculture. The pumping can induce seawater intrusion and land subsidence. Then in marine, seawater mixes with freshwater and it decreases salinity. Low salinity will influence marine ecosystem. The ecosystem will be disturbed by groundwater discharge if that water is contaminated. Based on the argue investigation of groundwater-seawater interactions is important and must be accurate because the results are used for coastal water management. To investigate the interactions data, i.e., lithology, pumping tests, hydrochemical data, sea level rise estimates, precipitation data, geophysics, environmental isotopes, and drilling information, should be compiled. The interaction can feed a model to determine how much groundwater extraction happening on coastal areas to prevent seawater intrusion and land subsidence. Water resources management on coasts should consider groundwater-seawater interactions.

  5. Intra-membrane molecular interactions of K+ channel proteins :

    Energy Technology Data Exchange (ETDEWEB)

    Moczydlowski, Edward G.

    2013-07-01

    Ion channel proteins regulate complex patterns of cellular electrical activity and ionic signaling. Certain K+ channels play an important role in immunological biodefense mechanisms of adaptive and innate immunity. Most ion channel proteins are oligomeric complexes with the conductive pore located at the central subunit interface. The long-term activity of many K+ channel proteins is dependent on the concentration of extracellular K+; however, the mechanism is unclear. Thus, this project focused on mechanisms underlying structural stability of tetrameric K+ channels. Using KcsA of Streptomyces lividans as a model K+ channel of known structure, the molecular basis of tetramer stability was investigated by: 1. Bioinformatic analysis of the tetramer interface. 2. Effect of two local anesthetics (lidocaine, tetracaine) on tetramer stability. 3. Molecular simulation of drug docking to the ion conduction pore. The results provide new insights regarding the structural stability of K+ channels and its possible role in cell physiology.

  6. MOLECULAR DYNAMICS SIMULATION OF LYSINE DENDRIMER AND SEMAX PEPTIDES INTERACTION

    Directory of Open Access Journals (Sweden)

    E. V. Popova

    2016-07-01

    Full Text Available The paper deals with the possibility of complex formation of therapeutic Semax peptides with lysine dendrimer by molecular modeling methods. Dendrimers are often used for delivery of drugs and biological molecules (e.g., DNA, peptides and polysaccharides. Since lysine dendrimers are less toxic than conventional synthetic dendrimers (e.g., polyamidoamine (PAMAM dendrimer, we chose them and studied two systems containing dendrimer and the different number of Semax peptides. The study was carried out by molecular dynamics method. It was obtained that the stable complexes were formed in both cases. The equilibrium structures of these complexes were investigated. These complexes can be used in the future in therapy of various diseases as Semax peptides have significant antioxidant, antihypoxic and neuroprotecting action.

  7. Decreased oxygen permeability of EVOH through molecular interactions

    Directory of Open Access Journals (Sweden)

    Zs. Peter

    2014-10-01

    Full Text Available Poly(ethylene-co-vinyl alcohol of 48 mol% ethylene content was modified with N,N'-bis(2,2,6,6-tetramethyl-4-piperidyl-isophthalamide (Nylostab SEED to decrease the oxygen permeability of the polymer. The additive was added in a wide concentration range from 0 to 10 wt%. The structure and properties of the polymer were characterized with various methods including differential scanning calorimetry, X-ray diffraction, mechanical testing, optical measurements and oxygen permeation. Interactions were estimated by molecular modeling and infrared spectroscopy. The results showed that oxygen permeation decreased considerably when the additive was added at less than 2.0 wt% concentration. The decrease resulted from the interaction of the hydroxyl groups of the polymer and the amide groups of the additive. The dissolution of the additive in the polymer led to decreased crystallinity, but also to decreased mobility of amorphous molecules. Stiffness and strength, but also deformability increased as a result. Above 2 wt% the additive forms a separate phase leading to the deterioration of properties. The success of the approach represents a novel way to control oxygen permeation in EVOH and in other polymers with similar functional groups capable of strong interactions.

  8. Molecular interactions in gelatin/chitosan composite films.

    Science.gov (United States)

    Qiao, Congde; Ma, Xianguang; Zhang, Jianlong; Yao, Jinshui

    2017-11-15

    Gelatin and chitosan were mixed at different mass ratios in solution forms, and the rheological properties of these film-forming solutions, upon cooling, were studied. The results indicate that the significant interactions between gelatin and chitosan promote the formation of multiple complexes, reflected by an increase in the storage modulus of gelatin solution. Furthermore, these molecular interactions hinder the formation of gelatin networks, consequently decreasing the storage modulus of polymer gels. Both hydrogen bonds and electrostatic interactions are formed between gelatin and chitosan, as evidenced by the shift of the amide-II bands of polymers. X-ray patterns of composite films indicate that the contents of triple helices decrease with increasing chitosan content. Only one glass transition temperature (T g ) was observed in composite films with different composition ratios, and it decreases gradually with an increase in chitosan proportion, indicating that gelatin and chitosan have good miscibility and form a wide range of blends. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Molecular investigations of β-thalassemic children in Erbil governorate

    Science.gov (United States)

    Hasan, Ahmad N.; Al-Attar, Mustafa S.

    2017-09-01

    The present work studies the molecular investigation of 40 thalassemic carriers using polymerase chain reaction. Forty thalassemic carriers who were registered and treated at Erbil thalassemic center and twenty apparently healthy children have been included in the present study. Ages of both groups ranged between 1-18 years. Four primers used to detect four different beta thalassemia mutations they were codon 8/9, codon 8, codon 41/42 and IVS-1-5. The two most common mutations detected among thalassemia group were Cd8/9 with 8 cases (20%) and Cd-8 with 6 cases (15%) followed by codon 41/42 with 4 cases (10%) which investigated and detected for the first time in Erbil governorate through the present study and finally IVS-1-5 with 3 cases (7.5%), while no any cases detected among control group.

  10. Lysozyme-magnesium aluminum silicate microparticles: Molecular interaction, bioactivity and release studies

    DEFF Research Database (Denmark)

    Kanjanakawinkul, Watchara; Medlicott, Natalie J.; Rades, Thomas

    2015-01-01

    The objectives of this study were to investigate the adsorption behavior of lysozyme (LSZ) onto magnesium aluminum silicate (MAS) at various pHs and to characterize the LSZ–MAS microparticles obtained from the molecular interaction between LSZ and MAS. The results showed that LSZ could be bound...... onto the MAS layers at different pHs, leading to the formation of LSZ–MAS microparticles. The higher preparation pH permitted greater adsorption affinity but a lower adsorption capacity of LSZ onto MAS. LSZ could interact with MAS via hydrogen bonds and electrostatic forces, resulting in the formation...

  11. Modelling interacting molecular motors with an internal degree of freedom

    Science.gov (United States)

    Pinkoviezky, Itai; Gov, Nir S.

    2013-02-01

    The mechanisms underlying the collective motion of molecular motors in living cells are not yet fully understood. One such open puzzle is the observed pulses of backward-moving myosin-X in the filopodia structure. Motivated by this phenomenon we introduce two generalizations of the ‘total asymmetric exclusion process’ (TASEP) that might be relevant to the formation of such pulses. The first is adding a nearest-neighbours attractive interaction between motors, while the second is adding an internal degree of freedom corresponding to a processive and immobile form of the motors. Switching between the two states occurs stochastically, without a conservation law. Both models show strong deviations from the mean field behaviour and lack particle-hole symmetry. We use approximations borrowed from the research on vehicular traffic models to calculate the current and jam size distribution in a system with periodic boundary conditions and introduce a novel modification to one of these approximation schemes.

  12. Modelling interacting molecular motors with an internal degree of freedom

    International Nuclear Information System (INIS)

    Pinkoviezky, Itai; Gov, Nir S

    2013-01-01

    The mechanisms underlying the collective motion of molecular motors in living cells are not yet fully understood. One such open puzzle is the observed pulses of backward-moving myosin-X in the filopodia structure. Motivated by this phenomenon we introduce two generalizations of the ‘total asymmetric exclusion process’ (TASEP) that might be relevant to the formation of such pulses. The first is adding a nearest-neighbours attractive interaction between motors, while the second is adding an internal degree of freedom corresponding to a processive and immobile form of the motors. Switching between the two states occurs stochastically, without a conservation law. Both models show strong deviations from the mean field behaviour and lack particle–hole symmetry. We use approximations borrowed from the research on vehicular traffic models to calculate the current and jam size distribution in a system with periodic boundary conditions and introduce a novel modification to one of these approximation schemes. (paper)

  13. Phase equilibria and molecular interaction studies on (naphthols + vanillin) systems

    International Nuclear Information System (INIS)

    Gupta, Preeti; Agrawal, Tanvi; Das, Shiva Saran; Singh, Nakshatra Bahadur

    2012-01-01

    Highlights: ► Phase equilibria of (naphthol + vanillin) systems have been studied for the first time. ► Eutectic type phase diagrams are obtained. ► Eutectic mixtures show nonideal behaviour. ► There is a weak molecular interaction between the components in the eutectic mixtures. ► α-Naphthol–vanillin eutectic is more stable as compared to β-naphthol–vanillin. - Abstract: Phase equilibria between (α-naphthol + vanillin) and (β-naphthol + vanillin) systems have been studied by thaw-melt method and the results show the formation of simple eutectic mixtures. Crystallization velocities of components and eutectic mixtures were determined at different stages under cooling. With the help of differential scanning calorimeter (DSC), the enthalpy of fusion of components and eutectic mixtures was determined and from the values excess thermodynamic functions viz., excess Gibbs free energy (G E ), excess entropy (S E ), excess enthalpy (H E ) of hypo-, hyper- and eutectic mixtures were calculated. Flexural strength measurements were made in order to understand the non-ideal nature of eutectics. FT-IR spectral studies indicate the formation of hydrogen bond in the eutectic mixture. Anisotropic and isotropic microstructural studies of components, hypo-, hyper- and eutectic mixtures were made. Jackson’s roughness parameter was calculated and found to be greater than 2 suggesting the faceted morphology with irregular structures. The overall results have shown that there is a weak molecular interaction between the components in the eutectic mixtures and the (α-naphthol + vanillin) eutectic is more stable as compared to the (β-naphthol + vanillin) eutectic system.

  14. A comprehensive molecular interaction map for rheumatoid arthritis.

    Science.gov (United States)

    Wu, Gang; Zhu, Lisha; Dent, Jennifer E; Nardini, Christine

    2010-04-16

    Computational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine--the scientific approach to medicine in tight relation with basic science--, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions that occur between molecules related to Rheumatoid Arthritis (RA). Due to the complexity of the disease and the numerous molecular players involved, we devised a method to construct a systemic network of interactions of the processes ongoing in patients affected by RA. The network is based on high-throughput data, refined semi-automatically with carefully curated literature-based information. This global network has then been topologically analysed, as a whole and tissue-specifically, in order to translate the experimental molecular connections into topological motifs meaningful in the identification of tissue-specific markers and targets in the diagnosis, and possibly in the therapy, of RA. We find that some nodes in the network that prove to be topologically important, in particular AKT2, IL6, MAPK1 and TP53, are also known to be associated with drugs used for the treatment of RA. Importantly, based on topological consideration, we are also able to suggest CRKL as a novel potentially relevant molecule for the diagnosis or treatment of RA. This type of finding proves the potential of in silico analyses able to produce highly refined hypotheses, based on vast experimental data, to be tested further and more efficiently. As research on RA is ongoing, the present map is in fieri, despite being--at the moment--a reflection of the state of the art. For this reason we make the network freely available in the standardised and easily exportable .xml CellDesigner format at 'www.picb.ac.cn/ClinicalGenomicNTW/temp.html' and 'www.celldesigner.org'.

  15. A comprehensive molecular interaction map for rheumatoid arthritis.

    Directory of Open Access Journals (Sweden)

    Gang Wu

    2010-04-01

    Full Text Available Computational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine--the scientific approach to medicine in tight relation with basic science--, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions that occur between molecules related to Rheumatoid Arthritis (RA.Due to the complexity of the disease and the numerous molecular players involved, we devised a method to construct a systemic network of interactions of the processes ongoing in patients affected by RA. The network is based on high-throughput data, refined semi-automatically with carefully curated literature-based information. This global network has then been topologically analysed, as a whole and tissue-specifically, in order to translate the experimental molecular connections into topological motifs meaningful in the identification of tissue-specific markers and targets in the diagnosis, and possibly in the therapy, of RA.We find that some nodes in the network that prove to be topologically important, in particular AKT2, IL6, MAPK1 and TP53, are also known to be associated with drugs used for the treatment of RA. Importantly, based on topological consideration, we are also able to suggest CRKL as a novel potentially relevant molecule for the diagnosis or treatment of RA. This type of finding proves the potential of in silico analyses able to produce highly refined hypotheses, based on vast experimental data, to be tested further and more efficiently. As research on RA is ongoing, the present map is in fieri, despite being--at the moment--a reflection of the state of the art. For this reason we make the network freely available in the standardised and easily exportable .xml CellDesigner format at 'www.picb.ac.cn/ClinicalGenomicNTW/temp.html' and 'www.celldesigner.org'.

  16. Molecular self-assembly for biological investigations and nanoscale lithography

    Science.gov (United States)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  17. Thermal and molecular investigation of laser tissue welding

    Energy Technology Data Exchange (ETDEWEB)

    Small, W., IV

    1998-06-01

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack oil both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub-surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of tile probability of long-term success. Molecular effects induced In the tissue by laser irradiation were investigated by measuring tile concentrations of specific collagen covalent crosslinks and characterizing the Fourier-Transform infrared (FTIR) spectra before and after the laser exposure.

  18. Molecular Investigation of Pediatric Portuguese Patients with Sensorineural Hearing Loss

    Directory of Open Access Journals (Sweden)

    Célia Nogueira

    2011-01-01

    Full Text Available The understanding of the molecular genetics in sensorineural hearing loss (SNHL has advanced rapidly during the last decade, but the molecular etiology of hearing impairment in the Portuguese population has not been investigated thoroughly. To provide appropriate genetic testing and counseling to families, we analyzed the whole mitochondrial genome in 95 unrelated children with SNHL (53 nonsyndromic and 42 syndromic and searched for variations in two frequent genes, GJB2 and GJB6, in the non-syndromic patients. Mutations in mtDNA were detected in 4.2% of the cases, including a hitherto undescribed change in the mtDNA-tRNATrp gene (namely, m.5558A>G. We also identified mono- or biallelic GJB2 mutations in 20 of 53 non-syndromic cases and also detected two novel mutations (p.P70R and p.R127QfsX84. Our data further reinforce the notion that genetic heterogeneity is paramount in children with SNHL.

  19. Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions.

    Directory of Open Access Journals (Sweden)

    Natalie S Scholes

    2016-05-01

    Full Text Available Transcriptional activation domains (ADs are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators.

  20. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  1. Molecular interactions between (--epigallocatechin gallate analogs and pancreatic lipase.

    Directory of Open Access Journals (Sweden)

    Shihui Wang

    Full Text Available The molecular interactions between pancreatic lipase (PL and four tea polyphenols (EGCG analogs, like (--epigallocatechin gallate (EGCG, (--gallocatechin gallate (GCG, (--epicatechin gallate (ECG, and (--epigallocatechin (EC, were studied from PL activity, conformation, kinetics and thermodynamics. It was observed that EGCG analogs inhibited PL activity, and their inhibitory rates decreased by the order of EGCG>GCG>ECG>EC. PL activity at first decreased rapidly and then slowly with the increase of EGCG analogs concentrations. α-Helix content of PL secondary structure decreased dependent on EGCG analogs concentration by the order of EGCG>GCG>ECG>EC. EGCG, ECG, and EC could quench PL fluorescence both dynamically and statically, while GCG only quenched statically. EGCG analogs would induce PL self-assembly into complexes and the hydrodynamic radii of the complexes possessed a close relationship with the inhibitory rates. Kinetics analysis showed that EGCG analogs non-competitively inhibited PL activity and did not bind to PL catalytic site. DSC measurement revealed that EGCG analogs decreased the transition midpoint temperature of PL enzyme, suggesting that these compounds reduced PL enzyme thermostability. In vitro renaturation through urea solution indicated that interactions between PL and EGCG analogs were weak and non-covalent.

  2. Investigating physics learning with layered student interaction networks

    DEFF Research Database (Denmark)

    Bruun, Jesper; Traxler, Adrienne

    Centrality in student interaction networks (SINs) can be linked to variables like grades [1], persistence [2], and participation [3]. Recent efforts in the field of network science have been done to investigate layered - or multiplex - networks as mathematical objects [4]. These networks can be e......, this study investigates how target entropy [5,1] and pagerank [6,7] are affected when we take time and modes of interaction into account. We present our preliminary models and results and outline our future work in this area....

  3. Thermal and molecular investigation of laser tissue welding

    Science.gov (United States)

    Small, Ward, IV

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack on both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of the probability of long-term success. Molecular effects induced in the tissue by laser irradiation were investigated by measuring the concentrations of specific collagen covalent crosslinks and measuring the infrared absorption spectra before and after the laser exposure. This investigation yielded results pertaining to both the methods and mechanisms of laser tissue welding. The combination of two-color infrared thermometry to obtain accurate surface temperatures free from emissivity bias and computer modeling illustrated the importance of including evaporation in the simulations, which effectively serves as an inherent cooling mechanism during laser irradiation. Moreover, the hydration state predicted by the model was useful in assessing the role of electrostatic versus covalent bonding in the fusion. These tools also helped elicit differences between dye- enhanced liquid solders and solid-matrix patches in laser-assisted tissue welding, demonstrating the significance of repeatable energy delivery. Surprisingly, covalent bonds

  4. Post-foil interaction in foil-induced molecular dissociation

    International Nuclear Information System (INIS)

    Faibis, A.; Kanter, E.P.; Koenig, W.; Plesser, I.; Vager, Z.

    1985-01-01

    The authors have investigated the foil-induced dissociation of 175- 250- keV/amu CH + , NH + , and OH + , FH + and NeH + ions by coincident detection of the fragment atoms. The dissociation energies corresponding to in-foil and post-foil interactions were deduced from the measured relative flight times of the fragment pairs to a set of detectors downstream from the target. The authors considered final states consisting of a) a proton and a heavy-ion and, b) a hydrogen atom and a heavy-ion. Surprisingly, in both cases the energy released in the post-target interaction shows a similar linear increase with the charge state of the heavy partner

  5. Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

    Science.gov (United States)

    Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

    2008-02-19

    Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

  6. Diffraction stress analysis of thin films; investigating elastic grain interaction

    International Nuclear Information System (INIS)

    Kumar, A.

    2005-12-01

    This work is dedicated to the investigation of specimens exhibiting anisotropic microstructures (and thus macroscopic elastic anisotropy) and/or inhomogeneous microstructures, as met near surfaces and in textured materials. The following aspects are covered: (i) Analysis of specimens with direction-dependent (anisotropic) elastic grain-interaction. Elastic grain-interaction determines the distribution of stresses and strains over the (crystallographically) differently oriented grains of a mechanically stressed polycrystal and the mechanical and diffraction (X-ray) elastic constants (relating (diffraction) lattice strains to mechanical stresses). Grain interaction models that allow for anisotropic, direction-dependent grain interaction have been developed very recently. The notion 'direction-dependent' grain-interaction signifies that different grain-interaction constraints prevail along different directions in a specimen. Practical examples of direction-dependent grain interaction are the occurrence of surface anisotropy in thin films and the surface regions of bulk polycrystals and the occurrence of grain-shape (morphological) texture. In this work, for the first time, stress analyses of thin films have been performed on the basis of these newly developed grain-interaction models. It has also been demonstrated that the identification of the (dominant) source of direction-dependent grain interaction is possible. The results for the grain interaction have been discussed in the light of microstructural investigations of the specimens by microscopic techniques. (ii) Analysis of specimens with depth gradients: Diffraction stress analysis can be hindered if gradients of the stress state, the composition or the microstructure occur in the specimen under investigation, as the so-called information depth varies in the course of a traditional stress measurement: Ambiguous results are thus generally obtained. In this work, a strategy for stress measurements at fixed

  7. Molecular interaction study of flavonoid derivative 3d with human serum albumin using multispectroscopic and molecular modeling approach.

    Science.gov (United States)

    Wei, Juntong; Jin, Feng; Wu, Qin; Jiang, Yuyang; Gao, Dan; Liu, Hongxia

    2014-08-01

    Human serum albumin (HSA) has been developed as a model protein to study drug-protein interaction. In the present work, the interaction between our synthesized flavonoid derivative 3d (possessing potent antitumor activity against HepG2 cells) and HSA was investigated using fluorescence spectroscopy, circular dichroism spectroscopy, UV-vis spectroscopy and molecular modeling approach. Fluorescence spectroscopy showed that the fluorescence of HSA can be quenched remarkably by 3d under physiological condition with a slight shift of maximum fluorescence emission bands from 360nm to 363nm. Calculated results from Stern-Volmer equation and modified Stern-Volmer equation indicated that the fluorescence was quenched by static quenching processing with association constant 5.26±0.04×10(4)L mol(-1) at 298K. After comprehensive consideration of the free energy change ΔG, enthalpy change ΔH and entropy change ΔS, electrostatic interactions were confirmed as the main factor that participate in stabilizing the 3d-HSA complex. Both dichroism spectroscopy and UV-vis spectroscopy indicated conformational change of HSA after binding to 3d. Moreover, the structure of HSA was loosened and the percentage of α-helix decreased with increasing concentration of 3d. Molecular modeling results demonstrated that 3d could bind to HSA well into subdomain IIA, which is related to its capability of deposition and delivery. Three cation-π interactions and three hydrogen bonds occurred between 3d and amino acid residuals ARG218, ARG222 and LYS199. In conclusion, flavonoid derivative 3d can bind to HSA with noncovalent bond in a relatively stable way, so it can be delivered by HSA in a circulatory system. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Virtual Manipulatives on the Interactive Whiteboard: A Preliminary Investigation

    Science.gov (United States)

    Mildenhall, Paula; Swan, Paul; Northcote, Maria; Marshall, Linda

    2008-01-01

    As part of the project titled "Hands-On Heads-On: The Effective Use of Manipulatives Both Virtual and Physical" being undertaken at Edith Cowan University, there was an investigation into the use of virtual manipulatives and the interactive whiteboard (IWB). Virtual manipulatives may be defined as a virtual representation of a physical…

  9. Investigating the amplitude of interactive footstep sounds and soundscape reproduction

    DEFF Research Database (Denmark)

    Turchet, Luca; Serafin, Stefania

    2013-01-01

    In this paper, we study the perception of amplitude of soundscapes and interactively generated footstep sounds provided both through headphones and a surround sound system. In particular, we investigate whether there exists a value for the amplitude of soundscapes and footstep sounds which is con...

  10. Investigating Stratification, Language Diversity and Mathematics Classroom Interaction

    Science.gov (United States)

    Barwell, Richard

    2016-01-01

    Research on the socio-political dimensions of language diversity in mathematics classrooms is under-theorised and largely focuses on language choice. These dimensions are, however, likely to influence mathematics classroom interaction in many other ways than participants' choice of language. To investigate these influences, I propose that the…

  11. A preliminary investigation into genotype x environment interaction ...

    African Journals Online (AJOL)

    The purpose of the study was to investigate a possible genotype by environment interaction in first calf South African Holstein cows for both production and reproduction traits. Data from 100 975 cows on a total mixed ration (TMR) and 22 083 pasture based cows were used. These cows were the progeny of 4 391 sires and ...

  12. Investigating the Nature of GxE Interaction under Different ...

    African Journals Online (AJOL)

    for this study were from Intermediate to Late Hybrid Trials (ILHT) conducted in ... This phenomenon, referred to as COI, introduces a degree of uncertainty into the ... Investigating the Nature of GxE Interaction under Different Management Systems [3]. Materials and Methods. Setup of the trial. The number of trial sites used for ...

  13. An Investigation of the Interaction between Resazurin and Cd 2+ ...

    African Journals Online (AJOL)

    The voltammetric behaviour of resazurin in the presence of Cd2+ and Zn2+ ions at a hanging mercury drop electrode (HMDE) was investigated by using square wave voltammetry (SWV), cyclic voltammetry (CV) and adsorptive square wave voltammetry (AdsSWV). The interaction of resazurin with Cd2+ and Zn2+ starts ...

  14. A probe to study the toxic interaction of tartrazine with bovine hemoglobin at the molecular level.

    Science.gov (United States)

    Li, Yating; Wei, Haoran; Liu, Rutao

    2014-03-01

    Tartrazine is an artificial azo dye commonly used in food products, but tartrazine in the environment is potentially harmful. The toxic interaction between tartrazine and bovine hemoglobin (BHb) was investigated using fluorescence, synchronous fluorescence, UV-vis absorption, circular dichroism (CD) and molecular modeling techniques under simulated physiological conditions. The fluorescence data showed that tartrazine can bind with BHb to form a complex. The binding process was a spontaneous molecular interaction, in which van der Waals' forces and hydrogen bonds played major roles. Molecular docking results showed that the hydrogen bonds exist between the oxygen atoms at position 31 of tartrazine and the nitrogen atom NZ7 on Lys99, and also between the oxygen atoms at position 15 of tartrazine and the nitrogen atom NZ7 on Lys104, Lys105. The results of UV-vis and CD spectra revealed that tartrazine led to conformational changes in BHb, including loosening of the skeleton structure and decreasing α helix in the secondary structure. The synchronous fluorescence experiment revealed that tartrazine binds into the hemoglobin central cavity, and this was verified using a molecular modeling study. Copyright © 2013 John Wiley & Sons, Ltd.

  15. Investigation of the Physical and Molecular Properties of Asphalt Binders Processed with Used Motor Oils

    Directory of Open Access Journals (Sweden)

    Mohyeldin Ragab

    2015-01-01

    Full Text Available In this work we investigated the performance aspects of addition of used motor oils (UMO to neat and crumb rubber modified asphalts (CRMA and related that to the change of molecular size distribution of modified asphalt’s fractions; asphaltenes, saturates, naphthene aromatics, and polar aromatics. Based on the results of temperature sweep viscoelastic tests, addition of crumb rubber modifier (CRM alone or with UMO results in the formation of internal network within the modified asphalt. Based on the results of short and long term aged asphalts, the utilization of combination of UMO and CRM enhanced the aging behavior of asphalt. Bending beam rheometer was utilized to investigate the low temperature behavior of UMO modified asphalts. Based on those tests, the utilization of the UMO and CRM enhanced the low temperature properties of asphalts. Based on the results of the asphalt separation tests and the Gel Permeation Chromatography (GPC analysis, it was found that saturates and naphthene aromatics are the two asphalt fractions that have similar molecular size fractions as those of UMO. However, UMO only shifts the molecular sizes of saturates after interaction with asphalt. Results also show that polar aromatics pose higher molecular size structures than UMO.

  16. Molecular interaction mechanism between 2-mercaptobenzimidazole and copper-zinc superoxide dismutase.

    Directory of Open Access Journals (Sweden)

    Yue Teng

    Full Text Available 2-Mercaptobenzimidazole (MBI is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment is potentially harmful. In the present work, the toxic interaction of MBI with the important antioxidant enzyme copper-zinc superoxide dismutase (Cu/ZnSOD was investigated using spectroscopic and molecular docking methods. MBI can interact with Cu/ZnSOD to form an MBI-Cu/ZnSOD complex. The binding constant, number of binding sites and thermodynamic parameters were measured, which indicated that MBI could spontaneously bind with Cu/ZnSOD with one binding site through hydrogen bonds and van der Waals forces. MBI bound into the Cu/ZnSOD interface of two subdomains, which caused some microenvironmental and secondary structure changes of Cu/ZnSOD and further resulted in the inhibition of Cu/ZnSOD activity. This work provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme Cu/ZnSOD. The estimated methods in this work may be applied to probe molecular interactions of biomacromolecules and other pollutants and drugs.

  17. Molecular Ecological Insights into Neotropical Bird-Tick Interactions.

    Science.gov (United States)

    Miller, Matthew J; Esser, Helen J; Loaiza, Jose R; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds' role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually-sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna). Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical-Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically-identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly-discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology and the dynamics of

  18. Molecular Ecological Insights into Neotropical Bird-Tick Interactions.

    Directory of Open Access Journals (Sweden)

    Matthew J Miller

    Full Text Available In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds' role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually-sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna. Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical-Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically-identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly-discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology

  19. Molecular Ecological Insights into Neotropical Bird–Tick Interactions

    Science.gov (United States)

    Esser, Helen J.; Loaiza, Jose R.; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds’ role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually–sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna). Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical–Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically–identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly–discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology and the

  20. Stable Molecular Diodes Based on π-π Interactions of the Molecular Frontier Orbitals with Graphene Electrodes.

    Science.gov (United States)

    Song, Peng; Guerin, Sarah; Tan, Sherman Jun Rong; Annadata, Harshini Venkata; Yu, Xiaojiang; Scully, Micheál; Han, Ying Mei; Roemer, Max; Loh, Kian Ping; Thompson, Damien; Nijhuis, Christian A

    2018-03-01

    In molecular electronics, it is important to control the strength of the molecule-electrode interaction to balance the trade-off between electronic coupling strength and broadening of the molecular frontier orbitals: too strong coupling results in severe broadening of the molecular orbitals while the molecular orbitals cannot follow the changes in the Fermi levels under applied bias when the coupling is too weak. Here, a platform based on graphene bottom electrodes to which molecules can bind via π-π interactions is reported. These interactions are strong enough to induce electronic function (rectification) while minimizing broadening of the molecular frontier orbitals. Molecular tunnel junctions are fabricated based on self-assembled monolayers (SAMs) of Fc(CH 2 ) 11 X (Fc = ferrocenyl, X = NH 2 , Br, or H) on graphene bottom electrodes contacted to eutectic alloy of gallium and indium top electrodes. The Fc units interact more strongly with graphene than the X units resulting in SAMs with the Fc at the bottom of the SAM. The molecular diodes perform well with rectification ratios of 30-40, and they are stable against bias stressing under ambient conditions. Thus, tunnel junctions based on graphene with π-π molecule-electrode coupling are promising platforms to fabricate stable and well-performing molecular diodes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Investigation on the toxic interaction of typical plasticizers with calf thymus DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Xiaojing [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Zong, Wansong, E-mail: gaocz@sdu.edu.cn [College of Population, Resources and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan 250014 (China); Liu, Chunguang; Liu, Yang [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Gao, Canzhu, E-mail: rutaoliu@sdu.edu.cn [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Liu, Rutao [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China)

    2015-05-15

    The interactions of typical plasticizers dimethyl phthalate (DMP), diethyl phthalate (DEP) and dibutyl phthalate (DBP) with calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopic techniques and molecular modeling. Experimental results indicated that the characteristic fluorescence intensity of phthalic acid rose with the increase of DNA concentration; while the characteristic fluorescence intensities of plasticizers decreased with the increase of DNA concentration. Experiments on native and denatured DNA determined that plasticizers interacted with DNA both in groove and electrostatic binding mode. The molecular modeling results further illustrated that there is groove binding between them; hydrogen bonding and Van der Waals interactions were the main forces. With the extension of branched-chains, the binding effects between plasticizers and DNA were weakened, which could be related to the increased steric hindrance. - Highlights: • This work established the binding mode of plasticizers with DNA on molecular level. • The mechanism was explored by fluorescence spectroscopic and molecular docking methods. • There are two kinds of binding mode between DMP, DEP, DBP and DNA, electrostatic and groove. • With the branched chain extension, the binding effect of plasticizers and DNA has been weakened.

  2. Thermodynamic Study of Molecular Interactions in Eutectic Mixtures Containing Camphene.

    Science.gov (United States)

    Okuniewski, Marcin; Paduszyński, Kamil; Domańska, Urszula

    2016-12-22

    Terpenes are an abundant and diverse class of chemicals having numerous applications in different areas of chemistry. Therefore, a detailed knowledge of physical and thermodynamic properties of terpenes and their mixtures with other compounds is highly desired. This paper reports both a thermodynamic study on solid-liquid equilibrium (SLE) phase diagrams in binary systems formed by (±)-camphene (a representative terpene) and one of the following solvents: n-decane, n-dodecane, 1-decanol, 1-dodecanol, phenylmethanol, 2-phenylethanol, 2-cyclohexylethanol. The observed trends in the measured SLE data are discussed in terms of structure (alkyl chain length, aromacity) of the solvent and molecular interactions. Modeling of the considered SLE phase diagrams with three well-established thermodynamic models, namely, modified UNIFAC (Dortmund), perturbed-chain statistical associating fluid theory (PC-SAFT) and conductor-like screening model for real solvents (COSMO-RS), is presented. A comparative analysis of their performance is given in terms of average absolute deviations between predicted and experimental SLE temperature.

  3. Interaction of diuron to human serum albumin: Insights from spectroscopic and molecular docking studies.

    Science.gov (United States)

    Chen, Huilun; Rao, Honghao; Yang, Jian; Qiao, Yongxiang; Wang, Fei; Yao, Jun

    2016-01-01

    This investigation was undertaken to determine the interaction of diuron with human serum albumin (HSA) was studied by monitoring the spectral behavior of diuron-HSA system. The fluorescence of HSA at 340 nm excited at 230 nm was obviously quenched by diuron due to dynamic collision and the quenching constant was of the order of 10(4) L mol(-1) at 310 K. However, no fluorescence quenching was observed when excited at 280 nm. Thermodynamic investigations revealed that the combination between diuron and HSA was entropy driven by predominantly hydrophobic interactions. The binding of diuron induced the drastic reduction in α-helix conformation and the significant enhancement in β-turn conformation of HSA. In addition, both sites marker competition study and molecular modeling simulation evidenced the binding of diuron to HSA primarily took place in subdomain IIIA (Sudlow's site II).

  4. Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

    Science.gov (United States)

    Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

    2012-07-15

    The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Simulating Molecular Interactions of Carbon Nanoparticles with a Double-Stranded DNA Fragment

    Directory of Open Access Journals (Sweden)

    Zhuang Wang

    2015-01-01

    Full Text Available Molecular interactions between carbon nanoparticles (CNPs and a double-stranded deoxyribonucleic acid (dsDNA fragment were investigated using molecular dynamics (MD simulations. Six types of CNPs including fullerenes (C60 and C70, (8,0 single-walled carbon nanotube (SWNT, (8,0 double-walled carbon nanotube (DWNT, graphene quantum dot (GQD, and graphene oxide quantum dot (GOQD were studied. Analysis of the best geometry indicates that the dsDNA fragment can bind to CNPs through pi-stacking and T-shape. Moreover, C60, DWNT, and GOQD bind to the dsDNA molecules at the minor groove of the nucleotide, and C70, SWNT, and GQD bind to the dsDNA molecules at the hydrophobic ends. Estimated interaction energy implies that van der Waals force may mainly contribute to the mechanisms for the dsDNA-C60, dsDNA-C70, and dsDNA-SWNT interactions and electrostatic force may contribute considerably to the dsDNA-DWNT, dsDNA-GQD, and dsDNA-GOQD interactions. On the basis of the results from large-scale MD simulations, it was found that the presence of the dsDNA enhances the dispersion of C60, C70, and SWNT in water and has a slight impact on DWNT, GQD, and GOQD.

  6. Experimental investigations and modelling of sodium-concrete interaction

    International Nuclear Information System (INIS)

    Schultheiss, G.F.; Deeg, H.J.

    1990-01-01

    The use of sodium as a coolant in liquid metal fast breeder reactors, fusion reactors, and solar plants requires special consideration of its chemical reactivity and related safety problems in the case of sodium leckage. On contact between hot sodium and concrete an interaction takes place resulting in energy release and hydrogen generation, which may contribute to containment loading by pressurization in a hypothetical accident situation. For this reason, sodium-concrete interactions were investigated experimentally and theoretically. The experiments revealed important effects of quartzitic material within the concrete and of the sodium temperature on the interaction mechanisms, the energy release and the consequent hydrogen production. The numerical model shows good agreement with the experimental results. (orig.) [de

  7. Molecular Dynamics Investigation of Efficient SO2 Absorption by ...

    Indian Academy of Sciences (India)

    ANIRBAN MONDAL

    TMG][L]) that absorbs an equimolar amount of SO2 through chemisorption.12 Subsequently, a sig- ...... Visual molecular dynamics J. Mol. Graphics 14 33. 83. Fiorin G, Klein M L and Hénin J 2013 Using collective variables to drive molecular ...

  8. Molecular interactions of alcohols with zeolite BEA and MOR frameworks.

    Science.gov (United States)

    Stückenschneider, Kai; Merz, Juliane; Schembecker, Gerhard

    2013-12-01

    Zeolites can adsorb small organic molecules such as alcohols from a fermentation broth. Also in the zeolite-catalyzed conversion of alcohols to biofuels, biochemicals, or gasoline, adsorption is the first step. Several studies have investigated the adsorption of alcohols in different zeolites experimentally, but computational investigations in this field have mostly been restricted to zeolite MFI. In this study, the adsorption of C1-C4 alcohols in BEA and MOR was investigated using density functional theory (DFT). Calculated adsorption geometries and the corresponding energies of the designed cluster models were comparable to periodic calculations, and the adsorption energies were in the same range as the corresponding computational and experimental values reported in the literature for zeolite MFI. Thus, BEA and MOR may be good adsorption materials for alcohols in the field of downstream processing and catalysis. Aside from the DFT calculations, adsorption isotherms were determined experimentally in this study from aqueous solutions. For BEA, the adsorption of significant amounts of alcohol from aqueous solution was observed experimentally. In contrast, MOR was loaded with only a very small amount of alcohol. Although differences were found between the affinities obtained from gas-phase DFT calculations and those observed experimentally in aqueous solution, the computational data presented here represent molecular level information on the geometries and energies of C1-C4 alcohols adsorbed in zeolites BEA and MOR. This knowledge should prove very useful in the design of zeolite materials intended for use in adsorption and catalytic processes, as it allows adsorption behavior to be predicted via judiciously designed computational models.

  9. Investigation of morphological features of six interacting galaxies. I

    International Nuclear Information System (INIS)

    Koroviakovskaia, A.A.

    1984-01-01

    The morphology of six groups of interacting galaxies in Vorontsov-Vel'iaminov's atlas is investigated by digital filtering methods using large-scale photographs obtained with the 6-m telescope. It is shown that of five groups of galaxies that might appear as chains in direct photographs, only one is probably a real chain. In the group VV 551, which was previously classified as a blue nest consisting of four or five members, only two spiral galaxies have been found

  10. Investigation into complexity and interaction in supervisory control

    International Nuclear Information System (INIS)

    Tholen, N.

    1989-01-01

    Optimizing Man-Machine Systems presupposes a sound knowledge of interactions involved. Two research facilities are described which are intended as a vehicle for investigating the influences of process and controller complexity, interface design and task. The processes on which they rely have much in common, but they each have their own strong points. Together they form a good basis for human supervisory control research. (author) 12 refs

  11. Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Gary J. Blanchard

    2009-06-30

    This work focuses on two broad issues. These are (1) the molecular origin of the chemical selectivity achieved with ultrathin polymer multilayers, and (2) how the viscoelastic properties of the polymer layers are affected by exposure to solvent and analytes. These issues are inter-related, and to understand them we need to design experiments that probe both the energetic and kinetic aspects of interfacial adsorption processes. This project focuses on controling the chemical structure, thickness, morphology and sequential ordering of polymer layers bound to interfaces using maleimide-vinyl ether and closely related alternating copolymerization chemistry and efficient covalent cross-linking reactions that allow for layer-by-layer polymer deposition. This chemistry has been developed during the funding cycle of this Grant. We have measure the equilibrium constants for interactions between specific layers within the polymer interfaces and size-controlled, surface-functionalized gold nanoparticles. The ability to control both size and functionality of gold nanoparticle model analytes allows us to evaluate the average “pore size” that characterizes our polymer films. We have measured the “bulk” viscosity and shear modulus of the ultrathin polymer films as a function of solvent overlayer identity using quartz crystal microbalance complex impedance measurements. We have measured microscopic viscosity at specific locations within the layered polymer interfaces with time-resolved fluorescence lifetime and depolarization techniques. We combine polymer, cross-linking and nanoparticle synthetic expertise with a host of characterization techniques, including QCM gravimetry and complex impedance analysis, steady state and time-resolved spectroscopies.

  12. Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications

    Science.gov (United States)

    Heinz, Hendrik; Pramanik, Chandrani; Heinz, Ozge; Ding, Yifu; Mishra, Ratan K.; Marchon, Delphine; Flatt, Robert J.; Estrela-Lopis, Irina; Llop, Jordi; Moya, Sergio; Ziolo, Ronald F.

    2017-02-01

    Nanostructures of diverse chemical nature are used as biomarkers, therapeutics, catalysts, and structural reinforcements. The decoration with surfactants has a long history and is essential to introduce specific functions. The definition of surfactants in this review is very broad, following its lexical meaning ;surface active agents;, and therefore includes traditional alkyl modifiers, biological ligands, polymers, and other surface active molecules. The review systematically covers covalent and non-covalent interactions of such surfactants with various types of nanomaterials, including metals, oxides, layered materials, and polymers as well as their applications. The major themes are (i) molecular recognition and noncovalent assembly mechanisms of surfactants on the nanoparticle and nanocrystal surfaces, (ii) covalent grafting techniques and multi-step surface modification, (iii) dispersion properties and surface reactions, (iv) the use of surfactants to influence crystal growth, as well as (v) the incorporation of biorecognition and other material-targeting functionality. For the diverse materials classes, similarities and differences in surfactant assembly, function, as well as materials performance in specific applications are described in a comparative way. Major factors that lead to differentiation are the surface energy, surface chemistry and pH sensitivity, as well as the degree of surface regularity and defects in the nanoparticle cores and in the surfactant shell. The review covers a broad range of surface modifications and applications in biological recognition and therapeutics, sensors, nanomaterials for catalysis, energy conversion and storage, the dispersion properties of nanoparticles in structural composites and cement, as well as purification systems and classical detergents. Design principles for surfactants to optimize the performance of specific nanostructures are discussed. The review concludes with challenges and opportunities.

  13. Lipid-based nanocarrier for quercetin delivery: system characterization and molecular interactions studies.

    Science.gov (United States)

    Hädrich, Gabriela; Monteiro, Samantha Oliveira; Rodrigues, Marisa Raquel; de Lima, Vânia Rodrigues; Putaux, Jean-Luc; Bidone, Juliana; Teixeira, Helder Ferreira; Muccillo-Baisch, Ana Luiza; Dora, Cristiana Lima

    2016-01-01

    The flavonoid quercetin (QU) is a naturally occurring compound with several biological activities. However, the oral bioavailability of this compound is very low due to the high pre-systemic metabolism in the colon and liver and its low water solubility. In this context, the development of QU-loaded nanocarriers (NEs) is a promising approach to improve the drug oral bioavailability. This study investigates the variation of the concentration of 12-hydroxystearic acid-polyethylene glycol copolymer, lecithin and castor oil (CO) as to increase the amount of QU encapsulated while maintaining physicochemical characteristics described in previous studies. To better understand the ability to load and release the drug, we investigated the molecular interactions between QU and NE. Lipid-based NEs were prepared using CO as oily phase and PEG 660-stearate and lecithin as surfactants. Hot solvent diffusion and phase inversion temperature were methods employed to produce NEs. The QU-NEs were investigated for physicochemical characteristics and in vitro drug release. Molecular interactions between QU and the NEs were monitored through the complementary infrared (Fourier transform infrared) and NMR. The results revealed that it was possible to incorporate higher amounts of QU in a lipid-based NE with a reduced size (20 nm). The system developed allow a sustained release of QU probably due to the shell formed by the surfactants around the NE and the flavonoid ordering effect in the emulsion hydrophobic regions, which may reduce the system permeability.

  14. Interaction of molecular oxygen with single wall nanotubes: Role of surfactant contamination

    International Nuclear Information System (INIS)

    Larciprete, R.; Goldoni, A.; Lizzit, S.

    2003-01-01

    The interaction of molecular oxygen with single wall nanotubes in the form of a commercial bucky paper was investigated by high resolution photoemission spectroscopy. Sodium contamination was found in the sample, which was completely removed only after prolonged heating at 1250 K. The C 1s core level spectrum measured on the sample annealed to 1020 K dramatically changed upon exposure to molecular oxygen. On the contrary, when exposing the Na-free SWNTs to several KL of O 2 , the sample remained oxygen free and no modification in the C 1s core level was observed. Therefore the observed sensitivity of the sample to O 2 was due to a Na mediated oxidation, determining a charge transfer from the C tubes to the Na-O complex

  15. Investigation of impurity defects in α-iron by molecular dynamics method

    International Nuclear Information System (INIS)

    Kevorkyan, Yu.R.

    1986-01-01

    Investigation of the configuration of impurity defects in α-iron by the molecular dynamics method is presented. The Jhonson model potential has been used to calculate the interaction of matrix atoms. The impurity-matrix atom interaction is described by the same form of the potential shifted along the axis of interatomic distances for a definite value. The correspondence between the shift value and change in the radius of the impurity defect is established on the basis of calculation of the relaxation volume. Possible configurations of the impurity - interstitial matrix atom complexes are obtained for the given model of the impurity defect, dimensional boundaries of possible transitions between different configurations are determined. Formation and bound energies, relaxation volumes of impurity defects are calculated

  16. Molecular epidemiological investigations of plague in Eastern Province of Zambia.

    Science.gov (United States)

    Nyirenda, Stanley S; Hang Ombe, Bernard M; Simulundu, Edgar; Mulenga, Evans; Moonga, Ladslav; Machang U, Robert S; Misinzo, Gerald; Kilonzo, Bukheti S

    2018-01-04

    Plague is a flea-borne zoonotic and invasive disease caused by a gram negative coccobacillus bacterium called Yersinia pestis. Plague has caused three devastating pandemics globally namely: the Justinian, Black Death and Oriental plague. The disease in the Eastern Province of Zambia has been reported in Nyimba and Sinda Districts in the past 15 years. The aim of this study was to investigate the molecular epidemiology of plague in the two affected districts. Polymerase Chain Reaction (PCR), targeting Plasminogen activator gene (pla gene) of Y. pestis, was performed on suspected human bubo aspirates (n = 7), rodents (n = 216), shrews (n = 27) and fleas (n = 1494). Of these, one positive sample from each source or host was subjected to sequencing followed by phylogenetic analysis. The plasminogen activator gene (pla gene) of Y. pestis was detected in 42.8% bubo aspirates, 6.9% rodents, 3.7% shrew and 0.8% fleas. The fleas were from pigs (n = 4), goats (n = 5) and rodents (n = 3). The sequencing and phylogenetic analysis suggested that the pla gene of Y. pestis in Nyimba and Sinda was similar and the isolates demonstrated a high degree of evolutionary relationship with Antiqua strains from the Republic of Congo and Kenya. It can be concluded that pla gene of Y. pestis was present in various hosts in the two districts and the strains circulating in each district were similar and resembles those in the Republic of Congo and Kenya.

  17. Molecular infection biology : interactions between microorganisms and cells

    National Research Council Canada - National Science Library

    Hacker, Jörg (Jörg Hinrich); Heesemann, Jurgen

    2002-01-01

    ...) Covers methods to analyze microbial pathogenicity, principles of gene regulation of virulence-associated genes, drug treatment and mechanisms of drug resistance, and molecular methods for diagnosis...

  18. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Directory of Open Access Journals (Sweden)

    Assem Barakat

    2015-11-01

    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  19. A Bone-Implant Interaction Mouse Model for Evaluating Molecular Mechanism of Biomaterials/Bone Interaction.

    Science.gov (United States)

    Liu, Wenlong; Dan, Xiuli; Wang, Ting; Lu, William W; Pan, Haobo

    2016-11-01

    The development of an optimal animal model that could provide fast assessments of the interaction between bone and orthopedic implants is essential for both preclinical and theoretical researches in the design of novel biomaterials. Compared with other animal models, mice have superiority in accessing the well-developed transgenic modification techniques (e.g., cell tracing, knockoff, knockin, and so on), which serve as powerful tools in studying molecular mechanisms. In this study, we introduced the establishment of a mouse model, which was specifically tailored for the assessment of bone-implant interaction in a load-bearing bone marrow microenvironment and could potentially allow the molecular mechanism study of biomaterials by using transgenic technologies. The detailed microsurgery procedures for developing a bone defect (Φ = 0.8 mm) at the metaphysis region of the mouse femur were recorded. According to our results, the osteoconductive and osseointegrative properties of a well-studied 45S5 bioactive glass were confirmed by utilizing our mouse model, verifying the reliability of this model. The feasibility and reliability of the present model were further checked by using other materials as objects of study. Furthermore, our results indicated that this animal model provided a more homogeneous tissue-implant interacting surface than the rat at the early stage of implantation and this is quite meaningful for conducting quantitative analysis. The availability of transgenic techniques to mechanism study of biomaterials was further testified by establishing our model on Nestin-GFP transgenic mice. Intriguingly, the distribution of Nestin + cells was demonstrated to be recruited to the surface of 45S5 glass as early as 3 days postsurgery, indicating that Nestin + lineage stem cells may participate in the subsequent regeneration process. In summary, the bone-implant interaction mouse model could serve as a potential candidate to evaluate the early stage tissue

  20. Investigations of the D-multi-ρ interactions

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, C.W. [Institut fuer Kernphysik (Theorie), Institute for Advanced Simulation, and Juelich Center for Hadron Physics, Forschungszentrum Juelich (Germany); Central South University, School of Physics and Electronics, Changsha (China)

    2017-09-15

    In the present work, which aims at searching for bound states, the interactions of the D-multi-ρ systems are investigated by means of the formalism of the fixed-center approximation to Faddeev equations. Reproducing the states of f{sub 2}(1270) and D{sub 1}(2420) dynamically in the two-body ρρ and ρD interactions, respectively, as the clusters of the fixed-center approximation, the state of D(3000){sup 0} is found as a molecule of D - f{sub 2} or ρ - D{sub 1} structures in the three-body interactions, where we determine its quantum number J{sup P} = 2{sup -} and find another possible state of D{sub 2}(3100) with isospin I = 3/2. In our results, there are some other predictions with uncertainties, a D{sub 3}(3160) state with I(J{sup P}) = (1)/(2)(3{sup +}) in the four-body interactions, a narrow D{sub 4}(3730) state with I(J{sup P}) = (1)/(2)(4{sup -}), a wide D{sub 4}(3410) state of I(J{sup P}) = (1)/(2)(4{sup -}), and another wide D{sub 4}(3770) state but with I(J{sup P}) = (3)/(2)(4{sup -}) in the five-body interactions, and a D{sub 5}(3570) state with I(J{sup P}) = (1)/(2)(5{sup +}) in the six-body interactions. (orig.)

  1. Contributions to Advances in Blend Pellet Products (BPP) Research on Molecular Structure and Molecular Nutrition Interaction by Advanced Synchrotron and Globar Molecular (Micro)Spectroscopy.

    Science.gov (United States)

    Guevara-Oquendo, VÍctor H; Yu, Peiqiang

    2018-04-13

    To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

  2. Synthesis, spectroscopic investigations, DFT studies, molecular docking and antimicrobial potential of certain new indole-isatin molecular hybrids: Experimental and theoretical approaches

    Science.gov (United States)

    Almutairi, Maha S.; Zakaria, Azza S.; Ignasius, P. Primsa; Al-Wabli, Reem I.; Joe, Isaac Hubert; Attia, Mohamed I.

    2018-02-01

    Indole-isatin molecular hybrids 5a-i have been synthesized and characterized by different spectroscopic methods to be evaluated as new antimicrobial agents against a panel of Gram positive bacteria, Gram negative bacteria, and moulds. Compound 5h was selected as a representative example of the prepared compounds 5a-i to perform computational investigations. Its vibrational properties have been studied using FT-IR and FT-Raman with the aid of density functional theory approach. The natural bond orbital analysis as well as HOMO and LUMO molecular orbitals investigations of compound 5h were carried out to explore its possible intermolecular delocalization or hyperconjugation and its possible interactions with the target protein. Molecular docking of compound 5h predicted its binding mode with the fungal target protein.

  3. Experimental investigation of the piano hammer-string interaction.

    Science.gov (United States)

    Birkett, Stephen

    2013-04-01

    Experimental techniques for investigating the piano hammer-string interaction are described. It is argued that the accuracy, consistency, and scope of conclusions of previous studies can be compromised by limitations of the conventional methods relating to key inputs; physical distortion; numerical distortion, particularly when differentiation or integration of measured signals is used to derive primary response variables; contact identification; and synchronization issues. These problems are discussed, and experimental methods that have been devised to avoid them are described and illustrated by detailed results from a study of the hammer-string interaction in a vertical piano. High resolution displacements are obtained directly by non-contact high-speed imaging and quantitative motion tracking. The attention focused on achieving very accurate and consistent temporal and spatial alignment, including the objective procedure used for contact identification, allows meaningful comparisons of responses from separate tests. String motion at the strike point and on each side of it, as well as hammer motion, is obtained for eight dynamic levels from 1.06 to 2.98 m/s impact velocity. Detailed observations of the force-compression behavior of the hammer interacting with real strings are presented. The direct effects of hammer shank deflection and agraffe string pulses on the interaction are also highlighted.

  4. Optoelectronic investigation of nanodiamond interactions with human blood

    Science.gov (United States)

    Ficek, M.; Wróbel, M. S.; Wasowicz, M.; Jedrzejewska-Szczerska, M.

    2016-03-01

    We present optoelectronic investigation of in vitro interactions of whole human blood with different nanodiamond biomarkers. Plasmo-chemical modifications of detonation nanodiamond particles gives the possibility for controlling their surface for biological applications. Optical investigations reveal the biological activity of nanodiamonds in blood dependent on its surface termination. We compare different types of nanodiamonds: commercial non-modified detonation nanodiamonds, and nanodiamonds modified by MW PACVD method with H2-termination, and chemically modified nanodiamond with O2-termination. The absorption spectra, and optical microscope investigations were conducted. The results indicate haemocompatibility of non-modified detonation nanodiamond as well as modified nanodiamonds, which enables their application for drug delivery, as well as sensing applications.

  5. Amino acids as co-amorphous stabilizers for poorly water-soluble drugs--Part 2: molecular interactions.

    Science.gov (United States)

    Löbmann, Korbinian; Laitinen, Riikka; Strachan, Clare; Rades, Thomas; Grohganz, Holger

    2013-11-01

    The formation of co-amorphous drug-drug mixtures has proved to be a powerful approach to stabilize the amorphous form and at the same time increase the dissolution of poorly water-soluble drugs. Molecular interactions in these co-amorphous formulations can play a crucial role in stabilization and dissolution enhancement. In this regard, Fourier-transform infrared spectroscopy (FTIR) is a valuable tool to analyze the molecular near range order of the compounds in the co-amorphous mixtures. In this study, several co-amorphous drugs--low molecular weight excipient blends--have been analyzed with FTIR spectroscopy. Molecular interactions of the drugs carbamazepine and indomethacin with the amino acids arginine, phenylalanine, and tryptophan were investigated. The amino acids were chosen from the biological target site of both drugs and prepared as co-amorphous formulations together with the drugs by vibrational ball milling. A detailed analysis of the FTIR spectra of these formulations revealed specific peak shifts in the vibrational modes of functional groups of drug and amino acid, as long as one amino acid from the biological target site was present in the blends. These peak shifts indicate that the drugs formed specific molecular interactions (hydrogen bonding and π-π interactions) with the amino acids. In the drug-amino acid mixtures that contained amino acids which were not present at the biological target site, no such interactions were identified. This study shows the potential of amino acids as small molecular weight excipients in co-amorphous formulations to stabilize the amorphous form of a poorly water-soluble drug through strong and specific molecular interactions with the drug. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. The selective interaction between silica nanoparticles and enzymes from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Xiaotian Sun

    Full Text Available Nanoscale particles have become promising materials in many fields, such as cancer therapeutics, diagnosis, imaging, drug delivery, catalysis, as well as biosensors. In order to stimulate and facilitate these applications, there is an urgent need for the understanding of the interaction mode between the nano-particles and proteins. In this study, we investigate the orientation and adsorption between several enzymes (cytochrome c, RNase A, lysozyme and 4 nm/11 nm silica nanoparticles (SNPs by using molecular dynamics (MD simulation. Our results show that three enzymes are adsorbed onto the surfaces of both 4 nm and 11 nm SNPs during our MD simulations and the small SNPs induce greater structural stabilization. The active site of cytochrome c is far away from the surface of 4 nm SNPs, while it is adsorbed onto the surface of 11 nm SNPs. We also explore the influences of different groups (-OH, -COOH, -NH2 and CH3 coated onto silica nanoparticles, which show significantly different impacts. Our molecular dynamics results indicate the selective interaction between silicon nanoparticles and enzymes, which is consistent with experimental results. Our study provides useful guides for designing/modifying nanomaterials to interact with proteins for their bio-applications.

  7. Spectroscopic investigations of pentobarbital interaction with human serum albumin

    Science.gov (United States)

    Darwish, Saqer M.; Abu sharkh, Sawsan E.; Abu Teir, Musa M.; Makharza, Sami A.; Abu-hadid, Mahmoud M.

    2010-01-01

    The interaction between pentobarbital and human serum albumin has been investigated. The basic binding interaction was studied by UV-absorption and fluorescence spectroscopy. From spectral analysis pentobarbital showed a strong ability to quench the intrinsic fluorescence of HSA through a static quenching procedure. The binding constant ( k) is estimated at 1.812 × 10 4 M -1 at 293 K. FT-IR spectroscopy with Fourier self-deconvolution technique was used to determine the protein secondary structure and drug binding mechanisms. The observed spectral changes of HSA-pentobarbital complex indicate a larger intensity decrease in the absorption band of α-helix relative to that of β-sheets. This variation in intensity is related indirectly to the formation of H-bonding in the complex molecules, which accounts for the different intrinsic propensities of α-helix and β-sheets.

  8. Advanced Characterization of Molecular Interactions in TALSPEAK-like Separations Systems

    Energy Technology Data Exchange (ETDEWEB)

    Nash, Kenneth [Washington State Univ., Pullman, WA (United States); Guelis, Artem [Argonne National Lab. (ANL), Argonne, IL (United States); Lumetta, Gregg J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Sinkov, Sergey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-10-21

    Combining unit operations in advanced aqueous reprocessing schemes brings obvious process compactness advantages, but at the same time greater complexity in process design and operation. Unraveling these interactions requires increasingly sophisticated analytical tools and unique approaches for adequate analysis and characterization that probe molecular scale interactions. Conventional slope analysis methods of solvent extraction are too indirect to provide much insight into such interactions. This project proposed the development and verification of several analytical tools based on studies of TALSPEAK-like aqueous processes. As such, the chemistry of trivalent fission product lanthanides, americium, curium, plutonium, neptunium and uranium figure prominently in these studies. As the project was executed, the primary focus fell upon the chemistry or trivalent lanthanides and actinides. The intent of the investigation was to compare and contrast the results from these various complementary techniques/studies to provide a stronger basis for predicting the performance of extractant/diluent mixtures as media for metal ion separations. As many/most of these techniques require the presence of metal ions at elevated concentrations, it was expected that these studies would take this investigation into the realm of patterns of supramolecular organization of metal complexes and extractants in concentrated aqueous/organic media. We expected to advance knowledge of the processes that enable and limit solvent extraction reactions as a result of the application of fundamental chemical principles to explaining interactions in complex media.

  9. Translational-rotational interaction in dynamics and thermodynamics of 2D atomic crystal with molecular impurity

    International Nuclear Information System (INIS)

    Antsygina, T.N.; Poltavskaya, M.I.; Chishko, K.A.

    2003-01-01

    The interaction between the rotational degrees of freedom of a diatomic molecular impurity and the phonon excitations of a two-dimensional atomic matrix commensurate with a substrate is investigated theoretically. It is shown, that the translational-rotational interaction changes the form of the rotational kinetic energy operator as compared to the corresponding expression for a free rotator, and also renormalized the parameters of the crystal field without change in its initial form. The contribution of the impurity rotational degrees of freedom to the low-temperature heat capacity for a dilute solution of diatomic molecules in an atomic two-dimensional matrix is calculated. The possibility of experimental observation of the effects obtained is discussed

  10. Investigation of molecular size of transcription factor TFIIE in solution.

    Science.gov (United States)

    Itoh, Yoshiyuki; Unzai, Satoru; Sato, Mamoru; Nagadoi, Aritaka; Okuda, Masahiko; Nishimura, Yoshifumi; Akashi, Satoko

    2005-11-15

    Human general transcription factor IIE (TFIIE), a component of a transcription preinitiation complex associated with RNA polymerase II, was characterized by size-exclusion chromatography, mass spectrometry, analytical ultracentrifugation, and small-angle X-ray scattering (SAXS). Recombinant human TFIIE was purified to homogeneity and shown to contain equimolar amounts of TFIIEalpha (50 kDa) and TFIIEbeta (35 kDa) by SDS-PAGE. In the analysis of size-exclusion chromatography of the purified sample, as already reported, TFIIE was shown to be a 170-kDa alpha(2)beta(2) heterotetramer. However, by using electrospray ionization mass spectrometry the purified sample gave the molecular mass of 84,152 +/- 5, indicating that TFIIE is an alphabeta heterodimer but not a heterotetramer. Analytical ultracentrifugation experiment of TFIIE provided that only a single component with the molecular mass of ca. 80,000 existed in solution, also suggesting an alphabeta heterodimer. In addition, its extraordinarily rod-like molecular shape was confirmed by SAXS. It is likely that the rod-like molecular shape of TFIIE has misled larger molecular size in size-exclusion chromatography, which was calibrated by globular proteins. It is demonstrated that TFIIE exists as a heterodimer under our present conditions in solution, although two molecules of heterodimer might be required for the formation of the preinitiation complex with RNA polymerase II for starting the transcription process. (c) 2005 Wiley-Liss, Inc.

  11. Investigating Atmospheric Oxidation with Molecular Dynamics Imaging and Spectroscopy

    Science.gov (United States)

    Merrill, W. G.; Case, A. S.; Keutsch, F. N.

    2013-06-01

    Volatile organic compounds (VOCs) in the Earth's atmosphere constitute trace gas species emitted primarily from the biosphere, and are the subject of inquiry for a variety of air quality and climate studies. Reactions intiated (primarily) by the hydroxyl radical (OH) lead to a myriad of oxygenated species (OVOCs), which in turn are prone to further oxidation. Investigations of the role that VOC oxidation plays in tropospheric chemistry have brought to light two troubling scenarios: (1) VOCs are responsible in part for the production of two EPA-regulated pollutants---tropospheric ozone and organic aerosol---and (2) the mechanistic details of VOC oxidation remain convoluted and poorly understood. The latter issue hampers the implementation of near-explicit atmospheric simulations, and large discrepancies in OH reactivity exist between measurements and models at present. Such discrepancies underscore the need for a more thorough description of VOC oxidation. Time-of-flight measurements and ion-imaging techniques are viable options for resolving some of the mechanistic and energetic details of VOC oxidation. Molecular beam studies have the advantage of foregoing unwanted bimolecular reactions, allowing for the characterization of specific processes which must typically compete with the complex manifold of VOC oxidation pathways. The focus of this work is on the unimolecular channels of organic peroxy radical intermediates, which are necessarily generated during VOC oxidation. Such intermediates may isomerize and decompose into distinct chemical channels, enabling the unambiguous detection of each pathway. For instance, a (1 + 1') resonance enhanced multiphoton ionization (REMPI) scheme may be employed to detect carbon monoxide generated from a particular unimolecular process. A number of more subtle mechanistic details may be explored as well. By varying the mean free path of the peroxy radicals in a flow tube, the role of collisional quenching in these unimolecular

  12. Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

    International Nuclear Information System (INIS)

    Sanz-Navarro, Carlos F.

    2002-01-01

    The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)

  13. Spectroscopic and molecular modeling investigation on the binding of a synthesized steroidal amide to protein

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hua-xin, E-mail: h.x.zhang@yeah.net; Liu, E.

    2014-09-15

    Owing to the various valuable biological activities, steroidal amides have become a hot topic in steroidal pharmaceutical chemistry. In this paper, an anti-tumor steroid derivate (DAAO) was synthesized and identified. The interaction between DAAO and human serum albumin (HSA) was studied by fluorescence spectra, circular dichroism (CD) spectra, molecular modeling and molecular probe techniques. The results suggested that DAAO had reacted with HSA through hydrogen bonds and van der Waals power. The formation of DAAO–HSA complex at ground state led to static quenching of HSA's fluorescence. The number of binding sites, binding constants, enthalpy change (ΔH{sup θ}), Gibbs free energy change (ΔG{sup θ}) and entropy change (ΔS{sup θ}) were calculated at different temperatures based on fluorescence quenching theory and classic equation. Molecular modeling investigation indicated that DAAO was more inclined to absorb on Sudlow's site I in subdomain IIA of HSA molecule on grounds of the lowest energy principle and steric hindrance effect. The binding location was further confirmed by fluorescence probe experiment using warfarin (site I probe) for displacement. Furthermore, the conformational changes of HSA in presence of DAAO were investigated by CD spectra. The results could provide new evidence explaining the relationship between the chemical structure and biological activity and may be useful for understanding the anti-cancer mechanism of steroidal drug. - Highlights: • A designed steroidal amide compound (DAAO) was synthesized by introducing amido bonds into a steroid nucleus. • DAAO binds to Sudlow's site I in HSA through hydrogen bonds and van der Waals power. • The interaction was a spontaneous and exothermic process with modest degree of reversibility. • The secondary structure of HSA and the microenvironment of TRP214 altered. • Amido bond in steroid nucleus (–NH–CO–) plays important role in stabling the structure of

  14. Investigation of hybrid molecular material prepared by ionic liquid ...

    Indian Academy of Sciences (India)

    It is fully characterized by CHN analysis, FTIR, XRD, UV-Vis-NIR DRS, 31P MAS NMR, TGA and SEM. The FTIR spectrum of the compound shows the fingerprint vibrational bands of both Keggin molecular anions and imidazolium cations. The aromatic C-H stretch region (2700-3250 cm-1) of imidazolium cation is split due ...

  15. [Molecular genetic investigation of sugar beet (Beta vulgaris L.)].

    Science.gov (United States)

    Butorina, A K; Kornienko, A V

    2011-10-01

    Molecular genetic studies of sugar beet (Beta vulgaris L.) are reviewed as a basis for the development of genomics of this species. The methods used to study structural and functional genomics are considered. The results and their application to increase the efficiency of sugar beet breeding are discussed.

  16. Investigation of hybrid molecular material prepared by ionic liquid ...

    Indian Academy of Sciences (India)

    Wintec

    A solid hybrid molecular material containing 1-butyl 3-methyl imidazolium cations and. Keggin anions of phosphotungstic acid has been synthesized. It is fully characterized by CHN analysis,. FTIR, XRD, UV-Vis-NIR DRS,. 31. P MAS NMR, TGA and SEM. The FTIR spectrum of the compound shows the fingerprint vibrational ...

  17. Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

    Indian Academy of Sciences (India)

    Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...

  18. Investigation of the limits of nanoscale filopodial interactions

    Directory of Open Access Journals (Sweden)

    Laura E McNamara

    2014-05-01

    Full Text Available Mesenchymal stem cells are sensitive to changes in feature height, order and spacing. We had previously noted that there was an inverse relationship between osteoinductive potential and feature height on 15-, 55- and 90 nm-high titania nanopillars, with 15 nm-high pillars being the most effective substrate at inducing osteogenesis of human mesenchymal stem cells. The osteoinductive effect was somewhat diminished by decreasing the feature height to 8 nm, however, which suggested that there was a cut-off point, potentially associated with a change in cell–nanofeature interactions. To investigate this further, in this study, a scanning electron microscopy/three-dimensional scanning electron microscopy approach was used to examine the interactions between mesenchymal stem cells and the 8 and 15 nm nanopillared surfaces. As expected, the cells adopted a predominantly filopodial mode of interaction with the 15 nm-high pillars. Interestingly, fine nanoscale membrane projections, which we have termed ‘nanopodia,’ were also employed by the cells on the 8 nm pillars, and it seems that this is analogous to the cells ‘clinging on with their fingertips’ to this scale of features.

  19. Theoretical investigation of interaction between the set of ligands and α7 nicotinic acetylcholine receptor

    Science.gov (United States)

    Glukhova, O. E.; Prytkova, T. R.; Shmygin, D. S.

    2016-03-01

    Nicotinic acetylcholine receptors (nAChRs) are neuron receptor proteins that provide a transmission of nerve impulse through the synapses. They are composed of a pentametric assembly of five homologous subunits (5 α7 subunits for α7nAChR, for example), oriented around the central pore. These receptors might be found in the chemical synapses of central and peripheral nervous system, and also in the neuromuscular synapses. Transmembrane domain of the one of such receptors constitutes ion channel. The conductive properties of ion channel strongly depend on the receptor conformation changes in the response of binding with some molecule, f.e. acetylcholine. Investigation of interaction between ligands and acetylcholine receptor is important for drug design. In this work we investigate theoretically the interaction between the set of different ligands (such as vanillin, thymoquinone, etc.) and the nicotinic acetylcholine receptor (primarily with subunit of the α7nAChR) by different methods and packages (AutodockVina, GROMACS, KVAZAR, HARLEM, VMD). We calculate interaction energy between different ligands in the subunit using molecular dynamics. On the base of obtained calculation results and using molecular docking we found an optimal location of different ligands in the subunit.

  20. Molecular aggregation in water : the interplay of hydrophobic and electrostatic interactions

    NARCIS (Netherlands)

    Buwalda, Rixt Tietje

    2001-01-01

    Hydrophobic interactions belong to the most important noncovalent interactions and play an important role in many (bio)chemical processes. A number of processes in aqueous solution like protein folding, surfactant aggregation or molecular recognition processes strongly rely on the interactions

  1. Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.

    Directory of Open Access Journals (Sweden)

    Tommi Aho

    2010-05-01

    Full Text Available Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need to integrate this information into a consistent reconstruction of the molecular interaction network. This work presents and validates RefRec, the most comprehensive molecular interaction network reconstruction currently available for yeast. The reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network from major biological databases. The core of the reconstruction is based on a reference object approach in which genes, transcripts, and proteins are identified using their primary sequences. This enables their unambiguous identification and non-redundant integration. The obtained total number of different molecular species and their connecting interactions is approximately 67,000. In order to demonstrate the capacity of RefRec for functional predictions, it was used for simulating the gene knockout damage propagation in the molecular interaction network in approximately 590,000 experimentally validated mutant strains. Based on the simulation results, a statistical classifier was subsequently able to correctly predict the viability of most of the strains. The results also showed that the usage of different types of molecular species in the reconstruction is important for accurate phenotype prediction. In general, the findings demonstrate the benefits of global reconstructions of molecular interaction networks. With all the molecular species and their physical interactions explicitly modeled, our

  2. Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: Advances toward treatment of hepatitis B virus infections

    Science.gov (United States)

    Shahabadi, Nahid; Falsafi, Monireh

    The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33 ± 0.2 × 104 L mol-1and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH = 34.4 kJ mol-1; ΔS = 184.32 J mol-1 K-1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

  3. Role of the Strength of Drug-Polymer Interactions on the Molecular Mobility and Crystallization Inhibition in Ketoconazole Solid Dispersions.

    Science.gov (United States)

    Mistry, Pinal; Mohapatra, Sarat; Gopinath, Tata; Vogt, Frederick G; Suryanarayanan, Raj

    2015-09-08

    The effects of specific drug-polymer interactions (ionic or hydrogen-bonding) on the molecular mobility of model amorphous solid dispersions (ASDs) were investigated. ASDs of ketoconazole (KTZ), a weakly basic drug, with each of poly(acrylic acid) (PAA), poly(2-hydroxyethyl methacrylate) (PHEMA), and polyvinylpyrrolidone (PVP) were prepared. Drug-polymer interactions in the ASDs were evaluated by infrared and solid-state NMR, the molecular mobility quantified by dielectric spectroscopy, and crystallization onset monitored by differential scanning calorimetry (DSC) and variable temperature X-ray diffractometry (VTXRD). KTZ likely exhibited ionic interactions with PAA, hydrogen-bonding with PHEMA, and weaker dipole-dipole interactions with PVP. On the basis of dielectric spectroscopy, the α-relaxation times of the ASDs followed the order: PAA > PHEMA > PVP. In addition, the presence of ionic interactions also translated to a dramatic and disproportionate decrease in mobility as a function of polymer concentration. On the basis of both DSC and VTXRD, an increase in strength of interaction translated to higher crystallization onset temperature and a decrease in extent of crystallization. Stronger drug-polymer interactions, by reducing the molecular mobility, can potentially delay the crystallization onset temperature as well as crystallization extent.

  4. IntAct: an open source molecular interaction database.

    Science.gov (United States)

    Hermjakob, Henning; Montecchi-Palazzi, Luisa; Lewington, Chris; Mudali, Sugath; Kerrien, Samuel; Orchard, Sandra; Vingron, Martin; Roechert, Bernd; Roepstorff, Peter; Valencia, Alfonso; Margalit, Hanah; Armstrong, John; Bairoch, Amos; Cesareni, Gianni; Sherman, David; Apweiler, Rolf

    2004-01-01

    IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains approximately 2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.

  5. On the use of test gases of various radii to investigate molecular sieving in leak channels.

    Science.gov (United States)

    Lim, William W; Bucknall, Martin P; Adler, Lewis; McKenzie, David R; Suaning, Gregg J

    2015-08-01

    Evidence of the effect of molecule size (molecular sieving) was discovered in leak channels similar to those found in hermetically sealed implantable bionics. A range of test gases of different molecular sizes was used to investigate the relative leak rates of several different samples. A contemporary model of molecular sieving is shown to be in partial agreement with our data.

  6. Polymorphism and disorder in caffeine: Dielectric investigation of molecular mobilities

    Science.gov (United States)

    Descamps, M.; Decroix, A. A.

    2014-12-01

    Using dielectric relaxation data we have characterized the molecular mobilities of caffeine both in phase I (stable and metastable) and in phase II. In phase I effects of sublimation and phase transformation kinetics were carefully considered. In plane rotational motions were followed on a wide temperature range. A noticeable antiferroelectric short range order developing at the approach of the glass-like transition is characterized. Condition for occurrence of a critical-like behaviour is discussed. At high temperature the emergence of an additional ultra slow relaxation process is highlighted. Possible molecular mechanisms are proposed for both processes. In phase II the existence of a less intense relaxation process is confirmed. Close similarity with the main process developing in phase I hints at a common origin of the dipolar motions. Careful consideration of recent structure determinations leads to suggest that this process is associated to similar molecular in plane rotations but developing at the surface of crystalline samples. Lower cooperativity at the surface is reflected in the smaller activation entropy of the relaxation.

  7. Molecular interaction fingerprint approaches for GPCR drug discovery

    NARCIS (Netherlands)

    Vass, M.; Kooistra, A.J.; Ritschel, T.; Leurs, R.; Esch, I.J. de; Graaf, C. de

    2016-01-01

    Protein-ligand interaction fingerprints (IFPs) are binary 1D representations of the 3D structure of protein-ligand complexes encoding the presence or absence of specific interactions between the binding pocket amino acids and the ligand. Various implementations of IFPs have been developed and

  8. Identifying gene-environment interactions in schizophrenia: contemporary challenges for integrated, large-scale investigations.

    Science.gov (United States)

    van Os, Jim; Rutten, Bart P; Myin-Germeys, Inez; Delespaul, Philippe; Viechtbauer, Wolfgang; van Zelst, Catherine; Bruggeman, Richard; Reininghaus, Ulrich; Morgan, Craig; Murray, Robin M; Di Forti, Marta; McGuire, Philip; Valmaggia, Lucia R; Kempton, Matthew J; Gayer-Anderson, Charlotte; Hubbard, Kathryn; Beards, Stephanie; Stilo, Simona A; Onyejiaka, Adanna; Bourque, Francois; Modinos, Gemma; Tognin, Stefania; Calem, Maria; O'Donovan, Michael C; Owen, Michael J; Holmans, Peter; Williams, Nigel; Craddock, Nicholas; Richards, Alexander; Humphreys, Isla; Meyer-Lindenberg, Andreas; Leweke, F Markus; Tost, Heike; Akdeniz, Ceren; Rohleder, Cathrin; Bumb, J Malte; Schwarz, Emanuel; Alptekin, Köksal; Üçok, Alp; Saka, Meram Can; Atbaşoğlu, E Cem; Gülöksüz, Sinan; Gumus-Akay, Guvem; Cihan, Burçin; Karadağ, Hasan; Soygür, Haldan; Cankurtaran, Eylem Şahin; Ulusoy, Semra; Akdede, Berna; Binbay, Tolga; Ayer, Ahmet; Noyan, Handan; Karadayı, Gülşah; Akturan, Elçin; Ulaş, Halis; Arango, Celso; Parellada, Mara; Bernardo, Miguel; Sanjuán, Julio; Bobes, Julio; Arrojo, Manuel; Santos, Jose Luis; Cuadrado, Pedro; Rodríguez Solano, José Juan; Carracedo, Angel; García Bernardo, Enrique; Roldán, Laura; López, Gonzalo; Cabrera, Bibiana; Cruz, Sabrina; Díaz Mesa, Eva Ma; Pouso, María; Jiménez, Estela; Sánchez, Teresa; Rapado, Marta; González, Emiliano; Martínez, Covadonga; Sánchez, Emilio; Olmeda, Ma Soledad; de Haan, Lieuwe; Velthorst, Eva; van der Gaag, Mark; Selten, Jean-Paul; van Dam, Daniella; van der Ven, Elsje; van der Meer, Floor; Messchaert, Elles; Kraan, Tamar; Burger, Nadine; Leboyer, Marion; Szoke, Andrei; Schürhoff, Franck; Llorca, Pierre-Michel; Jamain, Stéphane; Tortelli, Andrea; Frijda, Flora; Vilain, Jeanne; Galliot, Anne-Marie; Baudin, Grégoire; Ferchiou, Aziz; Richard, Jean-Romain; Bulzacka, Ewa; Charpeaud, Thomas; Tronche, Anne-Marie; De Hert, Marc; van Winkel, Ruud; Decoster, Jeroen; Derom, Catherine; Thiery, Evert; Stefanis, Nikos C; Sachs, Gabriele; Aschauer, Harald; Lasser, Iris; Winklbaur, Bernadette; Schlögelhofer, Monika; Riecher-Rössler, Anita; Borgwardt, Stefan; Walter, Anna; Harrisberger, Fabienne; Smieskova, Renata; Rapp, Charlotte; Ittig, Sarah; Soguel-dit-Piquard, Fabienne; Studerus, Erich; Klosterkötter, Joachim; Ruhrmann, Stephan; Paruch, Julia; Julkowski, Dominika; Hilboll, Desiree; Sham, Pak C; Cherny, Stacey S; Chen, Eric Y H; Campbell, Desmond D; Li, Miaoxin; Romeo-Casabona, Carlos María; Emaldi Cirión, Aitziber; Urruela Mora, Asier; Jones, Peter; Kirkbride, James; Cannon, Mary; Rujescu, Dan; Tarricone, Ilaria; Berardi, Domenico; Bonora, Elena; Seri, Marco; Marcacci, Thomas; Chiri, Luigi; Chierzi, Federico; Storbini, Viviana; Braca, Mauro; Minenna, Maria Gabriella; Donegani, Ivonne; Fioritti, Angelo; La Barbera, Daniele; La Cascia, Caterina Erika; Mulè, Alice; Sideli, Lucia; Sartorio, Rachele; Ferraro, Laura; Tripoli, Giada; Seminerio, Fabio; Marinaro, Anna Maria; McGorry, Patrick; Nelson, Barnaby; Amminger, G Paul; Pantelis, Christos; Menezes, Paulo R; Del-Ben, Cristina M; Gallo Tenan, Silvia H; Shuhama, Rosana; Ruggeri, Mirella; Tosato, Sarah; Lasalvia, Antonio; Bonetto, Chiara; Ira, Elisa; Nordentoft, Merete; Krebs, Marie-Odile; Barrantes-Vidal, Neus; Cristóbal, Paula; Kwapil, Thomas R; Brietzke, Elisa; Bressan, Rodrigo A; Gadelha, Ary; Maric, Nadja P; Andric, Sanja; Mihaljevic, Marina; Mirjanic, Tijana

    2014-07-01

    Recent years have seen considerable progress in epidemiological and molecular genetic research into environmental and genetic factors in schizophrenia, but methodological uncertainties remain with regard to validating environmental exposures, and the population risk conferred by individual molecular genetic variants is small. There are now also a limited number of studies that have investigated molecular genetic candidate gene-environment interactions (G × E), however, so far, thorough replication of findings is rare and G × E research still faces several conceptual and methodological challenges. In this article, we aim to review these recent developments and illustrate how integrated, large-scale investigations may overcome contemporary challenges in G × E research, drawing on the example of a large, international, multi-center study into the identification and translational application of G × E in schizophrenia. While such investigations are now well underway, new challenges emerge for G × E research from late-breaking evidence that genetic variation and environmental exposures are, to a significant degree, shared across a range of psychiatric disorders, with potential overlap in phenotype. © The Author 2014. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  9. Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach.

    Science.gov (United States)

    Cain, Stuart A; McGovern, Amanda; Small, Elaine; Ward, Lyle J; Baldock, Clair; Shuttleworth, Adrian; Kielty, Cay M

    2009-12-01

    Deciphering interacting networks of the extracellular matrix is a major challenge. We describe an affinity purification and mass spectrometry strategy that has provided new insights into the molecular interactions of elastic fibers, essential extracellular assemblies that provide elastic recoil in dynamic tissues. Using cell culture models, we defined primary and secondary elastic fiber interaction networks by identifying molecular interactions with the elastic fiber molecules fibrillin-1, MAGP-1, fibulin-5, and lysyl oxidase. The sensitivity and validity of our method was confirmed by identification of known interactions with the bait proteins. Our study revealed novel extracellular protein interactions with elastic fiber molecules and delineated secondary interacting networks with fibronectin and heparan sulfate-associated molecules. This strategy is a novel approach to define the macromolecular interactions that sustain complex extracellular matrix assemblies and to gain insights into how they are integrated into their surrounding matrix.

  10. Inhibitory effect of phloretin on α-glucosidase: Kinetics, interaction mechanism and molecular docking.

    Science.gov (United States)

    Han, Lin; Fang, Chun; Zhu, Ruixue; Peng, Qiang; Li, Ding; Wang, Min

    2017-02-01

    As the aglycone of phloridzin, phloretin belongs to dihydrochalcone with antioxidant, anti-inflammatory and antimicrobial activities. In this study, multispectroscopic techniques and molecular docking analysis were used to investigate the inhibitory activity and mechanisms of phloretin on α-glucosidase. The results showed that phloretin reversibly inhibited α-glucosidase in a mixed-type manner and the value of IC 50 was 31.26μgL -1 . The intrinsic fluorescence of α-glucosidase was quenched by the interactions with phloretin through a static quenching mechanism and spontaneously formed phloretin-α-glucosidase complex by the driving forces of van der Waals force and hydrogen bond. Atomic force microscope (AFM) studies and FT-IR measurements suggested that the interactions could change the micro-environments and conformation of the enzymes and the molecular docking analysis displayed the exact binding site of phloretin on α-glucosidase. These results indicated that phloretin is a strong α-glucosidase inhibitor, thus could be contribute to the improvement of diabetes mellitus. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Investigation of cellular responses upon interaction with silver nanoparticles

    Directory of Open Access Journals (Sweden)

    Subbiah R

    2015-08-01

    Full Text Available Ramesh Subbiah,1,2 Seong Beom Jeon,3,4 Kwideok Park,1,2 Sang Jung Ahn,4,5 Kyusik Yun3 1Center for Biomaterials, Korea Institute of Science and Technology, Seoul, 2Department of Biomedical Engineering, Korea University of Science and Technology, Daejon, 3Department of Bionanotechnology, Gachon University, Gyeonggi-do, 4Centre for Advanced Instrumentation, Korea Research Institute of Standard and Science, 5Major of Nano Science, Korea University of Science and Technology, Daejeon, Republic of Korea Abstract: In order for nanoparticles (NPs to be applied in the biomedical field, a thorough investigation of their interactions with biological systems is required. Although this is a growing area of research, there is a paucity of comprehensive data in cell-based studies. To address this, we analyzed the physicomechanical responses of human alveolar epithelial cells (A549, mouse fibroblasts (NIH3T3, and human bone marrow stromal cells (HS-5, following their interaction with silver nanoparticles (AgNPs. When compared with kanamycin, AgNPs exhibited moderate antibacterial activity. Cell viability ranged from ≤80% at a high AgNPs dose (40 µg/mL to >95% at a low dose (10 µg/mL. We also used atomic force microscopy-coupled force spectroscopy to evaluate the biophysical and biomechanical properties of cells. This revealed that AgNPs treatment increased the surface roughness (P<0.001 and stiffness (P<0.001 of cells. Certain cellular changes are likely due to interaction of the AgNPs with the cell surface. The degree to which cellular morphology was altered directly proportional to the level of AgNP-induced cytotoxicity. Together, these data suggest that atomic force microscopy can be used as a potential tool to develop a biomechanics-based biomarker for the evaluation of NP-dependent cytotoxicity and cytopathology. Keywords: AFM, roughness, nanoindentation, biomarker, cytotoxicity, biomechanics

  12. Investigation of syngas interactions in alcohol synthesis catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Akundi, M.A.

    1998-04-15

    The primary objectives of the project are to (a) synthesize, by controlled sequential and co-impregnation techniques, three distinct composition metal clusters (consisting of Cu-Co-Cr and Cu-Fe-Zn): rich in copper (Methanol selective), rich in ferromagnetic metal (Co or Fe-Hydrocarbon selective) and intermediate range (mixed alcohol catalysts); (b) investigate the changes in the magnetic character of the systems due to interaction with CO, through Zero-field Nuclear Magnetic Resonance (ZFNMR) study of cobalt and Magnetic character (saturation magnetization and coercive field) analysis of the composite catalyst of Vibrating Sample Magnetometry (VSM); (c) examine the changes in syngas adsorption character of the catalyst as the composition changes, by FTIR Spectroscopic analysis of CO stretching frequencies; (d) determine the nature and size of these intermetallic clusters by Scanning Electron Microscopy (SEM); and (e) perform catalytic runs on selected samples and analyze the correlations between the physical and chemical characteristics. The catalysts chosen have a greater promise for industrial application than the Rh and Mo based catalysts. Several groups preparing catalysts by synthetic routes have reported divergent results for activity and selectivity. Generally the research has followed an empirical path and less effort is devoted to analyze the mechanisms and the scientific basis. The primary intent of this study is to analyze the nature of the intermetallic and gas-metal interactions and examine the correlations to catalytic properties.

  13. Investigation on interaction of prulifloxacin with pepsin: A spectroscopic analysis

    Science.gov (United States)

    Huang, Yabei; Yan, Jie; Liu, Benzhi; Yu, Zhang; Gao, Xiaoyan; Tang, Yingcai; Zi, Yanqin

    2010-03-01

    The interaction between prulifloxacin, a kind of new oral taking antibiotic and pepsin, a kind of enzyme in the stomach has been investigated in vitro under a simulated physiological condition by different spectroscopic methods. The intrinsic fluorescence of pepsin was strongly quenched by prulifloxacin. This effect was rationalized in terms of a static quenching procedure. The binding parameters have been evaluated by fluorescence quenching methods. The negative value of Δ G0 reveals that the binding process is a spontaneous process. The binding distance R between donor (pepsin) and acceptor (prulifloxacin) was obtained according to the Förster's resonance energy transfer theory and found to be 0.95 nm. The results obtained herein will be of biological significance in pharmacology and clinical medicine.

  14. A molecular-genetic approach to studying source-sink interactions in Arabidopsis thalian. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, S. I.

    2000-06-01

    This is a final report describing the results of the research funded by the DOE Energy Biosciences Program grant entitled ''A Molecular-Genetic Approach to Studying Source-Sink Interactions in Arabidiopsis thaliana''.

  15. Interactions of mercury with different molecular weight fractions of humic substances in aquatic systems.

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, P.; Yao, K.M.; Chennuri, K.; Vudamala, K.; Babu, P.V.R.

    Interactions of mercury (Hg) with different molecular weight fractions of humic substances (HS) play an important role in controlling distribution, diffusion, speciation, and bioavailability of Hg in natural systems. This study suggests that Hg...

  16. Fragment molecular orbital method for studying lanthanide interactions with proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tsushima, Satoru [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Biophysics; Komeiji, Y. [National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan); Mochizuki, Y. [Rikkyo Univ., Tokyo (Japan)

    2017-06-01

    The binding affinity of the calcium-binding protein calmodulin towards Eu{sup 3+} was studied as a model for lanthanide protein interactions in the large family of ''EF-hand'' calcium-binding proteins.

  17. Molecular basis of indomethacin-human serum albumin interaction

    DEFF Research Database (Denmark)

    Trivedi, V D; Vorum, H; Honoré, B

    1999-01-01

    Studies on the strength and extent of binding of the non-steroidal anti-inflammatory drug indomethacin to human serum albumin (HSA) have provided conflicting results. In the present work, the serum-binding of indomethacin was studied in 55 mM sodium phosphate buffer (pH 7.0) at 28 degrees C......, by using a fluorescence quench titration technique. The interaction of indomethacin with human serum albumin has been studied as a function of temperature, ionic strength and pH. The results suggest that electrostatic interaction plays a major role in the binding. The possible role of lysine residues...... in this interaction was studied by modifying exposed and buried lysine residues of HSA with potassium cyanate and studying indomethacin binding with the modified HSA. The data suggest that the interaction takes place via a salt bridge formation between the carboxylate group of indomethacin and a buried lysine residue...

  18. Interactive domains in the molecular chaperone human alphaB crystallin modulate microtubule assembly and disassembly.

    Directory of Open Access Journals (Sweden)

    Joy G Ghosh

    2007-06-01

    Full Text Available Small heat shock proteins regulate microtubule assembly during cell proliferation and in response to stress through interactions that are poorly understood.Novel functions for five interactive sequences in the small heat shock protein and molecular chaperone, human alphaB crystallin, were investigated in the assembly/disassembly of microtubules and aggregation of tubulin using synthetic peptides and mutants of human alphaB crystallin.The interactive sequence (113FISREFHR(120 exposed on the surface of alphaB crystallin decreased microtubule assembly by approximately 45%. In contrast, the interactive sequences, (131LTITSSLSSDGV(142 and (156ERTIPITRE(164, corresponding to the beta8 strand and the C-terminal extension respectively, which are involved in complex formation, increased microtubule assembly by approximately 34-45%. The alphaB crystallin peptides, (113FISREFHR(120 and (156ERTIPITRE(164, inhibited microtubule disassembly by approximately 26-36%, and the peptides (113FISREFHR(120 and (131LTITSSLSSDGV(142 decreased the thermal aggregation of tubulin by approximately 42-44%. The (131LTITSSLSSDGV(142 and (156ERTIPITRE(164 peptides were more effective than the widely used anti-cancer drug, Paclitaxel, in modulating tubulinmicrotubule dynamics. Mutagenesis of these interactive sequences in wt human alphaB crystallin confirmed the effects of the alphaB crystallin peptides on microtubule assembly/disassembly and tubulin aggregation. The regulation of microtubule assembly by alphaB crystallin varied over a narrow range of concentrations. The assembly of microtubules was maximal at alphaB crystallin to tubulin molar ratios between 1:4 and 2:1, while molar ratios >2:1 inhibited microtubule assembly.Interactive sequences on the surface of human alphaB crystallin collectively modulate microtubule assembly through a dynamic subunit exchange mechanism that depends on the concentration and ratio of alphaB crystallin to tubulin. These are the first

  19. Molecular investigations into the mechanics of actin in different nucleotide states.

    Science.gov (United States)

    Lee, Ji Y; Iverson, Tyler M; Dima, Ruxandra I

    2011-01-13

    Actin plays crucial roles in the mechanical response of cells to applied forces. For example, during cell adhesion, under the action of forces transmitted through integrins, actin filaments (F-actin) induce intracellular mechanical movements leading to changes in the cell shape. Muscle contraction results from the interaction of F-actin with the molecular motor myosin. Thus, understanding the origin of actin's mechanical flexibility is required to understand the basis of fundamental cellular processes. F-actin results from the polymerization of globular actin (G-actin), which contains one tightly bound nucleotide (ATP or ADP). Experiments revealed that G-actin is more flexible than F-actin, but no molecular-level understanding of this differential behavior exists. To probe the basis of the mechanical behavior of actin, we study the force response of G-actin bound with ATP (G-ATP) or ADP (G-ADP). We investigate the global unfolding of G-actin under forces applied at its ends and its mechanical resistance along the actin-actin and actin-myosin bonds in F-actin. Our study reveals that the nucleotide plays an important role in the global unfolding of actin, leading to multiple unfolding scenarios which emphasize the differences between the G-ATP and G-ADP states. Furthermore, our simulations show that G-ATP is more flexible than G-ADP and that the actin-myosin interaction surface responds faster to force than the actin-actin interaction surface. The deformation of G-actin under tension revealed in our simulations correlates very well with experimental data on G-actin domain flexibility.

  20. Modeling of nanotoxicity molecular interactions of nanomaterials with bionanomachines

    CERN Document Server

    Zhou, Ruhong

    2015-01-01

    This book provides a comprehensive overview of the fundamentals of nanotoxicity modeling and its implications for the development of novel nanomedicines. It lays out the fundamentals of nanotoxicity modeling for an array of nanomaterial systems, ranging from carbon-based nanoparticles to noble metals, metal oxides, and quantum dots. The author illustrates how molecular (classical mechanics) and atomic (quantum mechanics) modeling approaches can be applied to bolster our understanding of many important aspects of this critical nanotoxicity issue. Each chapter is organized by types of nanomaterials for practicality, making this an ideal book for senior undergraduate students, graduate students, and researchers in nanotechnology, chemistry, physics, molecular biology, and computer science. It is also of interest to academic and industry professionals who work on nanodrug delivery and related biomedical applications, and aids readers in their biocompatibility assessment efforts in the coming age of nanotechnology...

  1. Interaction of molecular motors can enhance their efficiency

    Czech Academy of Sciences Publication Activity Database

    Slanina, František

    2008-01-01

    Roč. 84, č. 5 (2008), 50009/1-50009/6 ISSN 0295-5075 R&D Projects: GA ČR GA202/07/0404 Institutional research plan: CEZ:AV0Z10100520 Keywords : molecular motors * diffusion * colloids Subject RIV: BE - Theoretical Physics Impact factor: 2.203, year: 2008 http://iopscience.iop.org/0295-5075/84/5/50009/?ejredirect=.iopscience

  2. Molecular interactions between the olive and the fruit fly Bactrocera oleae

    Directory of Open Access Journals (Sweden)

    Corrado Giandomenico

    2012-06-01

    Full Text Available Abstract Background The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively. Results We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures. Conclusions This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction.

  3. Molecular interactions between the olive and the fruit fly Bactrocera oleae

    Science.gov (United States)

    2012-01-01

    Background The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively. Results We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures. Conclusions This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction. PMID:22694925

  4. Infectious Bronchitis Virus Variants: Molecular Analysis and Pathogenicity Investigation

    Directory of Open Access Journals (Sweden)

    Shu-Yi Lin

    2017-09-01

    Full Text Available Infectious bronchitis virus (IBV variants constantly emerge and pose economic threats to poultry farms worldwide. Numerous studies on the molecular and pathogenic characterization of IBV variants have been performed between 2007 and 2017, which we have reviewed herein. We noted that viral genetic mutations and recombination events commonly gave rise to distinct IBV genotypes, serotypes and pathotypes. In addition to characterizing the S1 genes, full viral genomic sequencing, comprehensive antigenicity, and pathogenicity studies on emerging variants have advanced our understanding of IBV infections, which is valuable for developing countermeasures against IBV field outbreaks. This review of IBV variants provides practical value for understanding their phylogenetic relationships and epidemiology from both regional and worldwide viewpoints.

  5. Investigating Viruses during the Transformation of Molecular Biology.

    Science.gov (United States)

    Moss, Bernard

    2017-03-10

    This Reflections article describes my early work on viral enzymes and the discovery of mRNA capping, how my training in medicine and biochemistry merged as I evolved into a virologist, the development of viruses as vaccine vectors, and how scientific and technological developments during the 1970s and beyond set the stage for the interrogation of nearly every step in the reproductive cycle of vaccinia virus (VACV), a large DNA virus with about 200 genes. The reader may view this article as a work in progress, because I remain actively engaged in research at the National Institutes of Health (NIH) notwithstanding 50 memorable years there. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Effect of Molecular Sizes of Chondroitin Sulfate on Interaction with L-Selectin

    Directory of Open Access Journals (Sweden)

    Naoko Igarashi

    2013-01-01

    Full Text Available Chondroitin sulfate (CS is a glycosaminoglycan (GAG side chain of proteoglycans (PGs which are widely distributed in the extracellular matrix and at cell surface. CS shows a highly structural diversity in not only molecular weight (MW but sulfonation pattern. CS has been reported to exert anti-inflammatory activity by having effects on cytokine production by helper T cells. In this study, we focused on the structures of CS chains, especially MW of CS, and investigated effect of the different MW of CS on binding affinity with L-selectin and cytokine production by murine splenocytes. Firstly, we fractionated CS by employing gel filtration chromatography and obtained several CS fractions with different MW. Then the interaction between fractionated CS and L-selectin was analyzed by surface plasmon resonance (SPR. Finally, the influence of MW of CS on cytokine production by murine splenocytes was investigated in vitro. The results showed that interferon-gamma production was significantly increased by mouse splenocytes cocultivated with CS. On the contrary, CS inhibited interleukin 5 production by murine splenocytes depending on MW of the cocultivated CS. These results strongly indicate the existence of the optimal molecular size for an anti-inflammatory effect of CS through cytokine production by murine splenocytes.

  7. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures

    Science.gov (United States)

    Caetano, Fabiana A.; Dirk, Brennan S.; Tam, Joshua H. K.; Cavanagh, P. Craig; Goiko, Maria; Ferguson, Stephen S. G.; Pasternak, Stephen H.; Dikeakos, Jimmy D.; de Bruyn, John R.; Heit, Bryan

    2015-01-01

    Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell. PMID:26657340

  8. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

    Directory of Open Access Journals (Sweden)

    Fabiana A Caetano

    2015-12-01

    Full Text Available Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

  9. The molecular mechanism for interaction of ceruloplasmin and myeloperoxidase

    Science.gov (United States)

    Bakhautdin, Bakytzhan; Bakhautdin, Esen Göksöy

    2016-04-01

    Ceruloplasmin (Cp) is a copper-containing ferroxidase with potent antioxidant activity. Cp is expressed by hepatocytes and activated macrophages and has been known as physiologic inhibitor of myeloperoxidase (MPO). Enzymatic activity of MPO produces anti-microbial agents and strong prooxidants such as hypochlorous acid and has a potential to damage host tissue at the sites of inflammation and infection. Thus Cp-MPO interaction and inhibition of MPO has previously been suggested as an important control mechanism of excessive MPO activity. Our aim in this study was to identify minimal Cp domain or peptide that interacts with MPO. We first confirmed Cp-MPO interaction by ELISA and surface plasmon resonance (SPR). SPR analysis of the interaction yielded 30 nM affinity between Cp and MPO. We then designed and synthesized 87 overlapping peptides spanning the entire amino acid sequence of Cp. Each of the peptides was tested whether it binds to MPO by direct binding ELISA. Two of the 87 peptides, P18 and P76 strongly interacted with MPO. Amino acid sequence analysis of identified peptides revealed high sequence and structural homology between them. Further structural analysis of Cp's crystal structure by PyMOL software unfolded that both peptides represent surface-exposed sites of Cp and face nearly the same direction. To confirm our finding we raised anti-P18 antisera in rabbit and demonstrated that this antisera disrupts Cp-MPO binding and rescues MPO activity. Collectively, our results confirm Cp-MPO interaction and identify two nearly identical sites on Cp that specifically bind MPO. We propose that inhibition of MPO by Cp requires two nearly identical sites on Cp to bind homodimeric MPO simultaneously and at an angle of at least 120 degrees, which, in turn, exerts tension on MPO and results in conformational change.

  10. Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx)

    Science.gov (United States)

    Orchard, Sandra; Kerrien, Samuel; Abbani, Sara; Aranda, Bruno; Bhate, Jignesh; Bidwell, Shelby; Bridge, Alan; Briganti, Leonardo; Brinkman, Fiona S. L.; Cesareni, Gianni; Chatr-aryamontri, Andrew; Chautard, Emilie; Chen, Carol; Dumousseau, Marine; Goll, Johannes; Hancock, Robert E. W.; Hannick, Linda I.; Jurisica, Igor; Khadake, Jyoti; Lynn, David J.; Mahadevan, Usha; Perfetto, Livia; Raghunath, Arathi; Ricard-Blum, Sylvie; Roechert, Bernd; Salwinski, Lukasz; Stümpflen, Volker; Tyers, Mike; Uetz, Peter; Xenarios, Ioannis; Hermjakob, Henning

    2013-01-01

    The IMEx consortium is an international collaboration between major public interaction data providers to share curation effort and make a non-redundant set of protein interactions available in a single search interface on a common website (www.imexconsortium.org). Common curation rules have been developed and a central registry is used to manage the selection of articles to enter into the dataset. The advantages of such a service to the user, quality control measures adopted and data distribution practices are discussed. PMID:22453911

  11. An experimental and numerical investigation on wave-mud interactions

    Science.gov (United States)

    Hsu, W. Y.; Hwung, H. H.; Hsu, T. J.; Torres-Freyermuth, A.; Yang, R. Y.

    2013-03-01

    Wave attenuation over a mud (kaolinite) layer is investigated via laboratory experiments and numerical modeling. The rheological behavior of kaolinite exhibits hybrid properties of a Bingham and pseudoplastic fluid. Moreover, the measured time-dependent velocity profiles in the mud layer reveal that the shear rate under wave loading is highly phase dependent. The measured shear rate and rheological data allow us to back-calculate the time-dependent viscosity of the mud layer under various wave loadings, which is also shown to fluctuate up to 1 order of magnitude during one wave period. However, the resulting time-dependent bottom stress is shown to only fluctuate within 25% of its mean. The back-calculated wave-averaged bottom stress is well correlated with the wave damping rate in the intermediate-wave energy condition. The commonly adopted constant viscosity assumption is then evaluated via linear and nonlinear wave-mud interaction models. When driving the models with measured wave-averaged mud viscosity (forward modeling), the wave damping rate is generally overpredicted under the low wave energy condition. On the other hand, when a constant viscosity is chosen to match the observed wave damping rate (inverse modeling), the predicted velocity profiles in the mud layer are not satisfactory and the corresponding viscosity is lower than the measured value. These discrepancies are less pronounced when waves become more energetic. Differences between the linear and nonlinear model results become significant under low-energy conditions, suggesting an amplification of wave nonlinearity due to non-Newtonian rheology. In general, the constant viscosity assumption for modeling wave-mud interaction is only appropriate for more energetic wave conditions.

  12. Ultrasonic study of molecular interaction in binary liquid mixtures at ...

    Indian Academy of Sciences (India)

    The variation of these parameters with composition of the mixture helps us in understanding the nature and extent of interaction between unlike molecules in the mixtures. Further, theoretical values of ultrasonic speed were evaluated using theories and empirical relations. The relative merits of these theories and relations ...

  13. Studies on Molecular Interaction in Ternary Liquid Mixtures

    Directory of Open Access Journals (Sweden)

    R. Uvarani

    2010-01-01

    Full Text Available Ultrasonic velocity, density and viscosity for the ternary liquid mixtures of cyclohexanone with 1-propanol and 1-butanol in carbon tetrachloride were measured at 303 K. The acoustical parameters and their excess values were calculated. The trends in the variation of these excess parameters were used to discuss the nature and strength of the interactions present between the component molecules.

  14. Molecular ecological insights into neotropical bird-tick interactions

    NARCIS (Netherlands)

    Miller, Matthew J.; Esser, Helen J.; Loaiza, Jose R.; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In

  15. Molecular Interaction Between Salivary Proteins and Food Tannins.

    Science.gov (United States)

    Silva, Mafalda Santos; García-Estévez, Ignacio; Brandão, Elsa; Mateus, Nuno; de Freitas, Victor; Soares, Susana

    2017-08-09

    Polyphenols interaction with salivary proteins (SP) has been related with organoleptic features such as astringency. The aim of this work was to study the interaction between some human SP and tannins through two spectroscopic techniques, fluorescence quenching, and saturation transfer difference-nuclear magnetic resonance (STD-NMR). Generally, the results showed a significant interaction between SP and both condensed tannins and ellagitannins. Herein, STD-NMR proved to be a useful tool to map tannins' epitopes of binding, while fluorescence quenching allowed one to discriminate binding affinities. Ellagitannins showed the greatest binding constants values (K SV from 20.1 to 94.1 mM -1 ; K A from 0.7 to 8.3 mM -1 ) in comparison with procyanidins (K SV from 5.4 to 40.0 mM -1 ; K A from 1.1 to 2.7 mM -1 ). In fact, punicalagin was the tannin that demonstrated the highest affinity for all three SP. Regarding SP, P-B peptide was the one with higher affinity for ellagitannins. On the other hand, cystatins showed in general the lower K SV and K A values. In the case of condensed tannins, statherin was the SP with the highest affinity, contrasting with the other two SP. Altogether, these results are evidence that the distinct SP present in the oral cavity have different abilities to interact with food tannins class.

  16. Guest:host interactions of lidocaine and prilocaine with natural cyclodextrins: Spectral and molecular modeling studies

    Science.gov (United States)

    Rajendiran, N.; Mohandoss, T.; Saravanan, J.

    2014-11-01

    Inclusion complex formation of two local anesthetics drugs (lidocaine (LC) and prilocaine (PC)) with α- and β-cyclodextrins (CDs) in aqueous solution were studied by absorption, fluorescence, time-resolved fluorescence and molecular modeling methods. The formation of inclusion complexes was confirmed by 1H NMR, FTIR, differential scanning calorimetry, SEM, TEM and X-ray diffractometry. Both drugs formed 1:1 inclusion complex and exhibit biexponential decay in water whereas triexponential decay in the CD solution. Nanosized self-aggregated particles of drug: CD complexes were found by TEM. Both experimental and theoretical studies revealed that the phenyl ring with the amide group of the drug is encapsulated in the hydrophobic CD nanocavity. Investigations of energetic and thermodynamic properties confirmed the stability of the inclusion complexes. van der Waals interactions are mainly responsible for enthalpy driven complex formation of LC and PC with CDs.

  17. Nuclear magnetic resonance studies of conformations and molecular interactions in lyotropic mesophases - Applications to solubilization problems

    International Nuclear Information System (INIS)

    Caniparoli, Jean-Philippe

    1988-01-01

    After having determined the structural properties of smectic liquid crystals made from double chain surfactants/water binary systems, residual anisotropic interactions and relaxation times measurements were used to investigate the molecular ordering. Phosphorus, deuterium and nitrogen NMR of the surfactant molecules evidenced their high degree of order and the strong anisotropy of their motions. Quantitative results depended on the surfactant polar head -phosphate or ammonium-, while they displayed little variations with the hydrocarbon tail size. The marked dependence of the order and dynamics of small solutes in a lamellar phase on their hydrophilic or hydrophobic behaviour was shown using the same methods. By means of para-magnetically induced relaxation, it was proved that the non-polar solute benzene is located in the organic domain of the liquid crystalline matrix. (author) [fr

  18. Chitosan nanoparticles-trypsin interactions: Bio-physicochemical and molecular dynamics simulation studies.

    Science.gov (United States)

    Salar, Safoura; Mehrnejad, Faramarz; Sajedi, Reza H; Arough, Javad Mohammadnejad

    2017-10-01

    Herein, we investigated the effect of the chitosan nanoparticles (CsNP) on the structure, dynamics, and activity of trypsin. The enzyme activity in complex with the nanoparticles slightly increased, which represents the interactions between the nanoparticles and the enzyme. The kinetic parameters of the enzyme, K m and k cat , increased after adding the nanoparticles, resulting in a slight increase in the catalytic efficiency (k cat /K m ). However, the effect of the nanoparticles on the kinetic stability of trypsin has not exhibited significant variations. Fluorescence spectroscopy did not show remarkable changes in the trypsin conformation in the presence of the nanoparticles. The circular dichroism (CD) spectroscopy results also revealed the secondary structure of trypsin attached to the nanoparticles slightly changed. Furthermore, we used molecular dynamics (MD) simulation to find more information about the interaction mechanisms between the nanoparticles and trypsin. The root mean square deviation (RMSD) of Cα atoms results have shown that in the presence of the nanoparticles, trypsin was stable. The simulation and the calculation of the binding free energy demonstrate that the nonpolar interactions are the most important forces for the formation of stable nanoparticle-trypsin complex. This study has explicitly elucidated that the nanoparticles have not considerable effect on the trypsin. Copyright © 2017. Published by Elsevier B.V.

  19. New insights into the molecular mechanisms of biomembrane structural changes and interactions by optical biosensor technology.

    Science.gov (United States)

    Lee, Tzong-Hsien; Hirst, Daniel J; Aguilar, Marie-Isabel

    2015-09-01

    Biomolecular-membrane interactions play a critical role in the regulation of many important biological processes such as protein trafficking, cellular signalling and ion channel formation. Peptide/protein-membrane interactions can also destabilise and damage the membrane which can lead to cell death. Characterisation of the molecular details of these binding-mediated membrane destabilisation processes is therefore central to understanding cellular events such as antimicrobial action, membrane-mediated amyloid aggregation, and apoptotic protein induced mitochondrial membrane permeabilisation. Optical biosensors have provided a unique approach to characterising membrane interactions allowing quantitation of binding events and new insight into the kinetic mechanism of these interactions. One of the most commonly used optical biosensor technologies is surface plasmon resonance (SPR) and there have been an increasing number of studies reporting the use of this technique for investigating biophysical analysis of membrane-mediated events. More recently, a number of new optical biosensors based on waveguide techniques have been developed, allowing membrane structure changes to be measured simultaneously with mass binding measurements. These techniques include dual polarisation interferometry (DPI), plasmon waveguide resonance spectroscopy (PWR) and optical waveguide light mode spectroscopy (OWLS). These techniques have expanded the application of optical biosensors to allow the analysis of membrane structure changes during peptide and protein binding. This review provides a theoretical and practical overview of the application of biosensor technology with a specific focus on DPI, PWR and OWLS to study biomembrane-mediated events and the mechanism of biomembrane disruption. This article is part of a Special Issue entitled: Lipid-protein interactions. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Molecular Investigation of the Stem Snap Point in Textile Hemp

    Directory of Open Access Journals (Sweden)

    Marc Behr

    2017-12-01

    Full Text Available Fibre crops are important natural resources, as they sustainably provide bast fibres, an economically-valuable raw material used in the textile and biocomposite sectors. Among fibre crops, textile hemp (Cannabis sativa L. is appreciated for its long and strong gelatinous bast fibres. The stem of fibre crops is a useful system for cell wall-oriented studies, because it shows a strong tissue polarity with a lignified inner core and a cellulosic hypolignified cortex, as well as a basipetal lignification gradient. Along the stem axis of fibre crops, a specific region, denoted snap point, marks the transition from elongation (above it to fibre thickening (below it. After empirically determining the snap point by tilting the plant, we divided the stem segment containing it into three non-overlapping consecutive regions measuring 1 cm each, and carried out targeted RT-qPCR on cell wall-related genes separately, in outer and inner tissues. Different gene clusters can be observed, two of which are the major gene groups, i.e., one group with members expressed at higher levels in the inner tissues, and one group whose genes are more expressed in the cortex. The present results provide a molecular validation that the snap point is characterised by a gradient of events associated with the shift from fibre elongation to thickening.

  1. The Cladosporium fulvum - tomato interaction : physiological and molecular aspects of pathogenesis

    NARCIS (Netherlands)

    Joosten, M.H.A.J.

    1991-01-01

    In this thesis research on the physiological and molecular aspects of pathogenesis in the interaction between tomato and Cladosporium fulvum Cooke (syn. Fulvia fulva [Cooke] Cif) is described. This plant-fungus interaction is envisaged to be based

  2. Molecular interactions in the betaine monohydrate-polyol deep eutectic solvents: Experimental and computational studies

    Science.gov (United States)

    Zahrina, Ida; Mulia, Kamarza; Yanuar, Arry; Nasikin, Mohammad

    2018-04-01

    DES (deep eutectic solvents) are a new class of ionic liquids that have excellent properties. The strength of interaction between molecules in the DES affects their properties and applications. In this work, the strength of molecular interactions between components in the betaine monohydrate salt and polyol (glycerol or/and propylene glycol) eutectic mixtures was studied by experimental and computational studies. The melting point and fusion enthalpy of the mixtures were measured using STA (Simultaneous Thermal Analyzer). The nature and strength of intermolecular interactions were observed by FT-IR and NMR spectroscopy. The molecular dynamics simulation was used to determine the number of H-bonds, percent occupancy, and radial distribution functions in the eutectic mixtures. The interaction between betaine monohydrate and polyol is following order: betaine monohydrate-glycerol-propylene glycol > betaine monohydrate-glycerol > betaine monohydrate-propylene glycol, where the latter is the eutectic mixture with the lowest stability, strength and extent of the hydrogen bonding interactions between component molecules. The presence of intra-molecular hydrogen bonding interactions, the inter-molecular hydrogen bonding interactions between betaine molecule and polyol, and also interactions between polyol and H2O of betaine monohydrate in the eutectic mixtures.

  3. Molecular Dynamics Methodologies for Probing Cannabinoid Ligand/Receptor Interaction

    Science.gov (United States)

    Lynch, Diane L.; Hurst, Dow P.; Shore, Derek M.; Pitman, Mike C.; Reggio, Patricia H.

    2018-01-01

    The cannabinoid type 1 and 2 G-protein-coupled receptors are currently important pharmacological targets with significant drug discovery potential. These receptors have been shown to display functional selectivity or biased agonism, a property currently thought to have substantial therapeutic potential. Although recent advances in crystallization techniques have provided a wealth of structural information about this important class of membrane-embedded proteins, these structures lack dynamical information. In order to fully understand the interplay of structure and function for this important class of proteins, complementary techniques that address the dynamical aspects of their function are required such as NMR as well as a variety of other spectroscopies. Complimentary to these experimental approaches is molecular dynamics, which has been effectively used to help unravel, at the atomic level, the dynamics of ligand binding and activation of these membrane-bound receptors. Here, we discuss and present several representative examples of the application of molecular dynamics simulations to the understanding of the signatures of ligand-binding and -biased signaling at the cannabinoid type 1 and 2 receptors. PMID:28750815

  4. Investigation of multilayer painting by means of molecular spectroscopy

    Directory of Open Access Journals (Sweden)

    Kadikova I.F.

    2017-01-01

    Full Text Available The study of paintings’ layer structure under microscope was implemented in the early XX century; since that time method of cross-section preparation as well as composition of embedded materials changed and capabilities of optical microscopy broadened. Nevertheless, until recently cross-sections were prepared only for analysis of paintings’ layer-specific structure, morphological and technological features, tracks of restoration treatments. Examination of chemical composition required additional sampling as well as division of these samples layer by layer in order to determine pigments and binding media; these procedures didn’t always lead to proper results. Micro-Raman and micro-FTIR spectroscopy allow carrying out investigation of painting cross-sections without any additional preliminary sampling; this is shown on example of investigation of a number of paintings.

  5. Molecular interactions in the placenta during malaria infection.

    Science.gov (United States)

    Mens, Petra F; Bojtor, Edward C; Schallig, Henk D F H

    2010-10-01

    Placental malaria is the placental sequestration of Plasmodium falciparum infected erythrocytes that accumulate in the intervillous space, resulting in pathological alterations. The intervillous space, the main compartment for exchange of nutrients and delivery of oxygen to the fetus, is of utmost importance for fetal development. Events leading to adverse outcomes of placental malaria can be summarized in four steps: (1) accumulation of P. falciparum infected erythrocytes; (2) infiltration of monocytes and macrophages; (3) alteration of the placental cytokine balance and (4) pathogenesis of adverse pregnancy outcomes. These events are triggered by chemokines and cytokines leading to impaired materno-fetal exchange and damage to the placenta. This review describes the events during placental malaria infection at molecular level and presents a simplified model describing all crucial steps leading to adverse pregnancy outcomes based on a review of recent literature (August 2009). Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  6. Interactions in charged colloidal suspensions: A molecular dynamics simulation study

    Science.gov (United States)

    Padidela, Uday Kumar; Behera, Raghu Nath

    2017-07-01

    Colloidal suspensions are extensively used in everyday life and find several applications in the pharmaceutical, chemical, food industries, etc. We present the classical molecular dynamics simulation results of the structural and transport properties of charged colloidal suspensions as a function of its size, charge and concentration. The system is viewed as a two-component (colloids and counterions) primitive model consisting of spherical colloid particle (macroion) and the counterions (micro-particles), which are treated explicitly. The solvent is treated as dielectric continuum. A systematic trend in the radial distribution functions g(r), potential of mean force W(r), different thermodynamic properties and diffusion coefficients is obtained as a function of colloid charge, size and concentration. An attractive minimum in W(r) is obtained at short interparticle distance.

  7. Molecular simulation of polar molecules interaction with MOFs family materials

    International Nuclear Information System (INIS)

    De Toni, M.

    2012-01-01

    The topic of this thesis is the adsorption of simple molecular fluids in nano-porous materials. Many industrial processes are based on this phenomenon, including ionic exchange, selective separation and heterogeneous catalysis. I used molecular simulation to study the adsorption properties of polar molecules of industrial interest (CO 2 and H 2 O) in a new class of crystalline microporous hybrid organic-inorganic materials called Metal-Organic Frameworks (MOFs). They have exceptional adsorption properties due to their topological variety and their versatility, allowed by the large range of possibilities offered by organic and coordination chemistry and functionalizations. I first studied the adsorption of CO 2 in a family of materials called IRMOFs, which share the same topology but have different porous volume, in order to characterize the effect of confinement on their adsorption performance. In particular, a general behavior has been highlighted: the critical temperature decreases when the confinement increases. Then, I looked at a recently synthesized cationic MOF called Zn2(CBTACN). After having localized the extra-framework halogen anions in the unit cell of the material, something which was not possible experimentally, I characterized CO 2 adsorption in this system first as a pure gas and then as a component of different mixtures. Finally, I was interested in the hydrothermal stability of MOFs, a crucial issue for their use in industrial applications. I observed the hydration mechanism of system that is analogous to the MOF-5 (IRMOF-0h) and shed light on some collaborative effects of the attack of water that were unknown to in the literature. (author)

  8. Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations.

    Science.gov (United States)

    Shawon, Jakaria; Khan, Akib Mahmud; Rahman, Adhip; Hoque, Mohammad Mazharol; Khan, Mohammad Abdul Kader; Sarwar, Mohammed G; Halim, Mohammad A

    2016-10-01

    Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of -8.7, -8.6 and -7.9 kcal/mol, respectively against 2KFN compared to the binding affinity -6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.

  9. Molecular interaction of Ornithobacterium rhinotracheale with eukaryotic cells

    NARCIS (Netherlands)

    Chansiripornchai, N. (Niwat)

    2004-01-01

    Ornithobacterium rhinotracheale (ORT) is a emerging gram negative bacterial pathogen in poultry. To facilitate the development of novel infection intervention and prevention strategies, the pathogenesis of ORT infection was investigated. In vitro infection assays demonstrated that ORT adhered to

  10. Molecular and Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017)

    Science.gov (United States)

    2017-10-01

    term goal is to identify molecular mechanisms regulating tau that can be used as diagnostics and to develop therapeutics for CTE. The immediate goal...AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017) PRINCIPAL...INTRODUCTION: Repetitive mild traumatic brain injury leads to neurological symptoms and chronic traumatic encephalopathy (CTE). The molecular changes

  11. Molecular dynamics simulations of protein-tyrosine phosphatase 1B: II. Substrate-enzyme interactions and dynamics

    DEFF Research Database (Denmark)

    Peters, Günther H.j.; Frimurer, T. M.; Andersen, J. N.

    2000-01-01

    Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme...... for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein...

  12. Correlations and symmetry of interactions influence collective dynamics of molecular motors

    International Nuclear Information System (INIS)

    Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

    2015-01-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

  13. Molecular Interaction of Pinic Acid with Sulfuric Acid

    DEFF Research Database (Denmark)

    Elm, Jonas; Kurten, Theo; Bilde, Merete

    2014-01-01

    from the corresponding ΔG values. The first two additions of sulfuric acid to pinic acid are found to be favorable with ΔG values of -9.06 and -10.41 kcal/mol. Addition of a third sulfuric acid molecule is less favorable and leads to a structural rearrangement forming a bridged sulfuric acid-pinic acid...... without the further possibility for attachment of either sulfuric acid or pinic acid. This suggests that pinic acid cannot be a key species in the first steps in nucleation, but the favorable interactions between sulfuric acid and pinic acid imply that pinic acid can contribute to the subsequent growth...

  14. Single NdPc2 molecules on surfaces. Adsorption, interaction, and molecular magnetism

    International Nuclear Information System (INIS)

    Fahrendorf, Sarah

    2013-01-01

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc 2 ) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc 2 ) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc 2 molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the spin

  15. Single NdPc{sub 2} molecules on surfaces. Adsorption, interaction, and molecular magnetism

    Energy Technology Data Exchange (ETDEWEB)

    Fahrendorf, Sarah

    2013-01-24

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc{sub 2}) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc{sub 2}) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc{sub 2} molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the

  16. Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

    Science.gov (United States)

    Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

    2018-02-05

    Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Thermal characterization of static and dynamical properties of the confined molecular systems interacting through dispersion force.

    Science.gov (United States)

    Ramos, Sergio Luis L M; Ogino, Michihiko; Oguni, Masaharu

    2015-01-28

    We investigated the thermal properties of liquid methylcyclohexane and racemic sec-butylcyclohexane, as representatives of a molecular system with only dispersion-force intermolecular interactions, confined in the pores (thickness/diameter d = 12, 6, 1.1 nm) of silica gels by adiabatic calorimetry. The results imply a heterogeneous picture for molecular aggregate under confinement consisting of an interfacial region and an inner pore one. In the vicinity of a glass-transition temperature T(g,bulk) of bulk liquid, two distinguishable relaxation phenomena were observed for the confined systems and their origins were attributed to the devitrification, namely glass transition, processes of (1) a layer of interfacial molecules adjacent to the pore walls and (2) the molecules located in the middle of the pore. A third glass-transition phenomenon was observed at lower temperatures and ascribed to a secondary relaxation process. The glass transition of the interfacial-layer molecules was found to proceed at temperatures rather above T(g,bulk), whereas that of the molecules located in the inner pore region occurred at temperatures below T(g,bulk). We discuss the reason why the molecules located in different places in the pores reveal the respectively different dynamical properties.

  18. Spectroscopy, calorimetry and molecular simulation studies on the interaction of catalase with copper ion.

    Science.gov (United States)

    Hao, Fang; Jing, Mingyang; Zhao, Xingchen; Liu, Rutao

    2015-02-01

    In this research, the binding mechanism of Cu(2+) to bovine liver catalase (BLC) was studied by fluorescence spectroscopy, ultraviolet-visible (UV-vis) absorption spectroscopy, circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC) and molecular docking methods. The cellar experiment was firstly carried out to investigate the inhibition effect of catalase. During the fluorescence quenching study, after correcting the inner filter effect (IFE), the fluorescence of BLC was found to be quenched by Cu(2+). The quenching mechanism was determined by fluorescence lifetime measurement, and was confirmed to be the dynamic mode. The secondary structure content of BLC was changed by the addition of Cu(2+), as revealed by UV-vis absorption and CD spectra, which further induces the decrease in BLC activity. Molecular simulation study indicates that Cu(2+) is located between two β-sheets and two random coils of BLC near to the heme group, and interacts with His 74 and Ser 113 residues near a hydrophilic area. The decrease of α-helix and the binding of His 74 are considered to be the major reason for the inhibition of BLC activity caused by Cu(2+). The ITC results indicate that the binding stoichiometry of Cu(2+) to catalase is 11.4. Moreover, the binding of Cu(2+) to BLC destroyed H-bonds, which was confirmed by the CD result. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Molecular interaction and energy transfer between human serum albumin and bioactive component Aloe dihydrocoumarin

    Science.gov (United States)

    Zhang, Xiu-Feng; Xie, Ling; Liu, Yang; Xiang, Jun-Feng; Li, Lin; Tang, Ya-Lin

    2008-10-01

    Aloe dihydrocoumarin is an antioxidant and a candidate of immunomodulatory drug on the immune system and can balance physiological reactive oxygen species (ROS) levels which may be useful to maintain homeostasis. In order to explore the mechanism of drug action at a molecular level, the binding of Aloe dihydrocoumarin with human serum albumin (HSA) has been investigated by fluorescence, ultraviolet (UV), circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, fluorescence dynamics, and molecular dynamic docking for the first time. We observed a quenching of fluorescence of HSA in the presence of Aloe dihydrocoumarin and also analyzed the quenching results using the Stern-Volmer equation and obtained high affinity binding to HSA. A Förster type fluorescence resonance energy transfer mechanism is involved in this quenching of Trp fluorescence by Aloe dihydrocoumarin. From the CD and FT-IR results, it is apparent that the interaction of Aloe dihydrocoumarin with HSA causes a conformational change of the protein, with the loss of α-helix stability and the gain of β-sheet and β-turn content. Data obtained by fluorescence spectroscopy, fluorescence dynamics, CD, and FT-IR experiments along with the docking studies suggest that Aloe dihydrocoumarin binds to residues located in subdomain IIA of HSA.

  20. Molecular Modeling of Interaction between Diabetic Drug and Antioxidant in Controlling Sucrose

    Science.gov (United States)

    Rakesh, Leela; Lee, Choon

    2009-09-01

    This article examined the possible protective effect of N-acetylcysteine (NAC) taurine, quercetin and Syringaldehyde dendritic antioxidants against the oxidative stress induced by diabetic or pre-diabetic patient case due to high sucrose intake by computer simulation. We also compared these results with the well-known diabetic drugs glizipid and Avandia. Towards this understanding we undertook a molecular level computer model in order to study the molecular interaction between high sugar content with antioxidant by varying ratios of sucrose molecules with and without the presence of diabetic drugs. From our study it shows that with the presence of various antioxidant combinations diabetics drugs could be much more beneficial to the patients in terms of its side effects such a heart attack. Many interesting results have been obtained by this study. The application of this driving force may be used to predict the feasibility and benefit in order to understand the high-sucrose diet-induced obesity, which certainly would bring new insights on obesity-related adverse control and may possibly suggest the impact of N-acetylcysteine and syringaldehyde in such cases. Hyperglycemia is an important predictor of cardiovascular mortality in patients with diabetes. We also investigated the hypothesis that diabetes or acute hyperglycemia attenuates the reduction of myocardial infarct size produced by activation of mitochondrial ATP-regulated potassium (KATP) channels. The results indicate that diabetes/hyperglycemia impairs activation of mitochondrial KATP channels.

  1. Circadian Rhythms in Fear Conditioning: An Overview of Behavioral, Brain System, and Molecular Interactions

    Directory of Open Access Journals (Sweden)

    Anne Albrecht

    2017-01-01

    Full Text Available The formation of fear memories is a powerful and highly evolutionary conserved mechanism that serves the behavioral adaptation to environmental threats. Accordingly, classical fear conditioning paradigms have been employed to investigate fundamental molecular processes of memory formation. Evidence suggests that a circadian regulation mechanism allows for a timestamping of such fear memories and controlling memory salience during both their acquisition and their modification after retrieval. These mechanisms include an expression of molecular clocks in neurons of the amygdala, hippocampus, and medial prefrontal cortex and their tight interaction with the intracellular signaling pathways that mediate neural plasticity and information storage. The cellular activities are coordinated across different brain regions and neural circuits through the release of glucocorticoids and neuromodulators such as acetylcholine, which integrate circadian and memory-related activation. Disturbance of this interplay by circadian phase shifts or traumatic experience appears to be an important factor in the development of stress-related psychopathology, considering these circadian components are of critical importance for optimizing therapeutic approaches to these disorders.

  2. Spectrofluoremetric and molecular docking study on the interaction of bisdemethoxycurcumin with bovine β-casein nanoparticles

    International Nuclear Information System (INIS)

    Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Keyhanfar, Mehrnaz; Behbahani, Mandana

    2013-01-01

    The interaction of bisdemethoxycurcumin (BDMC), as one of the main active component of turmeric (Curcuma longa L.), with bovine β-casein nanoparticle, as an efficient drug carrier system, was investigated using steady-state fluorescence spectroscopy and molecular docking calculations. Results of fluorescence quenching experiments, Forster energy transfer measurements and molecular docking calculations suggested that BDMC bind to the hydrophobic core of β-casein via formation of 3 hydrogen bonds and several vander Waals contacts that represented the encapsulation of BDMC in β-casein micelle nanoparticles. The binding parameters including number of substantive binding sites and the binding constants were evaluated by fluorescence quenching method. Additionally, the cytotoxicity of free BDMC and BDMC-β-casein complex in human breast cancer cell line MCF7 was evaluated in vitro. The study revealed the higher cytotoxic effects of encapsulated BDMC on MCF7 cells compared to equal dose of free BDMC. -- Highlights: • BDMC binds to the hydrophobic core of β-casein. • The effective encapsulation of BDMC in β-casein micelle nanoparticles was shown. • Enhanced cytotoxicity was observed for encapsulated BDMC in β-casein nanoparticles

  3. Spectrofluoremetric and molecular docking study on the interaction of bisdemethoxycurcumin with bovine β-casein nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Mehranfar, Fahimeh [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Bordbar, Abdol-Khalegh, E-mail: bordbar@chem.ui.ac.ir [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Keyhanfar, Mehrnaz; Behbahani, Mandana [Faculty of Advanced Sciences and Technologies, Department of Biotechnology, University of Isfahan, Isfahan, 81746-73441 (Iran, Islamic Republic of)

    2013-11-15

    The interaction of bisdemethoxycurcumin (BDMC), as one of the main active component of turmeric (Curcuma longa L.), with bovine β-casein nanoparticle, as an efficient drug carrier system, was investigated using steady-state fluorescence spectroscopy and molecular docking calculations. Results of fluorescence quenching experiments, Forster energy transfer measurements and molecular docking calculations suggested that BDMC bind to the hydrophobic core of β-casein via formation of 3 hydrogen bonds and several vander Waals contacts that represented the encapsulation of BDMC in β-casein micelle nanoparticles. The binding parameters including number of substantive binding sites and the binding constants were evaluated by fluorescence quenching method. Additionally, the cytotoxicity of free BDMC and BDMC-β-casein complex in human breast cancer cell line MCF7 was evaluated in vitro. The study revealed the higher cytotoxic effects of encapsulated BDMC on MCF7 cells compared to equal dose of free BDMC. -- Highlights: • BDMC binds to the hydrophobic core of β-casein. • The effective encapsulation of BDMC in β-casein micelle nanoparticles was shown. • Enhanced cytotoxicity was observed for encapsulated BDMC in β-casein nanoparticles.

  4. The interaction of plant-growth regulators with serum albumin: molecular modeling and spectroscopic methods.

    Science.gov (United States)

    Dong, Sheying; Li, Zhiqin; Shi, Ling; Huang, Guiqi; Chen, Shuangli; Huang, Tinglin

    2014-05-01

    The affinity between two plant-growth regulators (PGRs) and human serum albumin (HSA) was investigated by molecular modeling techniques and spectroscopic methods. The results of molecular modeling simulations revealed that paclobutrazol (PAC) could bind on both site I and site II in HSA where the interaction was easier, while uniconazole (UNI) could not bind with HSA. Furthermore, the results of fluorescence spectroscopy, three-dimensional (3D) fluorescence spectroscopy and circular dichroism (CD) spectroscopy suggested that PAC had a strong ability to quench the intrinsic fluorescence of HSA. The binding affinity (Kb) and the amounts of binding sites (n) between PAC and HSA at 291 K were estimated as 2.37×10(5) mol L(-1) and 1, respectively, which confirm that PAC mainly binds on site II of HSA. An apparent distance between the Trp214 and PAC was 4.41 nm. Additionally, the binding of PAC induced the conformational changes of disulfide bridges of HSA with the decrease of α-helix content. These studies provide more information on the potential toxicological effects and environmental risk assessment of PGRs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Study of interaction of butyl p-hydroxybenzoate with human serum albumin by molecular modeling and multi-spectroscopic method

    Energy Technology Data Exchange (ETDEWEB)

    Wang Qin, E-mail: wqing07@lzu.c [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Zhang Yaheng, E-mail: zhangyah04@lzu.c [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Sun Huijun, E-mail: sun.hui.jun-04@163.co [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Chen Hongli, E-mail: hlchen@lzu.edu.c [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Chen Xingguo, E-mail: chenxg@lzu.edu.c [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China)

    2011-02-15

    Study of the interaction between butyl p-hydroxybenzoate (butoben) and human serum albumin (HSA) has been performed by molecular modeling and multi-spectroscopic method. The interaction mechanism was predicted through molecular modeling first, then the binding parameters were confirmed using a series of spectroscopic methods, including fluorescence spectroscopy, UV-visible absorbance spectroscopy, circular dichroism (CD) spectroscopy and Fourier transform infrared (FT-IR) spectroscopy. The thermodynamic parameters of the reaction, standard enthalpy {Delta}H{sup 0} and entropy {Delta}S{sup 0}, have been calculated to be -29.52 kJ mol{sup -1} and -24.23 J mol{sup -1} K{sup -1}, respectively, according to the Van't Hoff equation, which suggests the van der Waals force and hydrogen bonds are the predominant intermolecular forces in stabilizing the butoben-HSA complex. Results obtained by spectroscopic methods are consistent with that of the molecular modeling study. In addition, alteration of secondary structure of HSA in the presence of butoben was evaluated using the data obtained from UV-visible absorbance, CD and FT-IR spectroscopies. - Research highlights: The interaction between butyl p-hydroxybenzoate with HSA has been investigated for the first time. Molecular modeling study can provide theoretical direction for experimental design. Multi-spectroscopic method can provide the binding parameters and thermodynamic parameters. These results are important for food safety and human health when using parabens as a preservative.

  6. Pathogenic Leptospira spp. in bats: Molecular investigation in Southern Brazil.

    Science.gov (United States)

    Mayer, Fabiana Quoos; Dos Reis, Emily Marques; Bezerra, André Vinícius Andrade; Cerva, Cristine; Rosa, Júlio; Cibulski, Samuel Paulo; Lima, Francisco Esmaile Sales; Pacheco, Susi Missel; Rodrigues, Rogério Oliveira

    2017-06-01

    The present study aimed to investigate the frequency of pathogenic Leptospira spp. in Brazilian bats and to determine possible risk factors associated to it. Ninety two bats of 12 species were evaluated. Whole genomic DNA from kidneys was extracted and real-time PCR specific to pathogenic Leptospira spp. was applied. Association between the frequency of specimens positive for Leptospira spp. and sex, age, bat species or family, season of collection, geographic localization and feeding habits was evaluated. The results showed that 39.13% of analyzed bats were found positive for Leptospira spp. Nine bat species had at least one positive result. There was no association among the evaluated variables and frequency of pathogenic Leptospira spp. Although the limitations due to lack of Leptospira spp. isolation, leptospiral carriage was demonstrated in bats of different species from southern Brazil, which reinforces the need for surveillance of infectious agents in wild animals. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Modeling of inhibitor-metalloenzyme interactions and selectivity using molecular mechanics grounded in quantum chemistry.

    Science.gov (United States)

    Garmer, D R; Gresh, N; Roques, B P

    1998-04-01

    We investigated the binding properties of the metalloprotease inhibitors hydroxamate, methanethiolate, and methylphosphoramidate to a model coordination site occurring in several Zn2+ metalloproteases, including thermolysin. This was carried out using both the SIBFA (sum of interactions between fragments ab initio-computed) molecular mechanics and the SCF/MP2 procedures for the purpose of evaluating SIBFA as a metalloenzyme modeling tool. The energy-minimized structures were closely similar to the X-ray crystallographic structures of related thermolysin-inhibitor complexes. We found that selectivity between alternative geometries and between inhibitors usually stemmed from multiple interaction components included in SIBFA. The binding strength sequence is hydroxamate > methanethiolate > or = methylphosphoramidate from multiple interaction components included in SIBFA. The trends in interaction energy components, rankings, and preferences for mono- or bidentate binding were consistent in both computational procedures. We also compared the Zn2+ vs. Mg2+ selectivities in several other polycoordinated sites having various "hard" and "soft" qualities. This included a hexahydrate, a model representing Mg2+/Ca2+ binding sites, a chlorophyll-like structure, and a zinc finger model. The latter three favor Zn2+ over Mg2+ by a greater degree than the hydrated state, but the selectivity varies widely according to the ligand "softness." SIBFA was able to match the ab initio binding energies by < 2%, with the SIBFA terms representing dispersion and charge-transfer contributing the most to Zn2+/Mg2+ selectivity. These results showed this procedure to be a very capable modeling tool for metalloenzyme problems, in this case giving valuable information about details and limitations of "hard" and "soft" selectivity trends.

  8. Interaction of von Willebrand factor domains with collagen investigated by single molecule force spectroscopy

    Science.gov (United States)

    Posch, Sandra; Obser, Tobias; König, Gesa; Schneppenheim, Reinhard; Tampé, Robert; Hinterdorfer, Peter

    2018-03-01

    von Willebrand factor (VWF) is a huge multimeric protein that plays a key role in primary hemostasis. Sites for collagen binding, an initial event of hemostasis, are located in the VWF-domains A1 and A3. In this study, we investigated single molecule interactions between collagen surfaces and wild type VWF A1A2A3 domain constructs, as well as clinically relevant VWF A3 domain point mutations, such as p.Ser1731Thr, p.Gln1734His, and p.His1786Arg. For this, we utilized atomic force microscopy based single molecular force spectroscopy. The p.Ser1731Thr mutant had no impact on the VWF-collagen type III and VI interactions, while the p.Gln1734His and p.His1786Arg mutants showed a slight increase in bond stability to collagen type III. This effect probably arises from additional hydrogen bonds that come along with the introduction of these mutations. Using the same mutants, but collagen type VI as a binding partner, resulted in a significant increase in bond stability. VWF domain A1 was reported to be essential for the interaction with collagen type VI and thus our findings strengthen the hypothesis that the VWF A1 domain can compensate for mutations in the VWF A3 domain. Additionally, our data suggest that the mutations could even stabilize the interaction between VWF and collagen without shear. VWF-collagen interactions seem to be an important system in which defective interactions between one VWF domain and one type of collagen can be compensated by alternative binding events.

  9. Profiling of Molecular Interactions in Real Time using Acoustic Detection

    Science.gov (United States)

    Godber, Benjamin; Frogley, Mark; Rehak, Marian; Sleptsov, Alexander; Thompson, Kevin S.J.; Uludag, Yildiz; Cooper, Matthew A.

    2007-01-01

    Acoustic sensors that exploit resonating quartz crystals to directly detect the binding of an analyte to a receptor are finding increasing utility in the quantification of clinically-relevant analytes. We have developed a novel acoustic detection technology, which we term Resonant Acoustic Profiling (RAP™). This technology builds on the fundamental basics of the “quartz crystal microbalance” or “QCM” with several key additional features including two- or four-channel automated sample delivery, in-line referencing and microfluidic sensor ‘cassettes’ that are pre-coated with easy-to-use surface chemistries. Example applications are described for the quantification of myoglobin concentration and its interaction kinetics, and for the ranking of enzyme-cofactor specificities. PMID:17129723

  10. Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Galo E. Balatti

    2017-10-01

    Full Text Available In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG model within the MARTINI force field; we simulated the peptide–lipid system from three different initial configurations: (a peptides in water in the presence of a pre-equilibrated lipid bilayer; (b peptides inside the hydrophobic core of the membrane; and (c random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide–lipid ratios. The exploration of the possible lipid–peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies.

  11. Interaction of vasicine with calf thymus DNA: Molecular docking, spectroscopic and differential scanning calorimetric insights

    Science.gov (United States)

    R. S., Sai Murali; R. S., Sai Siddhardha; Rajesh Babu, D.; Venketesh, S.; Basavaraju, R.; Nageswara Rao, G.

    2017-06-01

    The present study brings out the interaction between vasicine, an alkaloid and Adhatoda vasica Nees with double stranded DNA. The physico-chemical interaction between small molecules and nucleic acids is a major area of focus in screening drugs against various cancers. Molecular probing in our study using Molecular Operating Environment (MOE) has revealed interaction of vasicine with DNA double helix. Here we report the interaction of vasicine with Calf thymus DNA. We present for the first time the results obtained from UV-visible, fluorescence spectroscopic and differential scanning calorimetric techniques that suggest a moderate to strong electrostatic, hydrophobic and van der Waals interactions mediating the DNA binding properties of vasicine, leading to disruption of DNA secondary structure.

  12. STUDIES ON THE INTERACTION BETWEEN TRIPTOLIDE AND BOVINE SERUM ALBUMIN (BSA) BY SPECTROSCOPIC AND MOLECULAR MODELING METHODS.

    Science.gov (United States)

    Wang, Haidong; Shi, Hailang; Pang, Jie; Song, Xingfa; Xu, Caiyun; Sun, Zengxian

    2016-01-01

    Triptolide is a major active constituent isolated from Tripterygiumwilfordii Hook F, a Chinese herbal medicine. This study investigated the intermolecular interaction between triptolide and bovine serum albumin (BSA). The fluorescence, circular dichroism (CD) and molecular docking methods were used to investigate the intermolecular interaction between triptolide and BSA. The binding constant, the number of binding sites, binding subdomain and the thermodynamic parameters were measured. The results of this experiment revealed that the intrinsic fluorescence of BSA was effectively quenched by triptolide via static quenching. The experimental results of synchronous fluorescence and CD spectra showed that the conformation of BSA was changed in the presence of triptolide. It indicated that triptolide could spontaneously bind on site II (subdomain IIIA) of BSA mainly via hydrogen bonding interactions and Van der Waals force.

  13. Investigating the interactions of the enantiomers of phenylglycine ...

    Indian Academy of Sciences (India)

    about two orders of magnitude less than that in free water. Keywords. Nanostructure; zeolite; chirality; amino acid; molecular dynamics simulation. 1. Introduction. Domestic wastewaters contain the variety of organic contaminants such as pharmaceuticals and personal care products.1–3 Pharmaceuticals and antibiotics such.

  14. Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

    Science.gov (United States)

    Tsukanov, A. A.; Psakhie, S. G.

    2017-12-01

    The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

  15. An autosampling differential scanning calorimeter instrument for studying molecular interactions.

    Science.gov (United States)

    Plotnikov, Valerian; Rochalski, Andrew; Brandts, Michael; Brandts, John F; Williston, Samuel; Frasca, Verna; Lin, Lung-Nan

    2002-11-01

    A new ultrasensitive differential scanning calorimeter (DSC) instrument is described, which utilizes autosampling for continuous operation. High scanning rates to 250 deg/h with rapid cooling and equilibration between scans facilitates higher sample throughput up to 50 samples during each 24 h of unattended operation. The instrument is suited for those pharmaceutical applications where higher throughput is important, such as screening drug candidates for binding constant or screening solution conditions for stability of liquid protein formulations. Results are presented on the binding of five different anionic inhibitors to ribonuclease A, which included cytidine 2'-monophosphate (2'CMP), 3'CMP, uridine 3'-monophosphate, pyrophosphate, and phosphate. Binding constants K(B) (or dissociation constants K(d)) are obtained from the shift in the transition temperature T(M) for ribonuclease thermal unfolding in the presence of ligand relative to the transition temperature in the absence of ligand. Measured binding constants ranged from 155 M(-1) (K(d) = 6.45 mM) for the weak-binding phosphate anion to 13100 M(-1) (K(d) = 76.3 microM) for the strongest binding ligand, 2'CMP. The DSC method for measuring binding constants can also be extended to ultratight interactions involving either ligand-protein or protein-protein binding.

  16. Hydrogen bonding-assisted interaction between amitriptyline hydrochloride and hemoglobin: spectroscopic and molecular dynamics studies.

    Science.gov (United States)

    Maurya, Neha; Maurya, Jitendra Kumar; Kumari, Meena; Khan, Abbul Bashar; Dohare, Ravins; Patel, Rajan

    2017-05-01

    Herein, we have explored the interaction between amitriptyline hydrochloride (AMT) and hemoglobin (Hb), using steady-state and time-resolved fluorescence spectroscopy, UV-visible spectroscopy, and circular dichroism spectroscopy, in combination with molecular docking and molecular dynamic (MD) simulation methods. The steady-state fluorescence reveals the static quenching mechanism in the interaction system, which was further confirmed by UV-visible and time-resolved fluorescence spectroscopy. The binding constant, number of binding sites, and thermodynamic parameters viz. ΔG, ΔH, ΔS are also considered; result confirms that the binding of the AMT with Hb is a spontaneous process, involving hydrogen bonding and van der Waals interactions with a single binding site, as also confirmed by molecular docking study. Synchronous fluorescence, CD data, and MD simulation results contribute toward understanding the effect of AMT on Hb to interpret the conformational change in Hb upon binding in aqueous solution.

  17. Modelling social interaction as perceptual crossing: an investigation into the dynamics of the interaction process

    Science.gov (United States)

    Froese, Tom; Di Paolo, Ezequiel A.

    2010-03-01

    This paper continues efforts to establish a mutually informative dialogue between psychology and evolutionary robotics in order to investigate the dynamics of social interaction. We replicate a recent simulation model of a minimalist experiment in perceptual crossing and confirm the results with significantly simpler artificial agents. A series of psycho-physical tests of their behaviour informs a hypothetical circuit model of their internal operation. However, a detailed study of the actual internal dynamics reveals this circuit model to be unfounded, thereby offering a tale of caution for those hypothesising about sub-personal processes in terms of behavioural observations. In particular, it is shown that the behaviour of the agents largely emerges out of the interaction process itself rather than being an individual achievement alone. We also extend the original simulation model in two novel directions in order to test further the extent to which perceptual crossing between agents can self-organise in a robust manner. These modelling results suggest new hypotheses that can become the basis for further psychological experiments.

  18. Interaction of pathology and molecular characterization of thyroid cancers

    International Nuclear Information System (INIS)

    Williams, E.D.; Cherstvoy, E.; Egloff, B.; Hoefler, H.; Vecchio, G.; Bogdanova, T.; Bragarnik, M.; Tronko, N.D.

    1996-01-01

    This paper presents the results of joint studies of thyroid cancer in children under 15 years of age between departments in Cambridge, Brussels, Naples and Munich in the European Union, and departments in Minsk, Kiev and Obninsk in the newly independent states of Eastern Europe. The pathology of 264 cases of childhood thyroid cancer out of 430 that have occurred since 1990 in the 3 countries in which high levels of fallout from the Chernobyl accident occurred has been restudied by NIS and EU pathologists. The overall level of agreement reached was about 97%. The diagnosis was supported by immunocytochemistry and ISH for the differentiation markers, thyroglobulin and calcitonin, and the tumors were classified according to the WHO, with papillary carcinomas being further subclassified. 99% of the 134 Belarussian cases were papillary carcinomas, as were 94% of the 114 Ukrainian tumors. All 9 of the Russian cases available for study were papillary in type. 76 of 154 cases of childhood thyroid cancer reviewed over a 30 year period in England and Wales and were also studied, 68% of these were papillary carcinoma. Histological study showed that a subtype of papillary carcinoma, rarely found in adults, with a solid/follicular architecture occurred in children. It was found in 72% of the Belarussian papillary carcinomas, 76% of the Ukrainian cases, but only 40% of the England and Wales cases. Molecular biological studies showed that the proportion of cases of papillary carcinoma expressing the ret gene was not significantly different in the exposed and the unexposed tumors, studies of the type of translocation leading to ret gene expression are not yet conclusive. Ras gene mutations were found as expected in follicular carcinoma, but were absent from any papillary carcinoma, whether from exposed or unexposed cases. TSH receptor mutations, normally found in follicular tumors were not found in any papillary carcinomas, nor were any p53 mutations identified. All these results

  19. Optical spectroscopy and system–bath interactions in molecular aggregates with full configuration interaction Frenkel exciton model

    Energy Technology Data Exchange (ETDEWEB)

    Seibt, Joachim; Sláma, Vladislav; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz

    2016-12-20

    Highlights: • Standard Frenkel exciton model is extended to include inter-band coupling. • It is formally linked with configuration interaction method of quantum chemistry. • Spectral shifts due to inter-band coupling are found in molecular aggregates. • Effects of peak amplitude redistribution in two-dimensional spectra are found. - Abstract: Standard application of the Frenkel exciton model neglects resonance coupling between collective molecular aggregate states with different number of excitations. These inter-band coupling terms are, however, of the same magnitude as the intra-band coupling between singly excited states. We systematically derive the Frenkel exciton model from quantum chemical considerations, and identify it as a variant of the configuration interaction method. We discuss all non-negligible couplings between collective aggregate states, and provide compact formulae for their calculation. We calculate absorption spectra of molecular aggregate of carotenoids and identify significant band shifts as a result of inter-band coupling. The presence of inter-band coupling terms requires renormalization of the system–bath coupling with respect to standard formulation, but renormalization effects are found to be weak. We present detailed discussion of molecular dimer and calculate its time-resolved two-dimensional Fourier transformed spectra to find weak but noticeable effects of peak amplitude redistribution due to inter-band coupling.

  20. Large Scale Molecular Simulation of Nanoparticle-Biomolecule Interactions and their Implications in Nanomedicine

    Science.gov (United States)

    Zhou, Ruhong

    Nanoscale particles have become promising materials in various biomedical applications, however, in order to stimulate and facilitate these applications, there is an urgent need for a better understanding of their biological effects and related molecular mechanism/physics as well. In this talk, I will discuss some of our recent works, mostly molecular modelling, on nanotoxicity and their implications in de novo design of nanomedicine. We show that carbon-based nanoparticles (carbon nanotubes, graphene nanosheets, and fullerenes) can interact and disrupt the structures and functions of many important proteins. The hydrophobic interactions between the carbon nanotubes and hydrophobic residues, particularly aromatic residues through the so-called π- π stacking interactions, are found to play key roles. Meanwhile, metallofullerenol Gd@C82(OH)22 is found to inhibit tumour growth and metastases with both experimental and theoretical approaches. Graphene and graphene oxide (GO) nanosheets show strong destructive interactions to E. coli cell membranes (antibacterial activity) and A β amyloid fibrils (anti-AD, Alzheimer's disease, capability) with unique molecular mechanisms, while on the other hand, they also show a strong supportive role in enzyme immobilisation such as lipases through lid opening. In particular, the lid opening is assisted by lipase's sophisticated interaction with GO, which allows the adsorbed lipase to enhance its enzyme activity. The lipase enzymatic activity can be further optimized through fine tuning of the GO surface hydrophobicity. These findings might provide a better understanding of ``nanotoxicity'' at the molecular level with implications in de novo nanomedicine design.

  1. Experimental and theoretical investigation of a pyridine containing Schiff base: Hirshfeld analysis of crystal structure, interaction with biomolecules and cytotoxicity

    Science.gov (United States)

    Chithiraikumar, S.; Neelakantan, M. A.

    2016-03-01

    A pyridine containing Schiff base (E)-2-methoxy-6-(((pyridin-2-ylmethyl)imino)methyl) phenol (L) was isolated in single crystals. The molecular structure of L was studied by FT-IR, NMR, UV-Vis techniques, single crystal XRD analysis and computationally by DFT method. L prefers enol form in the solid state. Electronic spectrum of L was recorded in different organic solvents to investigate the dependence of tautomerism on solvent types. The polar solvents facilitate the proton transfer by decreasing the activation energy needed for transition state. Potential energy curve for the intramolecular proton transfer in the ground state is generated in gas and solution phases. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots were investigated. The percentages of various interactions were analyzed by fingerprint plots of Hirshfeld surface. The interaction of L with CT DNA was investigated under physiological conditions using UV-Vis spectroscopy, fluorescence quenching and molecular docking methods. Molecular docking studies reveal that binding of L to the groove of B-DNA is through hydrogen bonding and hydrophobic interactions. The in vitro cytotoxicity of L was carried out in two different human tumor cell lines, MCF 7 and MIA-Pa-Ca-2 exhibits moderate activity.

  2. Molecular mechanics and microcalorimetric investigations of the effects of molecular water on the aggregation of asphaltenes in solutions

    DEFF Research Database (Denmark)

    Murgich, J.; Lira-Galeana, C.; Garcia, Daniel Merino

    2002-01-01

    by titration calorimetry. A simple dimer dissociation model was used to derive the information about the heat and the constant of dissociation from asphaltenes of Mexico and Alaska obtained from the calorimetric data. The association enthalpies calculated were found to be in excellent agreement with those...... bond mechanism depends on the heteroatoms involved, the extension of the aromatic regions, and the steric interference present in the asphaltene molecules. The simulation results have been compared with experimental values of enthalpy of association of two different petroleum asphaltenes obtained...... measured, although the simulation only employed the interaction between averaged molecular structures....

  3. Armchair BN nanotubes--levothyroxine interactions: a molecular study.

    Science.gov (United States)

    Anota, E Chigo; Cocoletzi, Gregorio H; Ramírez, J F Sánchez

    2013-11-01

    The density functional theory has been applied to investigate the structural and electronic properties of single-wall boron nitride nanotubes (SW-BNNT) of (5,5) chirality, with surface and ends functionalized by the drug levothyroxine (C15H11NI4O4). The exchange-correlation energies have been modeled according to the Hamprecht-Cohen-Tozer-Handy functional within the generalized gradient approximation (HCTH-GGA) and a base function with double polarization has been used. The (5,5) BNNT-Levothyroxine structural optimization has been done considering the minimum energy criterion in nine possible atomic structures. Simulation results indicate that the preferential adsorption site (chemical adsorption) of the levothyroxine fragment is at the nanotube ends. The BNNT-Levothyroxine system polarity increases which indicates the possible dispersion and solubility both non-solvated and solvated in water. The BNNT-Levothyroxine solvated in water modifies its chemical reactivity which may allow the drug delivery within the biological systems. On the other hand, the decrease in the work function is important for the optoelectronic device design, which also makes these materials suitable to improve the field emission properties.

  4. [From Purkinje's pharmacologic observations to molecular drug interactions].

    Science.gov (United States)

    Kvĕtina, J

    1998-11-01

    The 650th anniversary of the foundation of Charles University (7 April 1348) in Prague has initiated a number of historical surveys of the subjects which has been taught at the University for a longer period of time. The disciplines connected with pharmacotherapy were being developed in an empirical conception at the University from the second half of the 14th century but the beginnings of experimental drug research date as late as the mid-19th century. The present survey of the history of "the sciences of medicaments" therefore attempts to outline in short entries the developmental stages of pharmaceutical and pharmacological investigations in the territory of Bohemia and Moravia in about recent 150 years. The arrangement of data is chronological; in the part covering the second half of the 20th century the research of a predominantly exploratory character (universities and academic institutions and their representatives) and research aimed primarily to innovate medicaments (research institutions of pharmaceutical industry and clinical pharmacology and some of their representatives) are treated separately.

  5. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    Science.gov (United States)

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  6. Spatial, temporal and functional molecular architecture of the munc18-syntaxin interaction

    OpenAIRE

    Smyth, Annya Mary

    2012-01-01

    Regulation of soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNARE) mediated exocytosis is dependent upon four key proteins; the vesicular SNARE synaptobrevin, target SNAREs SNAP-25 and syntaxin and the Sec1/Munc18 (SM) protein munc18-1. Despite the munc18-1-syntaxin interaction being central to regulated vesicle exocytosis the spatial and temporal pattern of their molecular distribution and interaction in neuroendocrine and neuronal cells remai...

  7. An allosteric model of the molecular interactions of excitation- contraction coupling in skeletal muscle

    OpenAIRE

    1993-01-01

    A contact interaction is proposed to exist between the voltage sensor of the transverse tubular membrane of skeletal muscle and the calcium release channel of the sarcoplasmic reticulum. This interaction is given a quantitative formulation inspired in the Monod, Wyman, and Changeux model of allosteric transitions in hemoglobin (Monod, J., J. Wyman, and J.-P. Changeux. 1965. Journal of Molecular Biology. 12:88- 118), and analogous to one proposed by Marks and Jones for voltage- dependent Ca ch...

  8. Electrochemical Investigation of the Interaction between Catecholamines and ATP.

    Science.gov (United States)

    Taleat, Zahra; Estévez-Herrera, Judith; Machado, José D; Dunevall, Johan; Ewing, Andrew G; Borges, Ricardo

    2018-02-06

    The study of the colligative properties of adenosine 5'-triphosphate (ATP) and catecholamines has received the attention of scientists for decades, as they could explain the capabilities of secretory vesicles (SVs) to accumulate neurotransmitters. In this Article, we have applied electrochemical methods to detect such interactions in vitro, at the acidic pH of SVs (pH 5.5) and examined the effect of compounds having structural similarities that correlate with functional groups of ATP (adenosine, phosphoric acid and sodium phosphate salts) and catecholamines (catechol). Chronoamperometry and fast scan cyclic voltammetry (FSCV) provide evidence compatible with an interaction of the catechol and adenine rings. This interaction is also reinforced by an electrostatic interaction between the phosphate group of ATP and the protonated ammonium group of catecholamines. Furthermore, chronoamperometry data suggest that the presence of ATP subtlety reduces the apparent diffusion coefficient of epinephrine in aqueous media that adds an additional factor leading to a slower rate of catecholamine exocytosis. This adds another plausible mechanism to regulate individual exocytosis events to alter communication.

  9. A preliminary investigation into genotype x environment interaction ...

    African Journals Online (AJOL)

    uvp

    2014-08-24

    Aug 24, 2014 ... 1 Department of Animal, Wildlife and Grassland Sciences, UFS, P.O. Box 339, Bloemfontein, 9300, South Africa;. 2INRA ... Bivariate analyses, fitting an animal model using the ASREML software, were used to obtain genetic correlations .... Genotype x environment interactions in conventional versus.

  10. Investigating the interactions of the enantiomers of phenylglycine ...

    Indian Academy of Sciences (India)

    So, movement, radius of gyration and angle of orientation of S-isomers inside nanopores are decreased, while R-isomers interact more strongly with each other. ... BC, Canada; School of Chemical Engineering- University College of Engineering-University of Tehran, Tehran, Iran; School of Chemistry- University College of ...

  11. Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C

    DEFF Research Database (Denmark)

    Kolovos, Petros; Brouwer, Rutger W W; Kockx, Christel E M

    2018-01-01

    -to-noise ratio. Its resolution is determined by the resulting fragment size of the chosen restriction enzyme, which can lead to sub-kilobase-pair resolution. T2C's high coverage allows the identification of the interactome of each individual DNA fragment, which makes binning of reads (often used in other methods......-domain interactions, as well as the composition of aggregated loops, interactions between nucleosomes, individual transcription factor binding sites, and promoters and enhancers. T2C can be performed by any investigator with basic skills in molecular biology techniques in ∼7-8 d. Data analysis requires basic...

  12. Understanding molecular interactions between scavenger receptor A and its natural product inhibitors through molecular modeling studies.

    Science.gov (United States)

    Pagare, Piyusha P; Zaidi, Saheem A; Zhang, Xiaomei; Li, Xia; Yu, Xiaofei; Wang, Xiang-Yang; Zhang, Yan

    2017-10-01

    Scavenger receptor A (SRA), as an immune regulator, has been shown to play important roles in lipid metabolism, cardiovascular diseases, and pathogen recognition. Several natural product inhibitors of SRA have been studied for their potential application in modulating SRA functions. To understand the binding mode of these inhibitors on SRA, we conducted systematic molecular modeling studies in order to identify putative binding domain(s) that may be responsible for their recognition to the receptor as well as their inhibitory activity. Treatment of SRA with one of the natural product inhibitors, rhein, led to significant dissociation of SRA oligomers to its trimer and dimer forms, which further supported our hypothesis on their putative mechanism of action. Such information is believed to shed light on design of more potent inhibitors for the receptor in order to develop potential therapeutics through immune system modulation. Published by Elsevier Inc.

  13. Multi-spectroscopic and molecular docking studies on the interaction of darunavir, a HIV protease inhibitor with calf thymus DNA

    Science.gov (United States)

    Shi, Jie-Hua; Zhou, Kai-Li; Lou, Yan-Yue; Pan, Dong-Qi

    2018-03-01

    Molecular interaction of darunavir (DRV), a HIV protease inhibitor with calf thymus deoxyribonucleic acid (ct-DNA) was studied in physiological buffer (pH 7.4) by multi-spectroscopic approaches hand in hand with viscosity measurements and molecular docking technique. The UV absorption and fluorescence results together revealed the formation of a DRV-ct-DNA complex having binding affinities of the order of 103 M- 1, which was more in keeping with the groove binding. The results that DRV bound to ct-DNA via groove binding mode was further evidenced by KI quenching studies, viscosity measurements, competitive binding investigations with EB and Rhodamine B and CD spectral analysis. The effect of ionic strength indicated the negligible involvement of electrostatic interaction between DRV and ct-DNA. The thermodynamic parameters regarding the binding interaction of DRV with ct-DNA in terms of enthalpy change (ΔH0) and entropy change (ΔS0) were - 63.19 kJ mol- 1 and - 141.92 J mol- 1 K- 1, indicating that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Furthermore, molecular simulation studies suggested that DRV molecule was prone to bind in the A-T rich region of the minor groove of DNA.

  14. Molecular modeling and multispectroscopic studies of the interaction of hepatitis B drug, adefovir dipivoxil with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Shahabadi, Nahid, E-mail: nahidshahabadi@yahoo.com [Department of Chemistry, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Falsafi, Monireh [Department of Chemistry, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Hadidi, Saba [Department of Chemistry, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2015-11-15

    The interaction of hepatitis B drug, adefovir dipivoxil with human serum albumin (HSA) was studied by using UV–vis, fluorometric, circular dichroism (CD) and molecular docking techniques. The results indicated that the binding of the drug to HSA caused fluorescence quenching through static quenching mechanism with binding constant of 1.3×103 M{sup −1}. The thermodynamic parameters indicated that the hydrophobic force contacts are the major forces in the stability of protein-drug complex (ΔH>0 and ΔS>0). The displacement experiments using the site probes viz., warfarin and ibuprofen showed that adefovir dipivoxil could bind to the site III of HSA. The results of CD and UV–vis spectroscopy indicated that the binding of the drug induced some conformational changes in HSA. Furthermore, the study of molecular docking also confirmed binding of adefovir dipivoxil to the site III of HSA by hydrophobic interaction. - Highlights: • The interaction of adefovir dipivoxil, drug for the treatment of HIV and HBV with human serum albumin (HSA) is investigated. • The drug bound to HSA by hydrophobic force and induced some conformational changes in HSA. • The study of molecular docking showed that adefovir dipivoxil could bind to the site III of HSA mainly.

  15. Molecular modeling and multispectroscopic studies of the interaction of hepatitis B drug, adefovir dipivoxil with human serum albumin

    International Nuclear Information System (INIS)

    Shahabadi, Nahid; Falsafi, Monireh; Hadidi, Saba

    2015-01-01

    The interaction of hepatitis B drug, adefovir dipivoxil with human serum albumin (HSA) was studied by using UV–vis, fluorometric, circular dichroism (CD) and molecular docking techniques. The results indicated that the binding of the drug to HSA caused fluorescence quenching through static quenching mechanism with binding constant of 1.3×103 M −1 . The thermodynamic parameters indicated that the hydrophobic force contacts are the major forces in the stability of protein-drug complex (ΔH>0 and ΔS>0). The displacement experiments using the site probes viz., warfarin and ibuprofen showed that adefovir dipivoxil could bind to the site III of HSA. The results of CD and UV–vis spectroscopy indicated that the binding of the drug induced some conformational changes in HSA. Furthermore, the study of molecular docking also confirmed binding of adefovir dipivoxil to the site III of HSA by hydrophobic interaction. - Highlights: • The interaction of adefovir dipivoxil, drug for the treatment of HIV and HBV with human serum albumin (HSA) is investigated. • The drug bound to HSA by hydrophobic force and induced some conformational changes in HSA. • The study of molecular docking showed that adefovir dipivoxil could bind to the site III of HSA mainly

  16. Molecular interactions of milk protein with phenolic components in oat-based liquid formulations following UHT treatment and prolonged storage.

    Science.gov (United States)

    Kaur, Jasmeet; Katopo, Lita; Ashton, John; Whitson, Andrew; Kasapis, Stefan

    2017-09-05

    Nowadays there is a growing demand for nutritionally balanced breakfast beverages enriched with functional ingredients including wholegrain oat, which is rich in phenolic acids. Such beverages typically contain added food ingredients (e.g. milk protein, sugar and lipids) and undergo thermal processing that initiates many molecular processes. Therefore, this work aims to investigate the molecular interactions between milk protein and phenolic acids that govern bioactivity in model oat-based beverages. Findings showed the susceptibility of ferulic and p-coumaric acids, in model oat beverages, to ultra-high temperature (UHT) processing at 145 °C for 8 s. Among model beverages, those with added milk protein demonstrated a considerable loss of phenolic acids following UHT processing due to the interaction between these micronutrients and the protein. The nature of molecular interactions was mainly categorized as covalent with hydrogen bonds playing a supportive role. UHT processing of oat-based beverage formulations facilitates the formation of protein-phenolic acid complexes, which are largely covalent and static in nature. This finding underlines the ability of UHT treatment to induce chemical modifications of food ingredients. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  17. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more

  18. Probing molecular interactions with methylene blue derivatized self-assembled monolayers

    Directory of Open Access Journals (Sweden)

    Eleni Koutsoumpeli

    2015-12-01

    Full Text Available The emergence of stratified and personalised medicine and the associated need for highly multiplexed detection strategies are driving the development of innovative sensor technology. Electronic immunosensor arrays capable of label-free and highly parallel monitoring of ligand binding have emerged as a particularly promising technology capable of meeting these new diagnostic challenges. In this study, we present an approach for interrogating molecular interactions electronically using redox active molecular monolayers. Specifically, we have synthesised self-assembled molecular monolayers assembled from long-chain alkanethiols (LCAT incorporating oligoethyleneglycol (OEG linkers that can be derivatized with a range of functional groups, including the redox active molecule methylene blue. Critically, we show that the electron transport properties of this redox-active monolayer are highly sensitive to the electrochemical environment, including the local concentration of protons and the electrostatic potential at the plane of electron transfer. Using a combination of cyclic voltammetry and QCM-D to study in detail the behaviour of the monolayer during functionalisation and analyte binding, we demonstrate that these redox properties can be exploited for the electrochemical sensing of molecular interactions (biotin–avidin in our case on SAMs. Given the versatility of LCAT-OEG monolayers, in terms of linker lengths, choice of functional group, and ability to create mixed component layers and the straight-forward assembly of mixed SAMs of high quality, our electrochemical sensing approach forms an excellent and generic label-free platform for probing a wide range of molecular interactions.

  19. Interplay between Long-Range Crystal Order and Short-Range Molecular Interactions Tunes Carrier Mobility in Liquid Crystal Dyes.

    Science.gov (United States)

    Tchamba Yimga, Nadine; Ramanan, Charusheela; Borchert, Holger; Parisi, Jürgen; Untenecker, Harald; Kirsch, Peer; von Hauff, Elizabeth

    2017-02-22

    We investigated the influence of molecular packing on the optical and electrical properties of the liquid crystalline dye 4,7-bis[5-(2-fluoro-4-pentyl-phenyl)-2-thienyl]-2,1,3-benzothiadiazole (FPPTB). FPPTB is crystalline at room temperature, exhibits a nematic phase at temperatures above 149 °C and is in an isotropic melt at temperatures above 230 °C. Solution processed FPPTB films were subject to thermal annealing through these phase transition temperatures and characterized with X-ray diffraction and polarized optical microscopy. Cooling FPPTB films from the nematic and isotropic phases increased crystal domain size, but also induced local structural variations in the molecular packing of crystalline FPPTB. The decrease in long-range order was correlated with an increase in short-range π-π interactions, leading to changes in molecular aggregation which persisted even when the FPPTB films were cooled to room temperature. Annealing-induced changes in molecular aggregation were confirmed with optical spectroscopy. The carrier mobility in FPPTB films increased over 2 orders of magnitude from (2.2 ± 0.4) × 10 -5 cm 2 V -1 s -1 in as-spun films to μ = (5.0 ± 0.8) × 10 -3 cm 2 V -1 s -1 in films cooled from the isotropic melt. We discuss the relationship between thermal stability and high carrier mobility values in terms of the interplay between long-range molecular order and increased π-π interactions between molecular pairs in the FPPTB film.

  20. Spectroscopic Parameter and Molecular Constant Investigations on Low-Lying States of BeF Radical

    Directory of Open Access Journals (Sweden)

    Jin Feng Sun

    2012-02-01

    Full Text Available The potential energy curves (PECs of X2Σ+, A2Πr and B2Σ+ states of BeF radical have been investigated using the complete active space self-consistent-field (CASSCF method, followed by the highly accurate valence internally contracted multireference configuration interaction (MRCI approach at the correlation-consistent basis sets, cc-pV5Z for Be and aug-cc-pV6Z for F. Based on the PECs of X2Σ+, A2Πr and B2Σ+ states, the spectroscopic parameters (De, Re, ωe, ωeχe, αe and Be have also been determined in the present work. With the PECs determined at the present level of theory, vibrational states have been predicted for each state when the rotational quantum number J equals zero (J = 0. The vibrational levels, inertial rotation and centrifugal distortion constants are determined for the three states, and the classical turning points are also calculated for the X2Σ+ state. Compared with the available experiments and other theories, it can be seen that the present spectroscopic parameter and molecular constant results are more fully in agreement with the experimental findings.

  1. A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

    International Nuclear Information System (INIS)

    Sun, Hui-Yong; Ji, Feng-Qin

    2012-01-01

    Highlights: ► The study revealed the detailed resistance mechanism of the non-active mutation C1156Y in ALK. ► C1156Y leads to crizotinib displacement and conformational changes in the binding cavity. ► The conformations cause a decline in the vdW and electrostatic energy between crizotinib and ALK. -- Abstract: Crizotinib is an anaplastic lymphoma kinase (ALK) inhibitor that has recently been approved in the US for the treatment of non-small cell lung carcinoma (NSCLC). Despite its outstanding safety and efficacy, several resistant mutations against crizotinib have been detected in the treatment of NSCLC. However, in contrast to the widely accepted mechanism of steric hindrance by mutations at the active site, the mechanism by which the C1156Y non-active site mutation confers resistance against crizotinib remains unclear. In the present study, the resistance mechanism of C1156Y in ALK was investigated using molecular dynamics simulations. The results suggest that despite the non-active site mutation, C1156Y causes the dislocation of crizotinib as well as the indirect conformational changes in the binding cavity, which results in a marked decrease in the van der Waals and electrostatic interactions between crizotinib and ALK. The obtained results provide a detailed explanation of the resistance caused by C1156Y and may give a vital clue for the design of drugs to combat crizotinib resistance.

  2. Immobilization of molecular cobalt electrocatalyst by hydrophobic interaction with hematite photoanode for highly stable oxygen evolution

    KAUST Repository

    Joya, Khurram

    2015-07-15

    A unique modification of a hematite photoanode with perfluorinated Co-phthalocyanine (CoFPc) by strong binding associated with hydrophobic interaction is demonstrated. The resultant molecular electrocatalyst – hematite photoanode hybrid material showed significant onset shift and high stability for photoelectrochemical oxidation evolution reaction (OER).

  3. Getting the ion-protein interactions right in molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Duboué-Dijon, Elise; Mason, Philip E.; Jungwirth, Pavel

    2017-01-01

    Roč. 46, Suppl 1 (2017), S66 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : ion-protein interaction * molecular dynamics simulations * neutron scattering * insulin Subject RIV: BO - Biophysics

  4. Investigation of sodium - carbon dioxide interactions with calorimetric studies

    International Nuclear Information System (INIS)

    Simon, N.; Latge, C.; Gicquel, L.

    2007-01-01

    The supercritical CO 2 Brayton cycle could be a promising option to enhance the competitiveness of future Sodium fast reactors but it is highly necessary to get thermodynamic and kinetics information on potential sodium-CO 2 chemical reactions and their consequences. We have studied the interaction between Na and CO 2 via calorimetric methods. These methods are able to point out exothermic/endothermic phenomena and to measure heat of chemical reactions. The main feature of the Na/CO 2 interaction seems to be its sharp dependence on temperature. At low temperature, below 500 C degrees, CO 2 and sodium react and exhibit an induction time which decreases when temperature increases. Above 500 C degrees, we observe a global phenomenon with a fast and instantaneous chemical reaction which may be understood as an auto-combustion of CO 2 in sodium. We clearly demonstrated that Na/CO 2 interaction does not proceed as an auto-catalytic process and is more satisfactorily explained by the occurring of an auto-combustion phenomenon

  5. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens

    2008-01-01

    is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...... Factors, Reporter Proteins and Reporter Complexes, and use this to decipher the logic of regulatory circuits playing a key role in yeast glucose repression and human diabetes. Conclusion: Reporter Features offer the opportunity to identify regulatory hot-spots in bio-molecular interaction networks...

  6. Cyrus Levinthal, the Kluge and the origins of interactive molecular graphics.

    Science.gov (United States)

    Francoeur, Eric

    2002-12-01

    In the mid-1960s, a group of scientists at Massachusetts Institute of Technology, led by Cyrus Levinthal, took hold of one of the early interactive graphics terminals and used it to visualize, study and model the structure of proteins and nucleic acids. From this encounter between cutting-edge computer technology and molecular biology emerged the crucial elements for the development of a research-technology field known today as interactive molecular graphics. The following account is not only about how computer graphics technology has literally changed the way scientists view the molecular realm, but also a look at how an epistemic and institutional space was created to integrate this technology into scientific research.

  7. Strong Hydrogen Bonded Molecular Interactions between Atmospheric Diamines and Sulfuric Acid.

    Science.gov (United States)

    Elm, Jonas; Jen, Coty N; Kurtén, Theo; Vehkamäki, Hanna

    2016-05-26

    We investigate the molecular interaction between methyl-substituted N,N,N',N'-ethylenediamines, propane-1,3-diamine, butane-1,4-diamine, and sulfuric acid using computational methods. Molecular structure of the diamines and their dimer clusters with sulfuric acid is studied using three density functional theory methods (PW91, M06-2X, and ωB97X-D) with the 6-31++G(d,p) basis set. A high level explicitly correlated CCSD(T)-F12a/VDZ-F12 method is used to obtain accurate binding energies. The reaction Gibbs free energies are evaluated and compared with values for reactions involving ammonia and atmospherically relevant monoamines (methylamine, dimethylamine, and trimethylamine). We find that the complex formation between sulfuric acid and the studied diamines provides similar or more favorable reaction free energies than dimethylamine. Diamines that contain one or more secondary amino groups are found to stabilize sulfuric acid complexes more efficiently. Elongating the carbon backbone from ethylenediamine to propane-1,3-diamine or butane-1,4-diamine further stabilizes the complex formation with sulfuric acid by up to 4.3 kcal/mol. Dimethyl-substituted butane-1,4-diamine yields a staggering formation free energy of -19.1 kcal/mol for the clustering with sulfuric acid, indicating that such diamines could potentially be a key species in the initial step in the formation of new particles. For studying larger clusters consisting of a diamine molecule with up to four sulfuric acid molecules, we benchmark and utilize a domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method. We find that a single diamine is capable of efficiently stabilizing sulfuric acid clusters with up to four acid molecules, whereas monoamines such as dimethylamine are capable of stabilizing at most 2-3 sulfuric acid molecules.

  8. Spectroscopic investigations of novel pharmaceuticals: Stability and resonant interaction with laser beam

    Science.gov (United States)

    Smarandache, Adriana; Boni, Mihai; Andrei, Ionut Relu; Handzlik, Jadwiga; Kiec-Kononowicz, Katarzyna; Staicu, Angela; Pascu, Mihail-Lucian

    2017-09-01

    This paper presents data about photophysics of two novel thio-hydantoins that exhibit promising pharmaceutical properties in multidrug resistance control. Time stability studies are necessary to establish the proper use of these compounds in different applications. As for their administration as drugs, it is imperative to know their shelf life, as well as storage conditions. At the same time, laser induced modified properties of the two new compounds are valuable to further investigate their specific interactions with other materials, including biological targets. The two new thio-hydantoins under generic names SZ-2 and SZ-7 were prepared as solutions in dimethyl sulfoxide at different concentrations, as well as in deionised water. For the stability assay they were kept in various light/temperature conditions up to 60 days. The stability was estimates based on UV-vis absorption measurements. The samples in bulk shape were exposed different time intervals to laser radiation emitted at 266 nm as the fourth harmonic of a Nd:YAG laser. The resonant interaction of the studied compounds with laser beams was analysed through spectroscopic methods UV-vis and FTIR absorption, as well as laser induced fluorescence spectroscopy. As for stability assay, only solutions kept in dark at 4 °C have preserved the absorption characteristics, considering the cumulated measuring errors, less than one week. The vibrational changes that occur in their FTIR and modified fluorescence spectra upon laser beam exposure are also discussed. A result of the experimental analysis is that modifications are induced in molecular structures of the investigated compounds by resonant interaction with laser radiation. This fact evidences that the molecules are photoreactive and their characteristics might be shaped through controlled laser radiation exposure using appropriate protocols. This conclusion opens many opportunities both in the biomedical field, but also in other industrial activities

  9. Investigation on the toxic interaction of superparamagnetic iron oxide nanoparticles with catalase

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Zehua [Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, China–America CRC for Environment and Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100 (China); Liu, Hongwei [Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, China–America CRC for Environment and Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100 (China); Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Hu, Xinxin; Song, Wei [Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, China–America CRC for Environment and Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100 (China); Liu, Rutao, E-mail: rutaoliu@sdu.edu.cn [Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, China–America CRC for Environment and Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100 (China)

    2015-03-15

    Superparamagnetic iron oxide nanoparticles (SPIONs) have been investigated for various applications in targeted drug delivery and magnetic resonance imaging. Given their clinical relevance, there is a need to understand these particles' potential cytotoxic effects and possible mechanisms of cytotoxicity. Using a variety of spectroscopic techniques, we investigated the interaction of SPIONs with catalase (CAT) in an aqueous environment. Catalase is an important enzyme that protects cells and tissues from oxidative damage by reactive oxygen species (ROS). Therefore, in this work, CAT served as a model protein for examining the physiological effects of SPIONs due to is function in eliminating H{sub 2}O{sub 2}. Synchronous fluorescence spectroscopy results showed that SPIONs have little effect on tryptophan residues in CAT. Data from circular dichroism (CD) and UV–vis spectroscopies showed that CAT α-helical content decreased from 32.4% to 29.1% in the presence of SPIONs. Moreover, a ca. 10% decrease in CAT activity was observed in the presence of SPIONs at a 20:1 particle:protein ratio. These results show that SPIONs can interact with proteins to alter both their structure and function. Further studies with CAT or other toxicologically relevant enzymes may be used for elucidating the mechanisms of SPION cytotoxicity. - Highlights: • This work established the binding mode of SPIONs with CAT on molecular level. • The interaction mechanism was explored by multiple spectroscopic techniques. • SPIONs can loosen the skeleton of protein and increase the exposure of amide moieties in the hydrophobic pocket. • SPIONs can inhibit CAT activity and trigger conformational changes in CAT.

  10. Investigation on the toxic interaction of superparamagnetic iron oxide nanoparticles with catalase

    International Nuclear Information System (INIS)

    Yu, Zehua; Liu, Hongwei; Hu, Xinxin; Song, Wei; Liu, Rutao

    2015-01-01

    Superparamagnetic iron oxide nanoparticles (SPIONs) have been investigated for various applications in targeted drug delivery and magnetic resonance imaging. Given their clinical relevance, there is a need to understand these particles' potential cytotoxic effects and possible mechanisms of cytotoxicity. Using a variety of spectroscopic techniques, we investigated the interaction of SPIONs with catalase (CAT) in an aqueous environment. Catalase is an important enzyme that protects cells and tissues from oxidative damage by reactive oxygen species (ROS). Therefore, in this work, CAT served as a model protein for examining the physiological effects of SPIONs due to is function in eliminating H 2 O 2 . Synchronous fluorescence spectroscopy results showed that SPIONs have little effect on tryptophan residues in CAT. Data from circular dichroism (CD) and UV–vis spectroscopies showed that CAT α-helical content decreased from 32.4% to 29.1% in the presence of SPIONs. Moreover, a ca. 10% decrease in CAT activity was observed in the presence of SPIONs at a 20:1 particle:protein ratio. These results show that SPIONs can interact with proteins to alter both their structure and function. Further studies with CAT or other toxicologically relevant enzymes may be used for elucidating the mechanisms of SPION cytotoxicity. - Highlights: • This work established the binding mode of SPIONs with CAT on molecular level. • The interaction mechanism was explored by multiple spectroscopic techniques. • SPIONs can loosen the skeleton of protein and increase the exposure of amide moieties in the hydrophobic pocket. • SPIONs can inhibit CAT activity and trigger conformational changes in CAT

  11. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA

    Science.gov (United States)

    Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

    2016-01-01

    A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

  12. Further investigations of the NN interaction in the Skyrme model

    International Nuclear Information System (INIS)

    Kaelbermann, G.; Eisenberg, J.M.

    1989-01-01

    We examine the influence of the coupling to NΔ and ΔΔ degrees of freedom for the NN interaction as derived in the Skyrme model, carrying out an extensive search for parameters in the basic Lagrangian that will yield both reasonable single-baryon results and appreciable attraction. Separately the free one-body skyrmeon solution and an improved two-body solution are inserted in the product ansatz for the two-body system both with and without time-dependent dynamical terms. No appreciable central attraction between nucleons is found with either of these approaches. (author)

  13. Microscopic investigation of the 12C + 12C interaction

    International Nuclear Information System (INIS)

    Baye, D.; Pecher, N.; Brussels Univ.

    1982-01-01

    The 12 C + 12 C system is studied in the framework of the generator coordinate method. Each 12 C nucleus is described by a closed psub(3/2) subshell. Phase shifts and resonances are determined for several effective two-body interactions involving a spin-orbit term. The existence and properties of simple local equivalent potentials for the 12 C + 12 C collision are discussed. The 12 C + 12 C system is too light to be well described by potentials independent of the angular momentum or weakly dependent on it. (orig.)

  14. Molecular characterization of protein kinase C delta (PKCδ)-Smac interactions.

    Science.gov (United States)

    Holmgren, Christian; Cornmark, Louise; Lønne, Gry Kalstad; Masoumi, Katarzyna Chmielarska; Larsson, Christer

    2016-05-23

    Protein kinase C δ (PKCδ) is known to be an important regulator of apoptosis, having mainly pro- but also anti-apoptotic effects depending on context. In a previous study, we found that PKCδ interacts with the pro-apoptotic protein Smac. Smac facilitates apoptosis by suppressing inhibitor of apoptosis proteins (IAPs). We previously established that the PKCδ-Smac complex dissociates during induction of apoptosis indicating a functional importance. Because the knowledge on the molecular determinants of the interaction is limited, we aimed at characterizing the interactions between PKCδ and Smac. We found that PKCδ binds directly to Smac through its regulatory domain. The interaction is enhanced by the PKC activator TPA and seems to be independent of PKCδ catalytic activity since the PKC kinase inhibitor GF109203X did not inhibit the interaction. In addition, we found that C1 and C2 domains from several PKC isoforms have Smac-binding capacity. Our data demonstrate that the Smac-PKCδ interaction is direct and that it is facilitated by an open conformation of PKCδ. The binding is mediated via the PKCδ regulatory domain and both the C1 and C2 domains have Smac-binding capacity. With this study we thereby provide molecular information on an interaction between two apoptosis-regulating proteins.

  15. Investigating Conversational Dynamics: Interactive Alignment, Interpersonal Synergy, and Collective Task Performance

    Science.gov (United States)

    Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    This study investigates interpersonal processes underlying dialog by comparing two approaches, "interactive alignment" and "interpersonal synergy", and assesses how they predict collective performance in a joint task. While the interactive alignment approach highlights imitative patterns between interlocutors, the synergy…

  16. Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Vincent Vagenende

    Full Text Available Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

  17. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    International Nuclear Information System (INIS)

    Carnevale, V.; Raugei, S.

    2009-01-01

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  18. The role of drug-polymer hydrogen bonding interactions on the molecular mobility and physical stability of nifedipine solid dispersions.

    Science.gov (United States)

    Kothari, Khushboo; Ragoonanan, Vishard; Suryanarayanan, Raj

    2015-01-05

    We investigated the influence of drug-polymer hydrogen bonding interactions on molecular mobility and the physical stability in solid dispersions of nifedipine with each of the polymers polyvinylpyrrolidone (PVP), hydroxypropylmethyl cellulose (HPMCAS), and poly(acrylic acid) (PAA). The drug-polymer interactions were monitored by FT-IR spectroscopy, the molecular mobility was characterized using broadband dielectric spectroscopy, and the crystallization kinetics was evaluated by powder X-ray diffractometry. The strength of drug-polymer hydrogen bonding, the structural relaxation time, and the crystallization kinetics were rank ordered as PVP > HPMCAS > PAA. At a fixed polymer concentration, the fraction of the drug bonded to the polymer was the highest with PVP. Addition of 20% w/w polymer resulted in ∼65-fold increase in the relaxation time in the PVP dispersion and only ∼5-fold increase in HPMCAS dispersion. In the PAA dispersions, there was no evidence of drug-polymer interactions and the polymer addition did not influence the relaxation time. Thus, the strongest drug-polymer hydrogen bonding interactions in PVP solid dispersions translated to the longest structural relaxation times and the highest resistance to drug crystallization.

  19. The interaction of 2-mercaptobenzimidazole with human serum albumin as determined by spectroscopy, atomic force microscopy and molecular modeling.

    Science.gov (United States)

    Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua

    2013-04-01

    The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

    Science.gov (United States)

    Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

    2018-05-01

    Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

  1. Human serum albumin interactions with C60 fullerene studied by spectroscopy, small-angle neutron scattering, and molecular dynamics simulations

    Science.gov (United States)

    Li, Song; Zhao, Xiongce; Mo, Yiming; Cummings, Peter T.; Heller, William T.

    2013-07-01

    Concern about the toxicity of engineered nanoparticles, such as the prototypical nanomaterial C60 fullerene, continues to grow. While, evidence continues to mount that C60 and its derivatives may pose health hazards, the specific molecular interactions of these particles with biological macromolecules require further investigation. In this article, we report combined experimental and theoretical studies on the interaction of one of the most prevalent proteins in the human body, human serum albumin (HSA), with C60 in an aqueous environment. The C60-HSA interaction was probed by circular dichroism (CD) spectroscopy, small-angle neutron scattering (SANS), and atomistic molecular dynamics (MD) simulations to understand C60-driven changes in the structure of HSA in solution. The CD spectroscopy demonstrates that the secondary structure of the protein decreases in α-helical content in response to the presence of C60 (0.68 nm in diameter). Similarly, C60 produces subtle changes in the solution conformation of HSA (an 8.0 nm × 3.8 nm protein), as evidenced by the SANS data and MD simulations, but the data do not indicate that C60 changes the oligomerization state of the protein, such as by inducing aggregation. The results demonstrate that the interaction is not highly disruptive to the protein in a manner that would prevent it from performing its physiological function.

  2. Human serum albumin interactions with C60 fullerene studied by spectroscopy, small-angle neutron scattering, and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Li, Song; Zhao, Xiongce; Mo, Yiming; Cummings, Peter T.; Heller, William T.

    2013-01-01

    Concern about the toxicity of engineered nanoparticles, such as the prototypical nanomaterial C 60 fullerene, continues to grow. While, evidence continues to mount that C 60 and its derivatives may pose health hazards, the specific molecular interactions of these particles with biological macromolecules require further investigation. In this article, we report combined experimental and theoretical studies on the interaction of one of the most prevalent proteins in the human body, human serum albumin (HSA), with C 60 in an aqueous environment. The C 60 –HSA interaction was probed by circular dichroism (CD) spectroscopy, small-angle neutron scattering (SANS), and atomistic molecular dynamics (MD) simulations to understand C 60 -driven changes in the structure of HSA in solution. The CD spectroscopy demonstrates that the secondary structure of the protein decreases in α-helical content in response to the presence of C 60 (0.68 nm in diameter). Similarly, C 60 produces subtle changes in the solution conformation of HSA (an 8.0 nm × 3.8 nm protein), as evidenced by the SANS data and MD simulations, but the data do not indicate that C 60 changes the oligomerization state of the protein, such as by inducing aggregation. The results demonstrate that the interaction is not highly disruptive to the protein in a manner that would prevent it from performing its physiological function

  3. Interaction of an antiepileptic drug, lamotrigine with human serum albumin (HSA): Application of spectroscopic techniques and molecular modeling methods.

    Science.gov (United States)

    Poureshghi, Fatemeh; Ghandforoushan, Parisa; Safarnejad, Azam; Soltani, Somaieh

    2017-01-01

    Lamotrigine (an epileptic drug) interaction with human serum albumin (HSA) was investigated by fluorescence, UV-Vis, FTIR, CD spectroscopic techniques, and molecular modeling methods. Binding constant (K b ) of 5.74×10 3 and number of binding site of 0.97 showed that there is a slight interaction between lamotrigine and HSA. Thermodynamic studies was constructed using the flourimetric titrations in three different temperatures and the resulted data used to calculate the parameters using Vant Hoff equation. Decreased Stern Volmer quenching constant by enhanced temperature revealed the static quenching mechanism. Negative standard enthalpy (ΔH) and standard entropy (ΔS) changes indicated that van der Waals interactions and hydrogen bonds were dominant forces which facilitate the binding of Lamotrigine to HSA, the results were confirmed by molecular docking studies which showed no hydrogen binding. The FRET studies showed that there is a possibility of energy transfer between Trp214 and lamotrigine. Also the binding of lamotrigine to HSA in the studied concentrations was not as much as many other drugs, but the secondary structure of the HSA was significantly changed following the interaction in a way that α-helix percentage was reduced from 67% to 57% after the addition of lamotrigine in the molar ratio of 4:1 to HSA. According to the docking studies, lamotrigine binds to IB site preferably. Copyright © 2016. Published by Elsevier B.V.

  4. A preliminary investigation of affective interaction in chronic pain couples.

    Science.gov (United States)

    Johansen, Ayna Beate; Cano, Annmarie

    2007-11-01

    The objective of this preliminary study was to examine the extent to which affective marital interaction related to depressive symptoms in persons with chronic pain and their spouses and to pain severity in persons with pain. Couples from the community completed self-report surveys and engaged in a videotaped conversation on a topic of mutual disagreement that was coded for three affect types (i.e., anger/contempt, sadness, humor). Humor was positively related to marital satisfaction in both partners. Spouse anger/contempt and sadness were positively related to depressive symptoms in spouses. Several significant interaction effects between couple pain status (i.e., whether one or both partners reported pain) and affect also emerged. Specifically, sadness in the participant designated as the person with pain was associated with greater depressive symptoms and pain severity when only he or she reported pain whereas sadness was related to fewer depressive symptoms and less pain severity when both partners reported pain. The relationships between spouse anger and spouse depressive symptoms and between spouse humor and pain severity in the person with pain were also moderated by couple pain status. These exploratory findings can be interpreted in light of emotion regulation and pain empathy theories. For example, partners who have not experienced pain themselves may fail to empathize with persons in pain, thus preventing effective emotion regulation. When both spouses report chronic pain, expressions of negative affect may instead promote emotion regulation because the affect is experienced with a spouse who may be more empathetic.

  5. Interaction of Flavonoids from Woodwardia unigemmata with Bovine Serum Albumin (BSA): Application of Spectroscopic Techniques and Molecular Modeling Methods.

    Science.gov (United States)

    Ma, Rui; Pan, Hong; Shen, Tao; Li, Peng; Chen, Yanan; Li, Zhenyu; Di, Xiaxia; Wang, Shuqi

    2017-08-09

    Phytochemical investigation on the methanol extract of Woodwardia unigemmata resulted in the isolation of seven flavonoids, including one new flavonol acylglycoside ( 1 ). The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis and comparison of literature data. The multidrug resistance (MDR) reversing activity was evaluated for the isolated compounds using doxorubicin-resistant K562/A02 cells model. Compound 6 showed comparable MDR reversing effect to verapamil. Furthermore, the interaction between compounds and bovine serum albumin (BSA) was investigated by spectroscopic methods, including steady-state fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular docking approach. The experimental results indicated that the seven flavonoids bind to BSA by static quenching mechanisms. The negative ΔH and ΔS values indicated that van der Waals interactions and hydrogen bonds contributed in the binding of compounds 2 - 6 to BSA. In the case of compounds 1 and 7 systems, the hydrophobic interactions play a major role. The binding of compounds to BSA causes slight changes in the secondary structure of BSA. There are two binding sites of compound 6 on BSA and site I is the main site according to the molecular docking studies and the site marker competitive binding assay.

  6. Molecular Understanding of Fullerene - Electron Donor Interactions in Organic Solar Cells

    KAUST Repository

    Ryno, Sean

    2016-09-13

    Organic solar cells hold promise of providing low-cost, renewable power generation, with current devices providing up to 13% power conversion efficiency. The rational design of more performant systems requires an in-depth understanding of the interactions between the electron donating and electron accepting materials within the active layers of these devices. Here, we explore works that give insight into the intermolecular interactions between electron donors and electron acceptors, and the impact of molecular orientations and environment on these interactions. We highlight, from a theoretical standpoint, the effects of intermolecular interactions on the stability of charge carriers at the donor/acceptor interface and in the bulk and how these interactions influence the nature of the charge transfer states as wells as the charge separation and charge transport processes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Molecular equilibrium structures from experimental rotational constants and calculated vibration-rotation interaction constants

    DEFF Research Database (Denmark)

    Pawlowski, F; Jorgensen, P; Olsen, Jeppe

    2002-01-01

    A detailed study is carried out of the accuracy of molecular equilibrium geometries obtained from least-squares fits involving experimental rotational constants B(0) and sums of ab initio vibration-rotation interaction constants alpha(r)(B). The vibration-rotation interaction constants have been...... calculated for 18 single-configuration dominated molecules containing hydrogen and first-row atoms at various standard levels of ab initio theory. Comparisons with the experimental data and tests for the internal consistency of the calculations show that the equilibrium structures generated using Hartree......-Fock vibration-rotation interaction constants have an accuracy similar to that obtained by a direct minimization of the CCSD(T) energy. The most accurate vibration-rotation interaction constants are those calculated at the CCSD(T)/cc-pVQZ level. The equilibrium bond distances determined from these interaction...

  8. Investigation on interaction between Ligupurpuroside A and pepsin by spectroscopic and docking methods

    Science.gov (United States)

    Shen, Liangliang; Xu, Hong; Huang, Fengwen; Li, Yi; Xiao, Huafeng; Yang, Zhen; Hu, Zhangli; He, Zhendan; Zeng, Zheling; Li, Yinong

    2015-01-01

    Ligupurpuroside A is one of the major glycoside in Ku-Din-Cha, a type of Chinese functional tea. In order to better understand its digestion and metabolism in humans, the interaction between Ligupurpuroside A and pepsin has been investigated by fluorescence spectra, UV-vis absorption spectra and synchronous fluorescence spectra along with molecular docking method. The fluorescence experiments indicate that Ligupurpuroside A can effectively quench the intrinsic fluorescence of pepsin through a combined quenching way at the low concentration of Ligupurpuroside A, and a static quenching procedure at the high concentration. The binding constant, binding sites of Ligupurpuroside A with pepsin have been calculated. The thermodynamic analysis suggests that non-covalent reactions, including electrostatic force, hydrophobic interaction and hydrogen bond are the main forces stabilizing the complex. According to the Förster's non-radiation energy transfer theory, the binding distance between pepsin and Ligupurpuroside A was calculated to be 3.15 nm, which implies that energy transfer occurs between pepsin and Ligupurpuroside A. Conformation change of pepsin was observed from UV-vis absorption spectra and synchronous fluorescence spectra under experimental conditions. In addition, all these experimental results have been validated by the protein-ligand docking studies which show that Ligupurpuroside A is located in the cleft between the domains of pepsin.

  9. Molecular analysis of the interaction between Olea europaea and the biotrophic fungus Spilocaea oleagina.

    Science.gov (United States)

    Benitez, Yoselin; Botella, Miguel A; Trapero, Antonio; Alsalimiya, Mohammed; Caballero, Jose Luis; Dorado, Gabriel; Muñoz-Blanco, Juan

    2005-07-01

    SUMMARY The mitosporic fungus Spilocaea oleagina is an obligate biotroph of olive (Olea europaea) causing a scab disease associated with leaf fall and substantial losses in production. Using differential display we have identified 162 cDNA fragments corresponding to transcripts that show altered abundance during the defence response of a resistant olive cultivar to S. oleagina. Detailed analyses of 21 selected genes by real-time quantitative RT-PCR revealed different kinetics of induction. Genes involved in signalling, transcriptional control, oxidative stress, biotic and abiotic stress, and several genes with unknown function were found to be induced rapidly after infection. In contrast, genes involved in metabolism and cellular maintenance showed delayed induction. The induction of the selected genes in a susceptible cultivar was delayed and/or reduced during the response to S. oleagina. Interestingly, the basal expression of some genes in the uninfected resistant cultivar was higher than in the susceptible one, suggesting a constitutive activation of defence responses. Expression of these genes in response to salicylic acid, methyl jasmonate, a mixture of both, ethephon, hydrogen peroxide, menadione and wounding was also investigated. The results are discussed in relation to the molecular bases and signalling events involved in this biotrophic interaction.

  10. Flavonoids as modulators of memory and learning: molecular interactions resulting in behavioural effects.

    Science.gov (United States)

    Rendeiro, Catarina; Guerreiro, João D T; Williams, Claire M; Spencer, Jeremy P E

    2012-05-01

    There is considerable interest in the potential of a group of dietary-derived phytochemicals known as flavonoids in modulating neuronal function and thereby influencing memory, learning and cognitive function. The present review begins by detailing the molecular events that underlie the acquisition and consolidation of new memories in the brain in order to provide a critical background to understanding the impact of flavonoid-rich diets or pure flavonoids on memory. Data suggests that despite limited brain bioavailability, dietary supplementation with flavonoid-rich foods, such as blueberry, green tea and Ginkgo biloba lead to significant reversals of age-related deficits on spatial memory and learning. Furthermore, animal and cellular studies suggest that the mechanisms underpinning their ability to induce improvements in memory are linked to the potential of absorbed flavonoids and their metabolites to interact with and modulate critical signalling pathways, transcription factors and gene and/or protein expression which control memory and learning processes in the hippocampus; the brain structure where spatial learning occurs. Overall, current evidence suggests that human translation of these animal investigations are warranted, as are further studies, to better understand the precise cause-and-effect relationship between flavonoid intake and cognitive outputs.

  11. Understanding trophic interactions of Orius spp. (Hemiptera: Anthocoridae) in lettuce crops by molecular methods.

    Science.gov (United States)

    Gomez-Polo, Priscila; Alomar, Oscar; Castañé, Cristina; Aznar-Fernández, Thaïs; Lundgren, Jonathan G; Piñol, Josep; Agustí, Nuria

    2016-02-01

    The aphid Nasonovia ribisnigri (Mosley) (Hemiptera: Aphididae) and the thrips Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) are common pests in Mediterranean lettuce crops, where Orius spp. are common generalist predators. Predation by Orius spp. was studied in a lettuce plot by conventional polymerase chain reaction (PCR) and real-time PCR analyses using specific primers of both main pests. Also, high-throughput sequencing was used to have a wider approach of the diet of these predators in natural field conditions. Molecular analyses indicated a higher predation on N. ribisnigri in spring and on F. occidentalis in summer. Predation on alternative prey, like Collembola, was also found in both seasons. Real-time PCR was more sensitive than conventional PCR in showing the target trophic links, whereas high-throughput sequencing revealed predation on other natural enemies - intraguild predation (IGP), showing other trophic interactions of Orius majusculus within the studied ecosystem. This study gives important information about the trophic relationships present in Mediterranean lettuce crops in different periods of the year. The detected predation by Orius spp. on alternative prey, as well as on other natural enemies, should be further investigated to clarify whether it adds or detracts to the biological control of N. ribisnigri and F. occidentalis. © 2015 Society of Chemical Industry.

  12. Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks.

    Science.gov (United States)

    Westergaard, David; Li, Jun; Jensen, Kasper; Kouskoumvekaki, Irene; Panagiotou, Gianni

    2014-05-17

    Epidemiological studies in the recent years have investigated the relationship between dietary habits and disease risk demonstrating that diet has a direct effect on public health. Especially plant-based diets -fruits, vegetables and herbs- are known as a source of molecules with pharmacological properties for treatment of several malignancies. Unquestionably, for developing specific intervention strategies to reduce cancer risk there is a need for a more extensive and holistic examination of the dietary components for exploring the mechanisms of action and understanding the nutrient-nutrient interactions. Here, we used colon cancer as a proof-of-concept for understanding key regulatory sites of diet on the disease pathway. We started from a unique vantage point by having a database of 158 plants positively associated to colon cancer reduction and their molecular composition (~3,500 unique compounds). We generated a comprehensive picture of the interaction profile of these edible and non-edible plants with a predefined candidate colon cancer target space consisting of ~1,900 proteins. This knowledge allowed us to study systematically the key components in colon cancer that are targeted synergistically by phytochemicals and identify statistically significant and highly correlated protein networks that could be perturbed by dietary habits. We propose here a framework for interrogating the critical targets in colon cancer processes and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. Our methodology for better delineating prevention of colon cancer by nutritional interventions relies heavily on the availability of information about the small molecule constituents of our diet and it can be expanded to any other disease class that previous evidence has linked to lifestyle.

  13. Molecular interactions between selected sodium salts of bile acids and morphine hydrochloride.

    Science.gov (United States)

    Poša, Mihalj; Csanádi, János; Kövér, Katalin E; Guzsvány, Valéria; Batta, Gyula

    2012-06-01

    The objective of this study was to understand the prolonged analgesic action of morphine hydrochloride observed in the presence of sodium 12-oxochenodeoxycholanate. Based on literature, this phenomenon may be due to the formation of aggregates in the cell between the molecules of bile acids and morphine. In addition to the sodium 12-oxochenodeoxycholanate, the present investigation also included salts of cholic and 7-oxodeoxycholic acids. Saturation transfer difference NMR experiments showed that morphine binds to the bile acid molecule close to the aromatic protons H1 and H2 provided that the concentration of the bile acid salt approaches the critical micellar concentration (CMC). The spin-lattice relaxation times (T(1)) of the affected protons decrease significantly in the presence of micellar solutions of the bile acid salts, and the most pronounced change in T(1) was observed for sodium 7-oxodeoxycholate. Diffusion-ordered NMR experiments suggested that morphine hydrochloride can interact only with sodium 7-oxochenodeoxycholate. It can be supposed that the molecular ratio of sodium 7-oxodeoxycholate and morphine hydrochloride in the mixed micelle is 2:1. The CMC values of mixed micelles do not differ from the CMC values of the micelle constituents, which suggests that the binding of morphine hydrochloride does not perturb the hydrophobic domain of the bile acid molecule. In the presence of bile acids, the transfer rate constant (k(12)) of morphine hydrochloride from the buffered aqueous solution to chloroform (model of the cell membrane) shows a decrease. A significant decrease of the k(12) was also observed in the presence of micellar solutions. Kinetic measurements indicated that, in addition to micellar interaction between morphine hydrochloride and sodium salts of bile acids, a complex may also be formed in chloroform via hydrogen bonds formed between the drug and bile acid molecules. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. Study on the molecular interaction of graphene quantum dots with human serum albumin: Combined spectroscopic and electrochemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Shan; Qiu, Hangna; Lu, Shuangyan; Zhu, Fawei [College of Chemistry and Material Science, Guangxi Teachers Education University, Nanning 530001 (China); Xiao, Qi, E-mail: qi.xiao@whu.edu.cn [College of Chemistry and Material Science, Guangxi Teachers Education University, Nanning 530001 (China); State Key Laboratory of Virology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072 (China)

    2015-03-21

    Highlights: • The interactions between GQDs and HSA were systematically investigated. • GQDs could quench the intrinsic fluorescence of HSA via static mode. • The binding site of GQDs was mainly located in site I of HSA. • The potential toxicity of GQDs resulted in the structural damage of HSA. - Abstract: Graphene quantum dots (GQDs) have attracted great attention in biological and biomedical applications due to their super properties, but their potential toxicity investigations are rarely involved. Since few studies have addressed whether GQDs could bind and alter the structure and function of human serum albumin (HSA), the molecular interaction between GQDs and HSA was systematically characterized by the combination of multispectroscopic and electrochemical approaches. GQDs could quench the intrinsic fluorescence of HSA via static mode. The competitive binding fluorescence assay revealed that the binding site of GQDs was site I of HSA. Some thermodynamic parameters suggested that GQDs interacted with HSA mainly through van der Waals interactions and hydrogen bonding interactions, and protonation might also participate in the process. As further revealed by FT-IR spectroscopy and circular dichroism technique, GQDs could cause the global and local conformational change of HSA, which illustrated the potential toxicity of GQDs that resulted in the structural damage of HSA. Electrochemical techniques demonstrated the complex formation between GQDs and HSA. Our results offered insights into the binding mechanism of GQDs with HSA and provided important information for possible toxicity risk of GQDs to human health.

  15. Interaction of bovine serum albumin with a psychotropic drug alprazolam: Physicochemical, photophysical and molecular docking studies

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Moumita; Paul, Shiv Shankar; Mukherjea, Kalyan K., E-mail: k_mukherjea@yahoo.com

    2013-10-15

    The interaction between alprazolam (Alp) and bovine serum albumin (BSA) has been investigated under physiological conditions by UV–vis, steady state as well as time-resolved fluorescence, circular dichroism (CD) spectroscopic and molecular docking studies. The binding constant K of Alp to BSA was found to be 1.8×10{sup 5} L mol{sup −1} from absorption data. Fluorometric studies suggested the formation of the Alp–BSA complex, while time-resolved fluorescence studies showed that the binding of Alp by BSA was mainly static and the effective rate constant is found to be 2.33×10{sup 13} L mol{sup −1} s{sup −1}. According to the modified Stern–Volmer equation, the Stern–Volmer quenching constants (K{sub SV}) between Alp and BSA at four different temperatures 295, 303, 308, 313 K were obtained to be 1.19×10{sup 5}, 1.05×10{sup 5}, 0.99×10{sup 5} and 0.90×10{sup 5} L mol{sup −1}, respectively. The change in enthalpy (ΔH) and entropy (ΔS) were calculated to be −11.66 and 57.64 J mol{sup −1} K{sup −1}, respectively, indicating that the interaction was hydrophobic in nature. Site marker competitive experiments suggested that the binding of Alp to BSA primarily took place in sub-domain IIA, whereas the binding distance (r) between Alp and the tryptophan residue of BSA was obtained to be 1.87 nm by Förster's theory of non-radiative energy transfer. The conformational studies by CD spectroscopy showed that the presence of Alp decreased the α-helical content of BSA and induced the unfolding of the polypeptide of the protein. The change in conformation was also supported by excitation–emission matrix spectroscopy (EEMS) studies. The molecular docking experiment supports the above results and effectively proves the binding of Alp to BSA. -- Highlights: • Alprazolam: a benzodiazepine drug with anxiolytic and anticonvulsant properties. • Alprazolam induces conformational change on the native as well as urea denatured BSA. • Alprazolam may

  16. Experimental Investigation of Hypersonic Flow and Plasma Aerodynamic Actuation Interaction

    International Nuclear Information System (INIS)

    Sun Quan; Cheng Bangqin; Li Yinghong; Cui Wei; Yu Yonggui; Jie Junhun

    2013-01-01

    For hypersonic flow, it was found that the most effective plasma actuator is derived from an electromagnetic perturbation. An experimental study was performed between hypersonic flow and plasma aerodynamic actuation interaction in a hypersonic shock tunnel, in which a Mach number of 7 was reached. The plasma discharging characteristic was acquired in static flows. In a hypersonic flow, the flow field can affect the plasma discharging characteristics. DC discharging without magnetic force is unstable, and the discharge channel cannot be maintained. When there is a magnetic field, the energy consumption of the plasma source is approximately three to four times larger than that without a magnetic field, and at the same time plasma discharge can also affect the hypersonic flow field. Through schlieren pictures and pressure measurement, it was found that plasma discharging could induce shockwaves and change the total pressure and wall pressure of the flow field

  17. Interaction of norfloxacin with bovine serum albumin studied by different spectrometric methods; displacement studies, molecular modeling and chemometrics approaches

    Energy Technology Data Exchange (ETDEWEB)

    Naseri, Abdolhossein, E-mail: a_naseri@tabrizu.ac.ir [Departments of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 51666-16471 (Iran, Islamic Republic of); Hosseini, Soheila [Departments of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 51666-16471 (Iran, Islamic Republic of); Rasoulzadeh, Farzaneh [Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Rashidi, Mohammad-Reza [Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Zakery, Maryam; Khayamian, Taghi [Department of Chemistry, College of Chemistry, Isfahan University of Technology, Isfahan 84154 (Iran, Islamic Republic of)

    2015-01-15

    Serum albumins as major target proteins can bind to other ligands leading to alteration of their pharmacological properties. The mechanism of interaction between norfloxacin (NFLX) with bovine serum albumin (BSA) was investigated. Fuorescence quenching of serum albumin by this drug was found to be a static quenching process. The binding sites number, n, apparent binding constant, K, and thermodynamic parameters were calculated at different temperatures. The distance, r, between donor, BSA, and acceptor, NFLX, was calculated according to the Forster theory of non-radiation energy transfer. Also binding characteristics of NFLX with BSA together with its displacement from its binding site by kanamycin and effect of common metal ions on binding constant were investigated by the spectroscopic methods. The conformational change in the secondary structure of BSA upon interaction with NFLX was investigated qualitatively from synchronous fluorescence spectra, Fourier Transform Infrared (FTIR) and circular dichroism (CD) spectrometric methods. Molecular docking studies were performed to obtain information on the possible residues involved in the interaction process and changes in accessible surface area of the interacting residues. The results showed that the conformation of BSA changed in the presence of NFLX. For the first time, displacement studies were used for this interaction; displacement studies showed that NFLX was displaced by phenylbutazon and ketoprofen but was not displaced by ibuprofen indicating that the binding site of NFLX on albumin was site I. In addition a powerful chemometrics method, multivariate curve resolution-alternating least square, was used for resolution of spectroscopic augmented data obtained in two different titration modes in order to extract spectral information regardless of spectral overlapping of components. - Highlights: • Interaction between norfloxacin and BSA is studied by spectral methods. • Chemometrics methods are used to

  18. Synthesis, characterization and biodistribution of bisphosphonates Sm-153 complexes: correlation with molecular modeling interaction studies

    Energy Technology Data Exchange (ETDEWEB)

    Neves, M. E-mail: mneves@itn.pt; Gano, L.; Pereira, N.; Costa, M.C.; Costa, M.R.; Chandia, M.; Rosado, M.; Fausto, R

    2002-04-01

    Bisphosphonates (BPs) are characterized by a P-C-P backbone structure and two phosphonic acid groups bonded to the same carbon, and are established as osteoclast-mediated bone resorption inhibitors. The nature of the groups attached to the central carbon atom are responsible in determining the potency of bisphosphonates as anti-resorption drugs. However, it is not yet clear the exact relationship between their molecular structure and pharmacologic activities. In this study, molecular geometries of pamidronate, alendronate and neridronate, differing only in the length of the aliphatic chains, were predicted by molecular mechanics and their interactions with hydroxyapatite, the main bone mineral component, were examined. We report the synthesis and radiochemical characterization of {sup 153}Sm complexes with pamidronate, alendronate and neridronate. Hydroxyapatite binding and biodistribution studies of these complexes have shown a good correlation with the theoretical molecular modeling interaction studies. So, it is possible to conclude that computational chemistry techniques are a good approach to evaluate specific interactions and may play a relevant role in determining the relative ability of BPs to mineral bone, and open new perspectives to the design of new BPs with increased pharmacological activity. These techniques could be extended to BPs as ligands to carrier radioactive metals, aiming for new bone therapeutic radiopharmaceuticals.

  19. Molecular dynamics simulations of the interaction between 60 deg. dislocation and self-interstitial cluster in silicon

    International Nuclear Information System (INIS)

    Jing Yuhang; Meng Qingyuan; Zhao Wei

    2009-01-01

    Molecular dynamics simulations are performed to investigate the interaction between 60 deg. shuffle dislocation and tetrainterstitial (I 4 ) cluster in silicon, using Stillinger-Weber (SW) potential to calculate the interatomic forces. Based on Parrinello-Rahman method, shear stress is exerted on the model to move the dislocation. Simulation results show that the I 4 cluster can bend the dislocation line and delay the dislocation movement. During the course of intersection the dislocation line sections relatively far away from the I 4 cluster accelerate first, and then decelerate. The critical shear stress unpinning the 60 deg. dislocation from the I 4 cluster decreases as the temperature increases in the models.

  20. Interaction between β-lactoglobulin and structurally different heteroexopolysaccharides investigated by solution scattering and analytical ultracentrifugation study

    DEFF Research Database (Denmark)

    Khan, Sanaullah; Birch, Johnny; Harris, Pernille

    Knowledge on molecular structure of exopolysaccharides (EPSs) and their roles in the associative interactions with proteins is essential to understand the relationship between their structure, physical and rheological properties. Despite their importance, no detailed molecular characterization...

  1. Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis.

    Science.gov (United States)

    Xue, Weiwei; Jin, Xiaojie; Ning, Lulu; Wang, Meixia; Liu, Huanxiang; Yao, Xiaojun

    2013-01-28

    The rapid emergence of cross-resistance to the integrase strand transfer inhibitors (INSTIs) has become a serious problem in the therapy of human immunodeficiency virus type 1 (HIV-1) infection. Understanding the detailed molecular mechanism of INSTIs cross-resistance is therefore critical for the development of new effective therapy against cross-resistance. On the basis of the homology modeling constructed structure of tetrameric HIV-1 intasome, the detailed molecular mechanism of the cross-resistance mutation E138K/Q148K to three important INSTIs (Raltegravir (RAL, FDA approved in 2007), Elvitegravir (EVG, FDA approved in 2012), and Dolutegravir (DTG, phase III clinical trials)) was investigated by using molecular dynamics (MD) simulation and residue interaction network (RIN) analysis. The results from conformation analysis and binding free energy calculation can provide some useful information about the detailed binding mode and cross-resistance mechanism for the three INSTIs to HIV-1 intasome. Binding free energy decomposition analysis revealed that Pro145 residue in the 140s 1oop (Gly140 to Gly149) of the HIV-1 intasome had strong hydrophobic interactions with INSTIs and played an important role in the binding of INSTIs to HIV-1 intasome active site. A systematic comparison and analysis of the RIN proves that the communications between the residues in the resistance mutant is increased when compared with that of the wild-type HIV-1 intasome. Further analysis indicates that residue Pro145 may play an important role and is relevant to the structure rearrangement in HIV-1 intasome active site. In addition, the chelating ability of the oxygen atoms in INSTIs (e.g., RAL and EVG) to Mg(2+) in the active site of the mutated intasome was reduced due to this conformational change and is also responsible for the cross-resistance mechanism. Notably, the cross-resistance mechanism we proposed could give some important information for the future rational design of novel

  2. Investigation of a V15 magnetic molecular nanocluster by the Monte Carlo method

    International Nuclear Information System (INIS)

    Khizriev, K. Sh.; Dzhamalutdinova, I. S.; Taaev, T. A.

    2013-01-01

    Exchange interactions in a V 15 magnetic molecular nanocluster are considered, and the process of magnetization reversal for various values of the set of exchange constants is analyzed by the Monte Carlo method. It is shown that the best agreement between the field dependence of susceptibility and experimental results is observed for the following set of exchange interaction constants in a V 15 magnetic molecular nanocluster: J = 500 K, J′ = 150 K, J″ = 225 K, J 1 = 50 K, and J 2 = 50 K. It is observed for the first time that, in a strong magnetic field, for each of the three transitions from low-spin to high-spin states, the heat capacity exhibits two closely spaced maxima

  3. Spectroscopic and molecular docking studies on the interaction of antiviral drug nevirapine with calf thymus DNA.

    Science.gov (United States)

    Moghadam, Neda Hosseinpour; Salehzadeh, Sadegh; Shahabadi, Nahid

    2017-09-02

    The interaction of calf thymus DNA with nevirapine at physiological pH was studied by using absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, salt effect studies and computational methods. The drug binds to ct-DNA in a groove binding mode, as shown by slight variation in the viscosity of ct-DNA. Furthermore, competitive fluorimetric studies with Hoechst 33258 indicate that nevirapine binds to DNA via groove binding. Moreover, the structure of nevirapine was optimized by DFT calculations and was used for the molecular docking calculations. The molecular docking results suggested that nevirapine prefers to bind on the minor groove of ct-DNA.

  4. Compensation effects in molecular interactions and the quantum chemical le Chatelier principle.

    Science.gov (United States)

    Mezey, Paul G

    2015-05-28

    Components of molecular interactions and various changes in the components of total energy changes during molecular processes typically exhibit some degrees of compensation. This may be as prominent as the over 90% compensation of the electronic energy and nuclear repulsion energy components of the total energy in some conformational changes. Some of these compensations are enhanced by solvent effects. For various arrangements of ions in a solvent, however, not only compensation but also a formal, mutual enhancement between the electronic energy and nuclear repulsion energy components of the total energy may also occur, when the tools of nuclear charge variation are applied to establish quantum chemically rigorous energy inequalities.

  5. Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

    Science.gov (United States)

    Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

    2012-10-01

    Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

  6. NMR (¹H, ROESY) spectroscopic and molecular modelling investigations of supramolecular complex of β-cyclodextrin and curcumin.

    Science.gov (United States)

    Jahed, Vahid; Zarrabi, Ali; Bordbar, Abdol-Khalegh; Hafezi, Mohammad Sadegh

    2014-12-15

    In this paper we have investigated the solubility enhancement of curcumin through inclusion complexation by β-cyclodextrin as well as the topology and geometry of interaction between curcumin and carrier. For this purpose, the phase solubility of curcumin was assessed using Higuchi and Connors method, and the inclusion complex was characterised by 1D (1)H and 2D ROESY NMR analysis, and finally confirmed by molecular modelling. The phase solubility diagram demonstrated the AL-type which confirms an increase in curcumin solubility by increasing the concentration of β-cyclodextrin. (1)H NMR and ROESY spectra results showed a cross-peak between H-3 proton of β-cyclodextrin and the aromatic rings group of curcumin. This revealed the hydrophobic interactions between aromatic rings of curcumin and the cavity of β-cyclodextrin. Finally, the enthalpy of formation was obtained from molecular modelling results which in turn indicated that the process is exothermic and low-energy interactions are involved in the inclusion complex formation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. AESOP: A Python Library for Investigating Electrostatics in Protein Interactions.

    Science.gov (United States)

    Harrison, Reed E S; Mohan, Rohith R; Gorham, Ronald D; Kieslich, Chris A; Morikis, Dimitrios

    2017-05-09

    Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Interaction between the SNR Sagittarius A East and the 50-km s-1 Molecular Cloud

    International Nuclear Information System (INIS)

    Tsuboi, Masato; Okumura, Sachiko K; Miyazaki, Atsushi

    2006-01-01

    We performed high-resolution observations of the Galactic Center 50-km s -1 molecular cloud in the CS J = 1 - 0 line using the Nobeyama Millimeter Array. The 50-km s -1 molecular cloud corresponds to a break in the Sagittarius (Sgr) A east shell. A very broad and negative velocity wing feature is detected at an apparent contact spot between the molecular cloud and the Sgr A east shell. The velocity width of the wing feature is over 50-km s -1 . The width is three times wider than those of typical Galactic Center clouds. This strongly suggests that the shell is interacting physically with the molecular cloud. The asymmetric velocity profile of the wing feature indicates that the Sgr A east shell expands and crashes into the far side of the molecular cloud. About 50 clumps are identified in the cloud using CLUMPFIND. The velocity width-size relation and the mass spectrum of clumps in the cloud are similar to those in Central Molecular Zone (CMZ)

  9. Molecular modeling of polymer composite interactions with analytes in electronic nose sensors for environmental monitoring in International Space Station

    Science.gov (United States)

    Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Zhou, H.; Manatt, K.

    2002-01-01

    We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL Electronic Nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings (with no hydrogens). The Dreiding 2.21 force field is used for the polymer and solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4- vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic (ammonia) and organic (methanol, toluene, hydrazine) compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites.

  10. Antiretroviral Drug Interactions: Overview of Interactions Involving New and Investigational Agents and the Role of Therapeutic Drug Monitoring for Management

    Directory of Open Access Journals (Sweden)

    R. Chris Rathbun

    2011-10-01

    Full Text Available Antiretrovirals are prone to drug-drug and drug-food interactions that can result in subtherapeutic or supratherapeutic concentrations. Interactions between antiretrovirals and medications for other diseases are common due to shared metabolism through cytochrome P450 (CYP450 and uridine diphosphate glucuronosyltransferase (UGT enzymes and transport by membrane proteins (e.g., p-glycoprotein, organic anion-transporting polypeptide. The clinical significance of antiretroviral drug interactions is reviewed, with a focus on new and investigational agents. An overview of the mechanistic basis for drug interactions and the effect of individual antiretrovirals on CYP450 and UGT isoforms are provided. Interactions between antiretrovirals and medications for other co-morbidities are summarized. The role of therapeutic drug monitoring in the detection and management of antiretroviral drug interactions is also briefly discussed.

  11. Final Report on Investigation of the Electron Interactions in Graphene

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Philip [Columbia University

    2015-02-14

    In graphene, combined with the real spin degree of freedom, which exhibits SU(2) symmetry, the total internal degrees of freedom of graphene carriers is thus described by a larger SU(4) symmetry, which produces a richer space for potential phenomena of emergent correlated electron phenomena. The major part of this proposal is exploring this unique multicomponent correlated system in the quantum limit. In the current period of DOE BES support we have made several key advances that will serve as a foundation for the new studies in this proposal. Employing the high-mobility encapsulated graphene heterostructures developed during the current phase of research, we have investigated spin and valley quantum Hall ferromagnetism in graphene and discovered a spin phase transition leading to a quantum spin Hall analogue. We have also observed the fractal quantum Hall effect arising from the Hofstadter’s butterfly energy spectrum. In addition, we have discovered multiband transport phenomena in bilayer graphene at high carrier densities.

  12. Theoretical investigation of electron-positive ion/atom interactions

    International Nuclear Information System (INIS)

    Msezane, A.Z.

    1992-01-01

    Very brief summaries are given on three research topics. Electron impact elastic, excitation, and total cross sections for K were investigated by using elaborate Cl target wave functions in the close-coupling approximation. Photoionization cross sections from ground-state Na were calculated near the 2s 2 2p 5 3s and 2s2p 6 3s inner-shell thresholds; also, the photoionization cross sections of excited 3p 2 P o and 3d 2 D states were calculated with the R-matrix methodology near the 2s2p 6 3s thresholds. A numerical approach was developed to calculate the charge transfer matrix elements for ion-atom(ion) collisions; this was used for the proton-hydrogen collision problem as an illustration

  13. Investigation of electron heating in laser-plasma interaction

    Directory of Open Access Journals (Sweden)

    A Parvazian

    2013-03-01

    Full Text Available  In this paper, stimulated Raman scattering (SRS and electron heating in laser plasma propagating along the plasma fusion is investigated by particle-in cell simulation. Applying an external magnetic field to plasma, production of whistler waves and electron heating associated with whistler waves in the direction perpendicular to external magnetic field was observed in this simulation. The plasma waves with low phase velocities, generated in backward-SRS and dominateing initially in time and space, accelerated the backward electrons by trapping them. Then these electrons promoted to higher energies by the forward-SRS plasma waves with high phase velocities. This tow-stage electron acceleration is more efficient due to the coexistence of these two instabilities.

  14. Molecular dynamics simulations of GPCR-cholesterol interaction: An emerging paradigm.

    Science.gov (United States)

    Sengupta, Durba; Chattopadhyay, Amitabha

    2015-09-01

    G protein-coupled receptors (GPCRs) are the largest class of molecules involved in signal transduction across cell membranes and represent major targets in the development of novel drug candidates. Membrane cholesterol plays an important role in GPCR structure and function. Molecular dynamics simulations have been successful in exploring the effect of cholesterol on the receptor and a general consensus molecular view is emerging. We review here recent molecular dynamics studies at multiple resolutions highlighting the main features of cholesterol-GPCR interaction. Several cholesterol interaction sites have been identified on the receptor that are reminiscent of nonannular sites. These cholesterol hot-spots are highly dynamic and have a microsecond time scale of exchange with the bulk lipids. A few consensus sites (such as the CRAC site) have been identified that correspond to higher cholesterol interaction. Interestingly, high plasticity is observed in the modes of cholesterol interaction and several sites have been suggested to have high cholesterol occupancy. We therefore believe that these cholesterol hot-spots are indicative of 'high occupancy sites' rather than 'binding sites'. The results suggest that the energy landscape of cholesterol association with GPCRs corresponds to a series of shallow minima interconnected by low barriers. These specific interactions, along with general membrane effects, have been observed to modulate GPCR organization. Membrane cholesterol effects on receptor structure and organization, that in turn influences receptor cross-talk and drug efficacy, represent a new frontier in GPCR research. This article is part of a Special Issue entitled: Lipid-protein interactions. Guest Editors: Amitabha Chattopadhyay and Jean-Marie Ruysschaert. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Molecular structure and interactions of nucleic acid components in nanoparticles: ab initio calculations

    International Nuclear Information System (INIS)

    Rubin, Yu.V.; Belous, L.F.

    2012-01-01

    Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150-200 atoms with enough large basis sets (for example, 6-31G * ). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 A on average, and the helical angle in a trimer is approximately equal to 30 o : The distance between phosphor atoms in neighboring chains is 13.1 A. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.

  16. Investigations of an O-H...S hydrogen bond via Car-Parrinello and path integral molecular dynamics.

    Science.gov (United States)

    Jezierska, Aneta; Panek, Jarosław J

    2009-06-01

    The presence of intramolecular hydrogen bonds influences the binding energy, tautomeric equilibrium, and spectroscopic properties of various classes of organic molecules. This article discusses the O-H...S bridge, one of the less commonly investigated types of intramolecular interactions. 3-mercapto-1,3-diphenylprop-2-en-1-one was considered as the model structure. This compound exhibits photochromic properties. Car-Parrinello molecular dynamics (CPMD) was applied to investigate the spectroscopic and molecular properties of this compound in the gas phase and in the solid state. The second part of the study is devoted to the effects of the quantization of nuclear motions, with special attention to the O-H...S moiety. Path integral molecular dynamics (PIMD) of the molecular crystal of 3-mercapto-1,3-diphenylprop-2-en-1-one was carried out for this purpose. The employment of this fully quantum mechanical technique enables one to study, in a time-averaged sense, the zero-point motion important for flat potential energy surfaces. Finally, the potentials of mean force (Pmfs) were calculated from the CPMD and PIMD data obtained for the solid-state calculations. The effect of including quantum nuclear motion was investigated. In the studied compound, quantum effects shortened the H-bridge and provided a better description of the free energy minimum. The computational results place this uncommon intramolecular H-bonding among the class of strong hydrogen bonds with large red shifts of O-H stretching modes, which correspond well with previously presented experimental data in the literature concerning this structure. 2008 Wiley Periodicals, Inc.

  17. Study of the interaction of multiply charged ions and complex systems of biological interest: effects of the molecular environment

    International Nuclear Information System (INIS)

    Capron, Michael

    2011-01-01

    This PhD thesis describes the experimental study of the interaction between slow multiply charged ions (tens of keV) and molecular systems of biological interest (amino acids and nucleobases). It is the aim to identify and to better understand the effect of a molecular environment on different collision induced phenomena. To do so, the time of flight spectra of cationic products emerging from collisions with isolated molecules as well as clusters are compared. It is shown that the molecular environment protects the molecule as it allows to distribute the transferred energies and charges over the whole system (global decrease of the fragmentation and quenching of some fragmentation channels). Furthermore, in the case of adenine clusters, the molecular environment weakens some intramolecular bonds. Moreover, products of chemical reactions are observed concerning proton transfer processes in hydrated cluster of adenine and the formation of peptides bonds between beta-alanine molecules in a cluster. The latter finding is studied as a function of the cluster size and type of the projectile. Some criteria for peptide bond formation, such as flexibility and geometry of the molecule, are investigated for different amino acids. (author)

  18. A raman microprobe investigation of the molecular architecture of loblolly pine tracheids

    Science.gov (United States)

    James S. Bond; Rajai H. Atalla

    1999-01-01

    Our understanding of the molecular architecture of intact, native plant cell walls is very limited. Traditional methods of investigation disturb the tissue to varying degrees and conclusions based on these methods may be intimately related to the technique used. A promising new technique to study native-state organization is polarized Raman spectroscopy. In this...

  19. Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

    Science.gov (United States)

    Ramya, L; Ramakrishnan, Vigneshwar

    2016-07-01

    Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts

    Science.gov (United States)

    Giorgino, Toni

    2014-03-01

    PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED’s rich syntax to define collective variables (CVs) and VMD’s chemically-aware atom selection language, while working within a natural point-and-click interface. Pre-defined templates and syntax mnemonics facilitate the definition of well-known reaction coordinates. Complex CVs, e.g. involving reference snapshots used for RMSD or native contacts calculations, can be built through dialogs that provide a synoptic view of the available options. Scripts can be either exported for use in simulation programs, or evaluated on the currently loaded molecular trajectories. Script development takes place without leaving VMD, thus enabling an incremental try-see-modify development model for molecular metrics.

  1. REVIEW - Advances on molecular studies of the interaction soybean - Asian rust

    Directory of Open Access Journals (Sweden)

    Aguida Maria Alves Pereira Morales

    2012-01-01

    Full Text Available Effective management practices are essential for controlling rust outbreaks. The main control methodused is the application of fungicides, which increases substantially the cost of production and is harmful to theenvironment. Prevention is still the best way to avoid more significant losses in soybean yields. Alternatives,such as planting resistant varieties to the fungus, are also important. The use of resistant or tolerant varietiesis the most promising method for controlling Asian soybean rust. Recently, five dominant genes resistant to soybean rust were described: Rpp1, Rpp2, Rpp3, Rpp4 and Rpp5. However, little is known about the molecular interaction among soybean plant and soybean rust and on the molecular pathway triggered by pathogen recognition. Understanding the molecular mechanisms involved in defense responses is of primary importance for planning strategies to control stress and, consequently, to increase plant adaptation to limiting conditions

  2. The dynamics of molecular interactions and chemical reactions at metal surfaces: testing the foundations of theory.

    Science.gov (United States)

    Golibrzuch, Kai; Bartels, Nils; Auerbach, Daniel J; Wodtke, Alec M

    2015-04-01

    We review studies of molecular interactions and chemical reactions at metal surfaces, emphasizing progress toward a predictive theory of surface chemistry and catalysis. For chemistry at metal surfaces, a small number of central approximations are typically made: (a) the Born-Oppenheimer approximation of electronic adiabaticity, (b) the use of density functional theory at the generalized gradient approximation level, (c) the classical approximation for nuclear motion, and (d) various reduced-dimensionality approximations. Together, these approximations constitute a provisional model for surface chemical reactivity. We review work on some carefully studied examples of molecules interacting at metal surfaces that probe the validity of various aspects of the provisional model.

  3. UNIQUAC interaction parameters for alkane/amine systems determined by Molecular Mechanics

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Klein, R. A.; Rasmussen, Kjeld

    1996-01-01

    UNIQUAC interaction parameters have been successfully determined for three alkane/primary amine systems using a Molecular Mechanics method called the Consistent Force Field. Interaction parameters for alkane/alkane and alkane/ketone systems had been determined previously using this method...... and in this contribution the method has been extended to polar systems with extensive hydrogen bonding. It is thus possible to predict reliable vapor liquid equilibrium data using pure component data only. A method for finding the global minimum on the potential energy surface of a pair of molecules was developed. Good...

  4. Interaction of sucralose with whey protein: Experimental and molecular modeling studies

    Science.gov (United States)

    Zhang, Hongmei; Sun, Shixin; Wang, Yanqing; Cao, Jian

    2017-12-01

    The objective of this research was to study the interactions of sucralose with whey protein isolate (WPI) by using the three-dimensional fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling. The results showed that the peptide strands structure of WPI had been changed by sucralose. Sucralose binding induced the secondary structural changes and increased content of aperiodic structure of WPI. Sucralose decreased the thermal stability of WPI and acted as a structure destabilizer during the thermal unfolding process of protein. In addition, the existence of sucralose decreased the reversibility of the unfolding of WPI. Nonetheless, sucralose-WPI complex was less stable than protein alone. The molecular modeling result showed that van der Waals and hydrogen bonding interactions contribute to the complexation free binding energy. There are more than one possible binding sites of WPI with sucralose by surface binding mode.

  5. Retracted: Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies.

    Science.gov (United States)

    Kim, Jehoon; Krebs, Mark R H; Trout, Bernhardt L

    2018-02-01

    Retraction: Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies by Jehoon Kim, Mark R. H. Krebs and Bernhardt L. Trout The above article from the Journal of Pharmacy and Pharmacology, first published online on 4 August 2017 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal Editor-in-Chief, Professor David Jones, and John Wiley & Sons Ltd. The authors discovered that the analysis of simulations was faulty making the data incorrect. Reference Kim J et al. Molecular characterization of excipients' preferential interactions with therapeutic monoclonal antibodies. J Pharm Pharmacol 2017. https://doi.org/10.1111/jphp.12787. © 2017 Royal Pharmaceutical Society.

  6. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

    Science.gov (United States)

    Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

    2013-01-01

    Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

  7. Molecular and biopharmaceutical investigation of alginate-inulin synbiotic coencapsulation of probiotic to target the colon.

    Science.gov (United States)

    Atia, Abdelbasset; Gomma, Ahmed I; Fliss, Ismail; Beyssac, Eric; Garrait, Ghislain; Subirade, Muriel

    2017-03-01

    Colon targeting, as a site-specific delivery for oral formulation, remains a major challenge, especially for sensitive bioactive components such as therapeutic forms of phages, live attenuated virus and prebiotics-probiotics association. Synbiotics could be used to protect encapsulated probiotics during the gastrointestinal tract and control their release in the colon. To achieve these goals, effective prebiotics, such as inulin, could be combined with alginate - the most exploited polymer used for probiotic encapsulation - in the form of beads. This work aimed to study the biopharmaceutical behaviour of alginate beads (A) and inulin-alginate beads of different inulin concentrations (5 or 20%) in 2% alginate (AI5, AI20). Beads were loaded with three probiotic strains (Pediococcus acidilactici Ul5, Lactobacillus reuteri and Lactobacillus salivarius). Dissolution of beads was studied by USP4 under conditions simulating the gastrointestinal condition. The survival rates of the bacterial strains were measured by a specific qPCR bacterial count. Mucoadhesiveness of beads was studied by an ex vivo method using intestinal mucosa. To understand the behaviour of each formulation, the ultrastructure of the polymeric network was studied using scanning electron microscopy (SEM). Molecular interactions between alginate and inulin were studied by Fourier transform infra-red spectroscopy (FTIR). Dissolution results suggested that the presence of inulin in beads provided more protection for the tested bacterial strains against the acidic pH. AI5 was the most effective formulation to deliver probiotics to the colon simulation conditions. FTIR and SEM investigations explained the differences in behaviour of each formula. The developed symbiotic form provided a promising matrix for the development of colonic controlled release systems.

  8. C60-DOM interactions and effects on C60 apparent solubility: a molecular mechanics and density functional theory study.

    Science.gov (United States)

    Wang, Zhuang; Chen, Jingwen; Sun, Qian; Peijnenburg, Willie J G M

    2011-08-01

    Dissolved organic matter (DOM) plays a critical role in the transport of carbon nano-particles (e.g. C(60)) in the aquatic environment. However, the mechanism for C(60)-DOM interactions and its environmental implications needs further investigations. In this study, the interaction of C(60) with relevant reference compounds of DOM (DOM(R)) is computationally simulated by molecular mechanics and density functional theory (DFT). All the C(60)-DOM(R) complexes are firstly optimized by classical annealing, and then DFT using the Dmol(3) code. The adsorption energies of C(60) on DOM(R) were computed. The computed electrostatic potential indicates that DOM(R) are electron acceptors in the C(60)-DOM(R) complexes, and the thermodynamic calculations indicate that electrostatic interaction is the dominant driving force for the C(60)-gallic acid complexation process in water. The presence of DOM(R) increases the apparent water solubility of C(60). It is also observed that the C(60) apparent water solubility decrease with the increase of the energy gaps of frontier molecular orbitals (E(LUMO)-E(HOMO)) for each C(60)-DOM(R) complex. These findings indicate that computational simulation is an important tool for predicting the behavior and fate of carbon nano-particles in the aquatic environment. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Mixtures of nonionic and anionic surfactants: interactions with low-molecular-mass homopeptides

    Czech Academy of Sciences Publication Activity Database

    Forgács, E.; Cserháti, T.; Deyl, Zdeněk; Mikšík, Ivan; Eckhardt, Adam

    2001-01-01

    Roč. 917, 1-2 (2001), s. 287-295 ISSN 0021-9673 R&D Projects: GA ČR GV203/96/K128; GA ČR GA203/99/0191; GA ČR GA203/00/D032 Institutional research plan: CEZ:AV0Z5011922 Keywords : molecular interactions * regression analysis * surfactants Subject RIV: BH - Optics, Masers, Lasers Impact factor: 2.793, year: 2001

  10. Quantum molecular modeling of the interaction between guanine and alkylating agents--2--nitrogen mustard.

    Science.gov (United States)

    Hamza, A; Broch, H; Vasilescu, D

    1996-06-01

    The alkylation mechanism of guanine by nitrogen mustard (HN2) was studied by using a supermolecular modeling at the ab initio 6-31G level. Our computations show that interaction of guanine with the aziridinium form of HN2 necessitates a transition state for the N7 alkylation route. The pathway of N7-guanine alkylation by nitrogen and sulfur mustards is discussed on the basis of the Molecular Electrostatic Potential and HOMO-LUMO properties of these molecules.

  11. Interaction of flavokawain B with lysozyme: A photophysical and molecular simulation study

    International Nuclear Information System (INIS)

    Feroz, Shevin R.; Teoh, Yue Jun; Mohamad, Saharuddin B.; Hong, Sok Lai; Malek, Sri N.A.; Tayyab, Saad

    2015-01-01

    Interaction of flavokawain B (FB), a therapeutic flavonoid with lysozyme (LYZ), was studied using various spectroscopic and molecular simulation techniques. The association constant, K a of the binding reaction was determined to be 2.79±0.16×10 4 M −1 at 25 °C based on fluorescence quenching titration results. Thermodynamic analysis of the binding data obtained at different temperatures along with molecular docking results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in FB–LYZ interaction. The binding reaction between FB and LYZ was found to affect the microenvironment around protein fluorophores (Tyr and Trp) as revealed by intrinsic and three-dimensional fluorescence results. A comparison of the LYZ thermograms, obtained by far-UV CD spectroscopy in the absence and the presence of FB, suggested improved protein thermal stability upon complexation with FB. Presence of metal ions was found to affect FB–LYZ interaction. Molecular docking predicted the formation of two hydrogen bonds between the oxygen atoms of FB and amino acid residues of LYZ (Asn-59 and Trp-63), located in the vicinity of the active site, in addition to various non-polar contacts. Molecular dynamics studies showed that the complex reached equilibrium during simulation, indicating the stability of the FB–LYZ complex. - Highlights: • Role of hydrogen bonds, hydrophobic and van der Waals forces in FB–LYZ interaction. • Moderate affinity between FB and LYZ. • Alteration in the microenvironment around protein fluorophores upon FB binding. • Presence of the FB binding locus in the vicinity of LYZ active site

  12. SChiSM2: creating interactive web page annotations of molecular structure models using Jmol.

    Science.gov (United States)

    Cammer, Stephen

    2007-02-01

    SChiSM2 is a web server-based program for creating web pages that include interactive molecular graphics using the freely-available applet, Jmol, for illustration. The program works with Internet Explorer and Firefox on Windows, Safari and Firefox on Mac OSX and Firefox on Linux. The program can be accessed at the following address: http://ci.vbi.vt.edu/cammer/schism2.html.

  13. Dipolar interactions, molecular flexibility, and flexoelectricity in bent-core liquid crystals.

    Science.gov (United States)

    Dewar, Alastair; Camp, Philip J

    2005-11-01

    The effects of dipolar interactions and molecular flexibility on the structure and phase behavior of bent-core molecular fluids are studied using Monte Carlo computer simulations. Some calculations of flexoelectric coefficients are also reported. The rigid cores of the model molecules consist of either five or seven soft spheres arranged in a "V" shape with external bend angle gamma. With purely repulsive sphere-sphere interactions and gamma = 0 degrees (linear molecules) the seven-sphere model exhibits isotropic, uniaxial nematic, and untilted and tilted smectic phases. With gamma > or = 20 degrees the untilted smectic phases disappear, while the system with gamma > or = 40 degrees shows a direct tilted smectic-isotropic fluid transition. The addition of electrostatic interactions between transverse dipole moments on the apical spheres is generally seen to reduce the degree of molecular inclination in tilted phases, and destabilizes the nematic and untilted smectic phases of linear molecules. The effects of adding three-segment flexible tails to the ends of five-sphere bent-core molecules are examined using configurational-bias Monte Carlo simulations. Only isotropic and smectic phases are observed. On the one hand, molecular flexibility gives rise to pronounced fluctuations in the smectic-layer structure, bringing the simulated system in better correspondence with real materials; on the other hand, the smectic phase shows almost no tilt. Lastly, the flexoelectric coefficients of various nematic phases--with and without attractive sphere-sphere interactions--are presented. The results are encouraging, but a large computational effort is required to evaluate the appropriate fluctuation relations reliably.

  14. Interaction of flavokawain B with lysozyme: A photophysical and molecular simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Feroz, Shevin R.; Teoh, Yue Jun [Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia); Mohamad, Saharuddin B. [Bioinformatics Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia); Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia); Hong, Sok Lai; Malek, Sri N.A. [Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia); Tayyab, Saad, E-mail: saadtayyab2004@yahoo.com [Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia); Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur (Malaysia)

    2015-04-15

    Interaction of flavokawain B (FB), a therapeutic flavonoid with lysozyme (LYZ), was studied using various spectroscopic and molecular simulation techniques. The association constant, K{sub a} of the binding reaction was determined to be 2.79±0.16×10{sup 4} M{sup −1} at 25 °C based on fluorescence quenching titration results. Thermodynamic analysis of the binding data obtained at different temperatures along with molecular docking results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in FB–LYZ interaction. The binding reaction between FB and LYZ was found to affect the microenvironment around protein fluorophores (Tyr and Trp) as revealed by intrinsic and three-dimensional fluorescence results. A comparison of the LYZ thermograms, obtained by far-UV CD spectroscopy in the absence and the presence of FB, suggested improved protein thermal stability upon complexation with FB. Presence of metal ions was found to affect FB–LYZ interaction. Molecular docking predicted the formation of two hydrogen bonds between the oxygen atoms of FB and amino acid residues of LYZ (Asn-59 and Trp-63), located in the vicinity of the active site, in addition to various non-polar contacts. Molecular dynamics studies showed that the complex reached equilibrium during simulation, indicating the stability of the FB–LYZ complex. - Highlights: • Role of hydrogen bonds, hydrophobic and van der Waals forces in FB–LYZ interaction. • Moderate affinity between FB and LYZ. • Alteration in the microenvironment around protein fluorophores upon FB binding. • Presence of the FB binding locus in the vicinity of LYZ active site.

  15. Interactions of cephalexin with bovine serum albumin: displacement reaction and molecular docking

    Directory of Open Access Journals (Sweden)

    Hamed Hamishehkar

    2016-09-01

    Conclusion: The outcomes of spectroscopic methods revealed that the conformation of BSA changed during drug-BSA interaction. The results of FRET propose that CPL quenches the fluorescence of BSA by static quenching and FRET. The displacement study showed that phenylbutazon and ketoprofen displaced CPL, indicating that its binding site on albumin is site I and Gentamicin cannot be displaced from the binding site of CPL. All results of molecular docking method agreed with the results of experimental data.

  16. Molecular Dynamic Analysis of Hyaluronic Acid and Phospholipid Interaction in Tribological Surgical Adjuvant Design for Osteoarthritis.

    Science.gov (United States)

    Siódmiak, Jacek; Bełdowski, Piotr; Augé, Wayne K; Ledziński, Damian; Śmigiel, Sandra; Gadomski, Adam

    2017-09-04

    Tribological surgical adjuvants constitute a therapeutic discipline made possible by surgical advances in the treatment of damaged articular cartilage beyond palliative care. The purpose of this study is to analyze interactions between hyaluronic acid and phospholipid molecules, and the formation of geometric forms, that play a role in the facilitated lubrication of synovial joint organ systems. The analysis includes an evaluation of the pathologic state to detail conditions that may be encountered by adjuvants during surgical convalescence. The synovial fluid changes in pH, hyaluronic acid polydispersity, and phospholipid concentration associated with osteoarthritis are presented as features that influence the lubricating properties of adjuvant candidates. Molecular dynamic simulation studies are presented, and the Rouse model is deployed, to rationalize low molecular weight hyaluronic acid behavior in an osteoarthritic environment of increased pH and phospholipid concentration. The results indicate that the hyaluronic acid radius of gyration time evolution is both pH- and phospholipid concentration-dependent. Specifically, dipalmitoylphosphatidylcholine induces hydrophobic interactions in the system, causing low molecular weight hyaluronic acid to shrink and at high concentration be absorbed into phospholipid vesicles. Low molecular weight hyaluronic acid appears to be insufficient for use as a tribological surgical adjuvant because an increased pH and phospholipid concentration induces decreased crosslinking that prevents the formation of supramolecular lubricating forms. Dipalmitoylphosphatidylcholine remains an adjuvant candidate for certain clinical situations. The need to reconcile osteoarthritic phenotypes is a prerequisite that should serve as a framework for future adjuvant design and subsequent tribological testing.

  17. ACCOUNTING OF MANY-PARTICLE INTERACTIONS IN MOLECULAR J-AGGREGATES AND NONLINEAR OPTICAL EFFECTS IN THESE SYSTEMS

    Directory of Open Access Journals (Sweden)

    N. A. Veretenov

    2014-09-01

    Full Text Available The paper deals with generalization of investigation materials performed by the authors in recent years and analysis of obtained results. The subject of the paper is accounting of many-particle interactions in molecular J-aggregates at their resonance excitation by laser radiation. In this case, not only twin interactions are taken into considerations, but also the interactions of a given particle with three and more particles simultaneously. Three basic directions can be denoted among carried out investigations. The first direction is connected with derivation (from the first principles of motion equations for molecular of J-aggregates in view of many-particle interactions, and also twin correlations between particles. The derivation of equations from the first principles leads in general to the system of coupled equations for the means of products of n operators relating to n different molecules. Since n increases in every following equation, the problems arise, connected with uncoupling of this system and also factorization of the means with the highest n. The most difficult and complicated problem in this process is correct calculation of relaxed terms, arising due to exciton-exciton annihilation. The first direction is connected concretely with solution of all above mentioned problems. Within the second direction the study of bistability has been carried out on the basis of obtained equations, in view of three-particle interactions. Meanwhile primary attention has been concentrated on analysis of homogeneous regimes in J-aggregates. It has been shown, in particular, that accounting of many-particle contributions leads to the shift of bistability boundary into region of smaller constants of exciton-exciton annihilation. And, at last, the third direction of investigations is connected with analysis of modulation instability for stationary states of J-aggregates considered earlier at bistability study. The study of stability region boundaries

  18. Investigating hadronic resonances in pp interactions with HADES

    Directory of Open Access Journals (Sweden)

    Przygoda Witold

    2015-01-01

    Full Text Available In this paper we report on the investigation of baryonic resonance production in proton-proton collisions at the kinetic energies of 1.25 GeV and 3.5 GeV, based on data measured with HADES. Exclusive channels npπ+ and ppπ0 as well as ppe+e− were studied simultaneously in the framework of a one-boson exchange model. The resonance cross sections were determined from the one-pion channels for Δ(1232 and N(1440 (1.25 GeV as well as further Δ and N* resonances up to 2 GeV/c2 for the 3.5 GeV data. The data at 1.25 GeV energy were also analysed within the framework of the partial wave analysis together with the set of several other measurements at lower energies. The obtained solutions provided the evolution of resonance production with the beam energy, showing a sizeable non-resonant contribution but with still dominating contribution of Δ(1232P33. In the case of 3.5 GeV data, the study of the ppe+e− channel gave the insight on the Dalitz decays of the baryon resonances and, in particular, on the electromagnetic transition form-factors in the time-like region. We show that the assumption of a constant electromagnetic transition form-factors leads to underestimation of the yield in the dielectron invariant mass spectrum below the vector mesons pole. On the other hand, a comparison with various transport models shows the important role of intermediate ρ production, though with a large model dependency. The exclusive channels analysis done by the HADES collaboration provides new stringent restrictions on the parameterizations used in the models.

  19. Molecular dynamics study of biodegradation of azo dyes via their interactions with AzrC azoreductase.

    Science.gov (United States)

    Haghshenas, Hamed; Kay, Maryam; Dehghanian, Fariba; Tavakol, Hossein

    2016-01-01

    Azo dyes are one of the most important class of dyes, which have been widely used in industries. Because of the environmental pollution of azo dyes, many studies have been performed to study their biodegradation using bacterial systems. In present work, the AzrC of mesophilic gram-positive Bacillus sp. B29 has been considered to study its interaction with five common azo dyes (orange G, acid red 88, Sudan I, orange I, and methyl red). The molecular dynamics simulations have been employed to study the interaction between AzrC and azo dyes. The trajectory was confirmed using root mean square deviation and the root mean square fluctuation analyses. Then, the hydrogen bond and alanine scanning analyses were performed to reveal active site residues. Phe105 (A), Phe125 (B), Phe172 (B), and Pro132 (B) have been found as the most important hydrophobic residues whereas Asn104 (A), Tyr127 (B), and Asn187 (A) have key role in making hydrogen bond. The results of molecular mechanics Poisson-Boltzmann surface area and molecular mechanics generalized Born surface area calculations proved that the hydrophobic azo dyes like Acid red 88 binds more tightly to the AzrC protein. The calculated data suggested MR A 121 (B) I as a potential candidate for improving the AzrC-MR interactions.

  20. Molecular dynamics simulations of the DNA interaction with metallic nanoparticles and TiO2 surfaces

    International Nuclear Information System (INIS)

    Kholmurodov, Kh.T.; Krasavin, E.A.; Dushanov, E.B.; Hassan, H.K.; Galal, A.; ElHabashy, H.A.; Sweilam, N.H.; Yasuoka, K.

    2013-01-01

    The understanding of the mechanism of DNA interactions and binding with metallic nanoparticles (NPs) and surfaces represents a great interest in today's medicine applications due to diagnostic and treatment of oncology diseases. Recent experimental and simulation studies involve the DNA interaction with highly localized proton beams or metallic NPs (such as Ag, Au, etc.), aimed at targeted cancer therapy through the injection of metal micro- or nanoparticles into the tumor tissue with consequent local microwave or laser heating. The effects of mutational structure changes in DNA and protein structures could result in destroying of native chemical (hydrogen) bonds or, on the contrary, creating of new bonds that do not normally exist there. The cause of such changes might be the alteration of one or several nucleotides (in DNA) or the substitution of specific amino acid residues (in proteins) that can lead to the essential structural destabilization or unfolding. At the atomic or molecular level, the replacement of one nucleotide by another (in DNA double helices) or replacement of one amino acid residue by another (in proteins) cause essential modifications of the molecular force fields of the environment that break locally important hydrogen bonds underlying the structural stability of the biological molecules. In this work, the molecular dynamics(MD) simulations were performed for four DNA models and the flexibilities of the purine and pyrimidine nucleotides during the interaction process with the metallic NPs and TiO 2 surface were clarified

  1. Investigation of a metal-organic interface. Realization and understanding of a molecular switch

    Energy Technology Data Exchange (ETDEWEB)

    Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

    2010-07-01

    The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

  2. Investigation of interactions between dendrimer-coated magnetite nanoparticles and bovine serum albumin

    International Nuclear Information System (INIS)

    Pan Bifeng; Gao Feng; Ao Limei

    2005-01-01

    We investigated the interactions between dendrimer-coated magnetite nanoparticles (MNPs) and the protein serum albumin. The investigation was based on the fluorescence quenching of tryptophan residue of serum albumin after binding with the dendrimer-coated magnetite nanoparticles. The extent of the interactions between bovine serum albumin and dendrimer-coated MNPs strongly depends on their surface groups and pH value

  3. Using Language Games as a Way to Investigate Interactional Engagement in Human-Robot Interaction

    DEFF Research Database (Denmark)

    Jensen, L. C.

    2016-01-01

    Social robots are employed in many classrooms and have been shown to aid learning. However, studies show that while schools intend for these robots to be social actors, they are not treated as such by the students. As the social factor is crucial for interactional engagement, this paper discusses...

  4. A structural investigation of the interaction of oxalic acid with Cu(110)

    Science.gov (United States)

    White, T. W.; Duncan, D. A.; Fortuna, S.; Wang, Y.-L.; Moreton, B.; Lee, T.-L.; Blowey, P.; Costantini, G.; Woodruff, D. P.

    2018-02-01

    The interaction of oxalic acid with the Cu(110) surface has been investigated by a combination of scanning tunnelling microscopy (STM), low energy electron diffraction (LEED), soft X-ray photoelectron spectroscopy (SXPS), near-edge X-ray absorption fine structure (NEXAFS) and scanned-energy mode photoelectron diffraction (PhD), and density functional theory (DFT). O 1s SXPS and O K-edge NEXAFS show that at high coverages a singly deprotonated monooxalate is formed with its molecular plane perpendicular to the surface and lying in the [ 1 1 bar 0 ] azimuth, while at low coverage a doubly-deprotonated dioxalate is formed with its molecular plane parallel to the surface. STM, LEED and SXPS show the dioxalate to form a (3 × 2) ordered phase with a coverage of 1/6 ML. O 1s PhD modulation spectra for the monooxalate phase are found to be simulated by a geometry in which the carboxylate O atoms occupy near-atop sites on nearest-neighbour surface Cu atoms in [ 1 1 bar 0 ] rows, with a Cusbnd O bondlength of 2.00 ± 0.04 Å. STM images of the (3 × 2) phase show some centred molecules attributed to adsorption on second-layer Cu atoms below missing [001] rows of surface Cu atoms, while DFT calculations show adsorption on a (3 × 2) missing row surface (with every third [001] Cu surface row removed) is favoured over adsorption on the unreconstructed surface. O 1s PhD data from dioxalate is best fitted by a structure similar to that found by DFT to have the lowest energy, although there are some significant differences in intramolecular bondlengths.

  5. Population reversal driven by unrestrained interactions in molecular dynamics simulations: A dialanine model

    Directory of Open Access Journals (Sweden)

    Filippo Pullara

    2015-10-01

    Full Text Available Standard Molecular Dynamics simulations (MD are usually performed under periodic boundary conditions using the well-established “Ewald summation”. This implies that the distance among each element in a given lattice cell and its corresponding element in another cell, as well as their relative orientations, are constant. Consequently, protein-protein interactions between proteins in different cells—important in many biological activities, such as protein cooperativity and physiological/pathological aggregation—are severely restricted, and features driven by protein-protein interactions are lost. The consequences of these restrictions, although conceptually understood and mentioned in the literature, have not been quantitatively studied before. The effect of protein-protein interactions on the free energy landscape of a model system, dialanine, is presented. This simple system features a free energy diagram with well-separated minima. It is found that, in the case of absence of peptide-peptide (p-p interactions, the ψ = 150° dihedral angle determines the most energetically favored conformation (global free-energy minimum. When strong p-p interactions are induced, the global minimum switches to the ψ = 0° conformation. This shows that the free-energy landscape of an individual molecule is dramatically affected by the presence of other freely interacting molecules of its same type. Results of the study suggest how taking into account p-p interactions in MD allows having a more realistic picture of system activity and functional conformations.

  6. Fundamental properties of molecules on surfaces. Molecular switching and interaction of magnetic molecules with superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hatter, Nino

    2016-12-14

    In this thesis, we investigate individual molecular switches and metal-organic complexes on surfaces with scanning tunneling microscopy (STM) and spectroscopy (STS) at low temperatures. One focus addresses the switching ability and mechanism of diarylethene on Ag(111). The other focus lies on resolving and tuning magnetic interactions of individual molecules with superconductors. 4,4'-(4,4'-(perfluorocyclopent-1-ene-1,2-diyl)bis (5-methylthiophene-4,2-diyl)dip yridine (PDTE) is a prototypical photochromic switch. We can induce a structural change of individual PDTE molecules on Ag(111) with the STM tip. This change is accompanied by a reduction of the energy gap between the occupied and unoccupied molecular orbitals. Density functional theory (DFT) calculations reveal that the induced switching corresponds to a ring-closing reaction from an open isomer in a flat adsorption configuration to a ring-closed isomer with its methyl groups in a cis configuration. The final product is thermodynamically stabilized by strong dispersion interactions with the surface. A linear dependence of the switching threshold with the tip-sample distance with a minimal threshold of 1.4 V is found, which we assign to a combination of an electric-field induced process and a tunneling-electron contribution. DFT calculations suggest a large activation barrier for a ring-closing reaction from the open flat configuration into the closed cis configuration. The interaction of magnetic molecules with superconductors is studied on manganese phthalocyanine (MnPc) adsorbed on Pb(111). We find triplets of Shiba states inside the superconducting gap. Different adsorption sites of MnPc provide a large variety of exchange coupling strengths, which lead to a collective energy shift of the Shiba triplets. We can assign the splitting of the Shiba states to be an effect of magnetic anisotropy in the system. A quantum phase transition from a ''Kondo screened'' to a &apos

  7. Murine transgenic embryonic stem cell lines for the investigation of sinoatrial node-related molecular pathways

    Directory of Open Access Journals (Sweden)

    Stefanie Schmitteckert

    2017-12-01

    Full Text Available The elucidation of molecular mechanisms that restrict the potential of pluripotent stem cells and promote cardiac lineage differentiation is of crucial relevance, since embryonic stem cells (ESCs hold great potential for cell based heart therapies. The homeodomain transcription factor Shox2 is essential for the development and proper function of the native cardiac pacemaker, the sinoatrial node. This prompted us to develop a cardiac differentiation model using ESC lines isolated from blastocysts of Shox2-deficient mice. The established cell model provides a fundamental basis for the investigation of molecular pathways under physiological and pathophysiological conditions for evaluating novel therapeutic approaches.

  8. Quasi- and inelastic neutron scattering to investigate the molecular dynamics of discotic molecules in the bulk

    Directory of Open Access Journals (Sweden)

    Krause Christina

    2015-01-01

    Full Text Available In- and quasielastic neutron scattering is employed to investigate both the vibrational density of states and the molecular dynamics of two homologous discotic liquid crystals (DLC with different length of the alkyl side chain based on a triphenylene derivate. For both compounds characteristic low frequency excess contributions to the vibrational density of states are found. Therefore it is concluded that these liquid crystals show a glass-like behaviour. Elastic scans further show that in these materials a rich molecular dynamics takes place.

  9. Molecular and Cellular Mechanisms of Sperm-Oocyte Interactions Opinions Relative to in Vitro Fertilization (IVF)

    Science.gov (United States)

    Anifandis, George; Messini, Christina; Dafopoulos, Konstantinos; Sotiriou, Sotiris; Messinis, Ioannis

    2014-01-01

    One of the biggest prerequisites for pregnancy is the fertilization step, where a human haploid spermatozoon interacts and penetrates one haploid oocyte in order to produce the diploid zygote. Although fertilization is defined by the presence of two pronuclei and the extraction of the second polar body the process itself requires preparation of both gametes for fertilization to take place at a specific time. These preparations include a number of consecutive biochemical and molecular events with the help of specific molecules and with the consequential interaction between the two gametes. These events take place at three different levels and in a precise order, where the moving spermatozoon penetrates (a) the outer vestments of the oocyte, known as the cumulus cell layer; (b) the zona pellucida (ZP); where exocytosis of the acrosome contents take place and (c) direct interaction of the spermatozoon with the plasma membrane of the oocyte, which involves a firm adhesion of the head of the spermatozoon with the oocyte plasma membrane that culminates with the fusion of both sperm and oocyte membranes (Part I). After the above interactions, a cascade of molecular signal transductions is initiated which results in oocyte activation. Soon after the entry of the first spermatozoon into the oocyte and oocyte activation, the oocyte’s coat (the ZP) and the oocyte’s plasma membrane seem to change quickly in order to initiate a fast block to a second spermatozoon (Part II). Sometimes, two spermatozoa fuse with one oocyte, an incidence of 1%–2%, resulting in polyploid fetuses that account for up to 10%–20% of spontaneously aborted human conceptuses. The present review aims to focus on the first part of the human sperm and oocyte interactions, emphasizing the latest molecular and cellular mechanisms controlling this process. PMID:25054321

  10. Molecular and Cellular Mechanisms of Sperm-Oocyte Interactions Opinions Relative to in Vitro Fertilization (IVF

    Directory of Open Access Journals (Sweden)

    George Anifandis

    2014-07-01

    Full Text Available One of the biggest prerequisites for pregnancy is the fertilization step, where a human haploid spermatozoon interacts and penetrates one haploid oocyte in order to produce the diploid zygote. Although fertilization is defined by the presence of two pronuclei and the extraction of the second polar body the process itself requires preparation of both gametes for fertilization to take place at a specific time. These preparations include a number of consecutive biochemical and molecular events with the help of specific molecules and with the consequential interaction between the two gametes. These events take place at three different levels and in a precise order, where the moving spermatozoon penetrates (a the outer vestments of the oocyte, known as the cumulus cell layer; (b the zona pellucida (ZP; where exocytosis of the acrosome contents take place and (c direct interaction of the spermatozoon with the plasma membrane of the oocyte, which involves a firm adhesion of the head of the spermatozoon with the oocyte plasma membrane that culminates with the fusion of both sperm and oocyte membranes (Part I. After the above interactions, a cascade of molecular signal transductions is initiated which results in oocyte activation. Soon after the entry of the first spermatozoon into the oocyte and oocyte activation, the oocyte’s coat (the ZP and the oocyte’s plasma membrane seem to change quickly in order to initiate a fast block to a second spermatozoon (Part II. Sometimes, two spermatozoa fuse with one oocyte, an incidence of 1%–2%, resulting in polyploid fetuses that account for up to 10%–20% of spontaneously aborted human conceptuses. The present review aims to focus on the first part of the human sperm and oocyte interactions, emphasizing the latest molecular and cellular mechanisms controlling this process.

  11. Study of the interaction between 8-azaguanine and bovine serum albumin using optical spectroscopy and molecular modeling methods.

    Science.gov (United States)

    Gong, Qiao-Ling; Hu, Xin-Gen; Fang, Guo-Yong; Li, Xin-Hua

    2012-02-01

    The interaction between 8-azaguanine (8-Azan) and bovine serum albumin (BSA) in Tris-HCl buffer solutions at pH 7.4 was investigated by means of fluorescence and ultraviolet-visible (UV-Vis) spectroscopy. At 298 K and 310 K, at a wavelength of excitation (λ (ex)) of 282 nm, the fluorescence intensity decreased significantly with increasing concentrations of 8-Azan. Fluorescence static quenching was observed for BSA, which was attributed to the formation of a complex between 8-Azan and BSA during the binding reaction. This was illuminated further by the UV-Vis absorption spectra and the decomposition of the fluorescence spectra. The thermodynamic parameters ∆G, ∆H, ∆S were calculated. The results showed that the forces acting between 8-Azan and BSA were typical hydrophobic forces, and that the interaction process was spontaneous. The interaction distance r between 8-Azan and BSA, evaluated according to fluorescence resonance energy transfer theory, suggested that there is a high possibility of energy transfer from BSA to 8-Azan. Theoretical investigations based on homology modeling and molecular docking suggested that binding between 8-Azan and BSA is dominated by hydrophilic forces and hydrogen bonding. The theoretical investigations provided a good structural basis to explain the phenomenon of fluorescence quenching between 8-Azan and BSA.

  12. Towards a molecular level understanding of the sulfanilamide-soil organic matter-interaction

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Ashour A., E-mail: ashour.ahmed@uni-rostock.de [University of Rostock, Institute of Physics, Albert-Einstein-Str. 23-24, D-18059 Rostock (Germany); Steinbeis GmbH & Co. KG für Technologietransfer, 70174 Stuttgart (Germany); University of Cairo, Faculty of Science, Department of Chemistry, 12613 Giza (Egypt); Thiele-Bruhn, Sören, E-mail: thiele@uni-trier.de [University of Trier, Soil Science, D-54286 Trier (Germany); Leinweber, Peter, E-mail: peter.leinweber@uni-rostock.de [Steinbeis GmbH & Co. KG für Technologietransfer, 70174 Stuttgart (Germany); University of Rostock, Soil Science, D-18051 Rostock (Germany); Kühn, Oliver, E-mail: oliver.kuehn@uni-rostock.de [University of Rostock, Institute of Physics, Albert-Einstein-Str. 23-24, D-18059 Rostock (Germany)

    2016-07-15

    Sorption experiments of sulfanilamide (SAA) on well-characterized samples of soil size-fractions were combined with the modeling of SAA-soil-interaction via quantum chemical calculations. Freundlich unit capacities were determined in batch experiments and it was found that they increase with the soil organic matter (SOM) content according to the order fine silt > medium silt > clay > whole soil > coarse silt > sand. The calculated binding energies for mass-spectrometrically quantified sorption sites followed the order ionic species > peptides > carbohydrates > phenols and lignin monomers > lignin dimers > heterocyclic compounds > fatty acids > sterols > aromatic compounds > lipids, alkanes, and alkenes. SAA forms H-bonds through its polar centers with the polar SOM sorption sites. In contrast dispersion and π-π-interactions predominate the interaction of the SAA aromatic ring with the non-polar moieties of SOM. Moreover, the dipole moment, partial atomic charges, and molecular volume of the SOM sorption sites are the main physical properties controlling the SAA-SOM-interaction. Further, reasonable estimates of the Freundlich unit capacities from the calculated binding energies have been established. Consequently, we suggest using this approach in forthcoming studies to disclose the interactions of a wide range of organic pollutants with SOM. - Highlights: • Experiment and theory showed that SAA obeys a site-specific sorption on soil surfaces. • SAA-SOM-interaction increases by increasing polarity of SOM sorption site. • H-bonds, dispersion, and π-π-interactions were observed for SAA-SOM-interaction. • Dipole moment and atomic charges of SOM sorption sites control SAA-SOM-interaction. • The Freundlich unit capacities were estimated from the calculated binding energies. • The current SOM model is flexible to describe interactions of SOM with other pollutants.

  13. SUDDEN UNEXPLAINED JUVENILE DEATH AND THE ROLE OF MEDICOLEGAL INVESTIGATION: UPDATE ON MOLECULAR AUTOPSY

    Directory of Open Access Journals (Sweden)

    Antonina Argo

    2012-04-01

    Full Text Available In the past few years, contributions of molecular biology assays to the investigation of sudden juvenile death have permitted to clarify some of the pathogenetic aspects of sudden arrhythmic death, opening the way to preventive action on victims’ relatives. We reviewed literature on the genetics of sudden juvenile death, and on molecular biology assays performed on autoptic samples. Biological investigation permits the detection of genetic mutations underlying the susceptibility to sudden cardiac death of individuals with rare inherited forms of arrhythmia (Long QT Syndrome, Brugada Syndrome, Lev’s disease etc. through the analysis of critical sequences codifying for ion channel subunits (HERG, KvLQT1, MinK, Mirp1, SCN5A, KCNQ1, KCNH2, KCNE1, KCNE2. The main objective of post-mortem investigation in sudden juvenile death is the detection of treatable monogenic inherited disorders, in order to prevent further deaths among the relatives of the deceased patient.

  14. A model for studying molecular plant-bacteria interactions in the flight experimet

    Science.gov (United States)

    Kovtunovych, G.; Lar, O.; Kovalchuk, M.; Negrutska, V.; Rogutski, I.; Kozyrovska, N.; Kordyum, V.

    The ability to grow plants in space self-perpetuating gardens is actual for providing an advanced life support system for humans during extended missions. Nevertheless, studies of molecular mechanisms of plant-bacteria interactions in the flight experiments are still in their infancy. Space factors affect cell microenvironment and signal transduction through membranes, and it may result in induction in bacteria of some genes regulated by the systems, sensing environmental signals. In space a risk of genetic rearrangements is increased, and some changes in bacterial DNA expected. As a consequence, bacteria may exhibit novel characters, e.g., pathogenicity. During the previous our experience we have determined an increase of internal colonisation of the rice roots with bacteria in space flight. It is important to characterise molecular-genetic plant-bacteria interactions influenced with physical factors. Genes coding for bacterial pectinases provide a suitable model for studies of well integrated objectives, concerning plant-bacteria interactions. From examining a mode of expression of pectinases encoding genes of a plant-associated bacterium and nucleotide polymorphism within pectate lyase- and polygalacturonase encoding genes in microcosm experiments in earth and space flight we get new knowledges about understanding some physical factors as the environmental signals and the possible risk of changes in interactions of bacteria with the plant.

  15. Advances on plant-pathogen interactions from molecular toward systems biology perspectives.

    Science.gov (United States)

    Peyraud, Rémi; Dubiella, Ullrich; Barbacci, Adelin; Genin, Stéphane; Raffaele, Sylvain; Roby, Dominique

    2017-05-01

    In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant-pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant-pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant-pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

  16. Molecular investigations of a locally acquired case of melioidosis in Southern AZ, USA.

    Directory of Open Access Journals (Sweden)

    David M Engelthaler

    2011-10-01

    Full Text Available Melioidosis is caused by Burkholderia pseudomallei, a Gram-negative bacillus, primarily found in soils in Southeast Asia and northern Australia. A recent case of melioidosis in non-endemic Arizona was determined to be the result of locally acquired infection, as the patient had no travel history to endemic regions and no previous history of disease. Diagnosis of the case was confirmed through multiple microbiologic and molecular techniques. To enhance the epidemiological analysis, we conducted several molecular genotyping procedures, including multi-locus sequence typing, SNP-profiling, and whole genome sequence typing. Each technique has different molecular epidemiologic advantages, all of which provided evidence that the infecting strain was most similar to those found in Southeast Asia, possibly originating in, or around, Malaysia. Advancements in new typing technologies provide genotyping resolution not previously available to public health investigators, allowing for more accurate source identification.

  17. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    Science.gov (United States)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  18. Spectroscopic analysis of 8-hydroxyquinoline derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Sureshkumar, B.; Mary, Y. Sheena; Resmi, K. S.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Narayana, B.; Suma, S.

    2018-03-01

    Two 8-hydroxyquinoline derivatives, 5,7-dichloro-8-hydroxyquinoline (57DC8HQ) and 5-chloro-7-iodo-8-hydroxy quinoline (5CL7I8HQ) have been investigated in details by means of spectroscopic characterization and computational molecular modelling techniques. FT-IR and FT-Raman experimental spectroscopic approaches have been utilized in order to obtain detailed spectroscopic signatures of title compounds, while DFT calculations have been used in order to visualize and assign vibrations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the title molecules exhibit NLO properties. The evaluated HOMO and LUMO energies demonstrate the chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyperconjugative interactions and charge delocalization. DFT calculations have been also used jointly with MD simulations in order to investigate in details global and local reactivity properties of title compounds. Also, molecular docking has been also used in order to investigate affinity of title compounds against decarboxylase inhibitor and quinoline derivatives can be a lead compounds for developing new antiparkinsonian drug.

  19. Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

    Directory of Open Access Journals (Sweden)

    Cusick Michael E

    2007-10-01

    Full Text Available Abstract Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. Results The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. Conclusion The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.

  20. Separation and characterization of resins and asphaltenes coming from Castilla crude Evaluation of their molecular interaction

    International Nuclear Information System (INIS)

    Navarro, Lina; Alvarez, Mario; Grosso, Jorge Luis; Navarro, Uriel

    2004-01-01

    The study of resins and asphaltenes, the heaviest fractions of oil, has become an area of interest due to the abundance of heavy crude oils in Colombia and Latin America. We studied the chemical composition of the heavy fractions of Castilla crude oil, evaluated some of its molecular parameters and found evidence of the interaction between the resins extracted from the crude with the asphaltenes of the original crude. With this objective, we carried out at the pilot plant level precipitation of the resin-asphaltene (R-A) aggregate by adding and mixing under controlled conditions, a paraffin solvent, from the Apiay refinery, called Apiasol. By extracting Soxhlet with the same solvent, resin 1 of aggregate R-A was separated. Resin ll defined as the soluble fraction that is part of the maltenes, was separated from the deasphalted crude by open column chromatography, using alumina as support, according to the SAR method (Saturated, Aromatics, Resins). The fractions of resins and the asphaltenes obtained, were characterized by: Nuclear Magnetic Resonance (NMR), FT-lR, DRX, elementary analysis (C, H, N, S), metal content (Ni and V), distribution of molecular weight by GPC, and average molecular weight by VPO. The results obtained show evidence that resin l which is part of the aggregate has less average molecular weight than resin ll which is present in the fraction of maltenes. In addition, some changes were found in the elementary analysis of among the resins. On the one hand, and taking into account the existing theories of molecular interactions among these fractions, it was found that the resins l separated from the R-A aggregate, when added to the crude, they stabilize their asphaltenes. This evaluation was carried out by analyzing the flocculation point of the crude and its mixtures with 1,9% and 3,8% of resin l, when they are titrated with a precipitating agent in an NIR cell that works with high pressure and temperature

  1. Multi-spectroscopic investigation of the binding interaction of fosfomycin with bovine serum albumin

    Directory of Open Access Journals (Sweden)

    Manjunath D. Meti

    2015-08-01

    Full Text Available The interaction between fosfomycin (FOS and bovine serum albumin (BSA has been investigated effectively by multi-spectroscopic techniques under physiological pH 7.4. FOS quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites n and observed binding constant KA were measured by the fluorescence quenching method. The thermodynamic parameters ΔG0, ΔH0 and ΔS0 were calculated at different temperatures according to the van’t Hoff equation. The site of binding of FOS in the protein was proposed to be Sudlow’s site I based on displacement experiments using site markers viz. warfarin, ibuprofen and digitoxin. The distance r between the donor (BSA and acceptor (FOS molecules was obtained according to the Förster theory. The effect of FOS on the conformation of BSA was analyzed using synchronous fluorescence spectra (SFS, circular dichroism (CD and 3D fluorescence spectra. A molecular modeling study further confirmed the binding mode obtained by the experimental studies. Keywords: Fosfomycin, Serum albumin, Spectroscopic methods, Synchronous fluorescence, 3D spectra

  2. Investigation of the molecular conformations of ethanol using electron momentum spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ning, C G; Luo, Z H; Huang, Y R; Liu, K; Zhang, S F; Deng, J K [Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084 (China); Hajgato, B; Morini, F; Deleuze, M S [Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek (Belgium)], E-mail: ningcg@tsinghua.edu.cn, E-mail: djk-dmp@tsinghua.edu.cn, E-mail: michael.deleuze@uhasselt.be

    2008-09-14

    The valence electronic structure and momentum-space electron density distributions of ethanol have been investigated with our newly constructed high-resolution electron momentum spectrometer. The measurements are compared to thermally averaged simulations based on Kohn-Sham (B3LYP) orbital densities as well as one-particle Green's function calculations of ionization spectra and Dyson orbital densities, assuming Boltzmann's statistical distribution of the molecular structure over the two energy minima defining the anti and gauche conformers. One-electron ionization energies and momentum distributions in the outer-valence region were found to be highly dependent upon the molecular conformation. Calculated momentum distributions indeed very sensitively reflect the distortions and topological changes that molecular orbitals undergo due to the internal rotation of the hydroxyl group, and thereby exhibit variations which can be traced experimentally. The B3LYP model Kohn-Sham orbital densities are overall in good agreement with the experimental distributions, and closely resemble benchmark ADC(3) Dyson orbital densities. Both approaches fail to quantitatively reproduce the experimental momentum distributions characterizing the highest occupied molecular orbital. Since electron momentum spectroscopy measurements at various electron impact energies indicate that the plane wave impulse approximation is valid, this discrepancy between theory and experiment is tentatively ascribed to thermal disorder, i.e. large-amplitude and thermally induced dynamical distortions of the molecular structure in the gas phase.

  3. Investigation of coherent molecular resonances in quantum dot–metallic nanoparticle systems using their spontaneous emission

    International Nuclear Information System (INIS)

    Sadeghi, S.M.; Patty, K.D.

    2014-01-01

    In the presence of metallic nanoparticles the nature of the optical excitations (pumping) of semiconductor quantum dots can be determined by their molecular states and resonances formed via coherent coupling of excitons and plasmons. We show that the spontaneous emission of such quantum dots can provide key information regarding formation and characteristics of such molecular properties. This includes an ultra-fast switching process associated with optical transition between the molecular states of the quantum dot-metallic nanoparticle system or its plasmonic meta-resonance when the intensity of the laser field responsible for the exciton–plasmon coupling reaches a critical value. We also show that by varying the intensity of this laser, the spontaneous emission exhibits characteristic features indicating tunability of the molecular resonances and excitation-power dependence of plasmonic fields of the metallic nanoparticles. - Highlights: • Investigation of collective molecular properties of quantum dot-metallic nanoparticle systems. • Impact of such collective properties on the optical excitation of quantum dots. • Effects of exciton–plasmon coupling in the spontaneous emission of the quantum dots. • Signatures of plasmonic meta-resonances in the fluorescence of quantum dots

  4. Investigation of Nascent Base Pair and Polymerase Behavior in the Presence of Mismatches in DNA Polymerase I Using Molecular Dynamics.

    Science.gov (United States)

    Yeager, Andrew; Humphries, Kathryn; Farmer, Ellen; Cline, Gene; Miller, Bill R

    2018-02-26

    Optimizing DNA polymerases for a broad range of tasks requires an understanding of the factors influencing polymerase fidelity, but many details of polymerase behavior remain unknown, especially in the presence of mismatched nascent base pairs. Using molecular dynamics, the large fragment of Bacillus stearothermophilus DNA polymerase I is simulated in the presence of all 16 possible standard nucleoside triphosphate-template (dNTP-dN) pairs, including four Watson-Crick pairs and 12 mismatches. The precatalytic steps of nucleotide addition from nucleotide insertion to immediately preceding catalysis are explored using three starting structures representing different stages of nucleotide addition. From these simulations, interactions between dNTPs and the DNA-protein complex formed by the polymerase are elucidated. Patterns of large-scale conformational shifts, classification of nucleotide pairs based on composition, and investigation of the roles of residues interacting with dNTPs are completed on 50+ μs of simulation. The role of molecular dynamics in studies of polymerase behavior is discussed.

  5. Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer.

    Science.gov (United States)

    Latysheva, Natasha S; Oates, Matt E; Maddox, Louis; Flock, Tilman; Gough, Julian; Buljan, Marija; Weatheritt, Robert J; Babu, M Madan

    2016-08-18

    Gene fusions are common cancer-causing mutations, but the molecular principles by which fusion protein products affect interaction networks and cause disease are not well understood. Here, we perform an integrative analysis of the structural, interactomic, and regulatory properties of thousands of putative fusion proteins. We demonstrate that genes that form fusions (i.e., parent genes) tend to be highly connected hub genes, whose protein products are enriched in structured and disordered interaction-mediating features. Fusion often results in the loss of these parental features and the depletion of regulatory sites such as post-translational modifications. Fusion products disproportionately connect proteins that did not previously interact in the protein interaction network. In this manner, fusion products can escape cellular regulation and constitutively rewire protein interaction networks. We suggest that the deregulation of central, interaction-prone proteins may represent a widespread mechanism by which fusion proteins alter the topology of cellular signaling pathways and promote cancer. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  6. The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel.

    Directory of Open Access Journals (Sweden)

    Samira Yazdi

    2016-01-01

    Full Text Available Voltage-gated potassium (KV channels are membrane proteins that respond to changes in membrane potential by enabling K+ ion flux across the membrane. Polyunsaturated fatty acids (PUFAs induce channel opening by modulating the voltage-sensitivity, which can provide effective treatment against refractory epilepsy by means of a ketogenic diet. While PUFAs have been reported to influence the gating mechanism by electrostatic interactions to the voltage-sensor domain (VSD, the exact PUFA-protein interactions are still elusive. In this study, we report on the interactions between the Shaker KV channel in open and closed states and a PUFA-enriched lipid bilayer using microsecond molecular dynamics simulations. We determined a putative PUFA binding site in the open state of the channel located at the protein-lipid interface in the vicinity of the extracellular halves of the S3 and S4 helices of the VSD. In particular, the lipophilic PUFA tail covered a wide range of non-specific hydrophobic interactions in the hydrophobic central core of the protein-lipid interface, while the carboxylic head group displayed more specific interactions to polar/charged residues at the extracellular regions of the S3 and S4 helices, encompassing the S3-S4 linker. Moreover, by studying the interactions between saturated fatty acids (SFA and the Shaker KV channel, our study confirmed an increased conformational flexibility in the polyunsaturated carbon tails compared to saturated carbon chains, which may explain the specificity of PUFA action on channel proteins.

  7. MOLECULAR DYNAMICS STUDY OF INTERACTIONS OF POLYMYXIN B3 AND ITS ALA-MUTANTS WITH LIPOPOLYSACCHARIDE

    Directory of Open Access Journals (Sweden)

    Lisnyak Yu. V.

    2015-12-01

    Full Text Available Introduction. Emergence of nosocomial bacterial pathogens (especially Gram-negative bacteria with multiple resistance against almost all available antibiotics is a growing medical problem. No novel drugs targeting multidrug-resistant Gram-negative bacteria have been developed in recent years. In this context, there has been greatly renewed interest to cyclic lipodecapeptides polymyxins. Polymyxins exhibit rapid bactericidal activity, they are specific and highly potent against Gramnegative bacteria, but have potential nephrotoxic side effects. So polymyxins are attractive lead compounds to develop analogues with improved microbiological, pharmacological and toxicological properties. A detailed knowledge of the molecular mechanisms of polymyxin interactions with its cell targets is a prerequisite for the purposeful improvement of its therapeutic properties. The primary cell target of a polymyxin is a lipopolysaccharide (LPS in the outer membrane of Gram-negative bacteria. The binding site of polymyxin on LPS has been supposed to be Kdo2-lipid A fragment. Methods. For all molecular modeling and molecular dynamics simulation experiments the YASARA suite of programs was used. Complex of antimicrobial peptide polymyxin В3 (PmB3 with Kdo2-lipid A portion of E. coli lipopolysaccharide was constructed by rigid docking with flexible side chains of the peptide. By alanine scanning of polymyxin В3 bound to LPS followed by simulated annealing minimization of the complexes in explicit water environment, the molecular aspects of PmB3-LPS binding have been studied by 20 ns molecular dynamics simulations at 298 K and pH 7.0. The AMBER03 force field was used with a 1.05 nm force cutoff. To treat long range electrostatic interactions the Particle Mesh Ewald algorithm was used. Results. Ala-mutations of polymyxin’s residues Dab1, Dab3, Dab5, Dab8 and Dab9 in the PmB3-LPS complex caused sustained structural changes resulting in the notable loss in stability of

  8. Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole

    Science.gov (United States)

    Sheena Mary, Y.; Al-Shehri, Mona M.; Jalaja, K.; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Temiz-Arpaci, Ozlem; Van Alsenoy, C.

    2017-04-01

    Antimicrobial active 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole (NATPB) was synthesized and observed IR, Raman bands are compared with the theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number splits into a doublet with a noted difference and is red shifted from the computed value, which indicates the weakening of NH bond resulting in proton transfer to the neighbouring oxygen atom. The HOMO-LUMO plots reveal the charge transfer in the molecular system through the conjugated paths. The electrophilic and nucleophilic reactive sites are identified from the MEP plot. Mapping of average local ionization energy (ALIE) values to the electron density surface served us as a tool for prediction of molecule sites possibly prone to electrophilic attacks. Other important reactive centres of the title molecule were detected by calculations of Fukui functions. Calculations of bond dissociation energies (BDE) for hydrogen abstraction were used in order to assess whether the NATPB molecules is prone to autoxidation mechanism or not, while BDE of the remaining single acyclic bonds were used in order to determine the weakest bond. Interaction properties with water were investigated by molecular dynamics (MD) simulations and calculations of radial distribution functions (RDFs). The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations (MICs) ranging between 32 and 128 μg/ml. The compound exhibited significant antibacterial activity (32 μg/ml) against an antibiotic resistant E. faecalis isolate, at same potency with the compared standard drugs vancomycin and gentamycin sulfate. The molecular docking studies show that the compound might exhibit inhibitory activity against CDK inhibitors.

  9. Exploring molecular and spin interactions of Tellurium adatom in reduced graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Alegaonkar, Ashwini [Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411 007, MS (India); Alegaonkar, Prashant [Department of Applied Physics, Defence Institute of Advance Technology, Girinagar, Pune, 411 025, MS (India); Pardeshi, Satish, E-mail: skpar@chem.unipune.ac.in [Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411 007, MS (India)

    2017-07-01

    The transport of spin information fundamentally requires favourable molecular architecture and tunable spin moments to make the medium pertinent for spintronic. We report on achieving coherent molecular-spin parameters for rGO due to Tellurium (Te) adatom. Initially, GO prepared using graphite, was modified into rGO by in situ incorporation of 1 (w/w)% of Te. Both the systems were subjected to ESCA, FTIR, Raman dispersion, ESR spectroscopy, and electron microscopy. Analysis revealed that, Te substantially reacted with epoxides, carbonyl, and carboxylate groups that improved C-to-O ratio by twice. However, the spin splitting character, between Te and C, seems to be quenched. Moreover, Te altered the dynamical force constant between C-C and C=C that generated the mechanical stress within rGO network. The layer conjugation, nature of folding, symmetry, and electronic states of the edges were also affected by precipitation and entrapment of Te. The calculated dynamic molecular Raman and ESR spin parameters indicated that, Te acted as a bridging element for long range spin transport. This is particularly due to, the p-orbital moments of Te contributing, vectorially, to spin relaxation process operative at broken inversion symmetry sites. Our study suggests that, facile addition of Te in rGO is useful to achieve favourable spintronic properties. - Highlights: • Spin interactions and molecular dynamics modification due to Tellurium adatom in rGO. • Molecular level manipulation of Tellurium adatom for favourable spintronic properties. • Bychocov-Rashaba coupling are the operative channels in rGO. • Extrinsic coupling component get added vectorially by Tellurium. • Te-rGO is a viable medium for molecular spintronics.

  10. Interactions of Borneol with DPPC Phospholipid Membranes: A Molecular Dynamics Simulation Study

    Directory of Open Access Journals (Sweden)

    Qianqian Yin

    2014-11-01

    Full Text Available Borneol, known as a “guide” drug in traditional Chinese medicine, is widely used as a natural penetration enhancer in modern clinical applications. Despite a large number of experimental studies on borneol’s penetration enhancing effect, the molecular basis of its action on bio-membranes is still unclear. We carried out a series of coarse-grained molecular dynamics simulations with the borneol concentration ranging from 3.31% to 54.59% (v/v, lipid-free basis to study the interactions of borneol with aDPPC(1,2-dipalmitoylsn-glycero-3-phosphatidylcholine bilayer membrane, and the temperature effects were also considered. At concentrations below 21.89%, borneol’s presence only caused DPPC bilayer thinning and an increase in fluidity; A rise in temperature could promote the diffusing progress of borneol. When the concentration was 21.89% or above, inverted micelle-like structures were formed within the bilayer interior, which led to increased bilayer thickness, and an optimum temperature was found for the interaction of borneol with the DPPC bilayer membrane. These findings revealed that the choice of optimal concentration and temperature is critical for a given application in which borneol is used as a penetration enhancer. Our results not only clarify some molecular basis for borneol’s penetration enhancing effects, but also provide some guidance for the development and applications of new preparations containing borneol.

  11. Pressure Enhancement in Confined Fluids: Effect of Molecular Shape and Fluid-Wall Interactions.

    Science.gov (United States)

    Srivastava, Deepti; Santiso, Erik E; Gubbins, Keith E

    2017-10-24

    Recently, several experimental and simulation studies have found that phenomena that normally occur at extremely high pressures in a bulk phase can occur in nanophases confined within porous materials at much lower bulk phase pressures, thus providing an alternative route to study high-pressure phenomena. In this work, we examine the effect on the tangential pressure of varying the molecular shape, strength of the fluid-wall interactions, and pore width, for carbon slit-shaped pores. We find that, for multisite molecules, the presence of additional rotational degrees of freedom leads to unique changes in the shape of the tangential pressure profile, especially in larger pores. We show that, due to the direct relationship between the molecular density and the fluid-wall interactions, the latter have a large impact on the pressure tensor. The molecular shape and pore size have a notable impact on the layering of molecules in the pore, greatly influencing both the shape and scale of the tangential pressure profile.

  12. Molecular identification of blow flies recovered from human cadavers during crime scene investigations in Malaysia.

    Science.gov (United States)

    Kavitha, Rajagopal; Nazni, Wasi Ahmad; Tan, Tian Chye; Lee, Han Lim; Isa, Mohd Noor Mat; Azirun, Mohd Sofian

    2012-12-01

    Forensic entomology applies knowledge about insects associated with decedent in crime scene investigation. It is possible to calculate a minimum postmortem interval (PMI) by determining the age and species of the oldest blow fly larvae feeding on decedent. This study was conducted in Malaysia to identify maggot specimens collected during crime scene investigations. The usefulness of the molecular and morphological approach in species identifications was evaluated in 10 morphologically identified blow fly larvae sampled from 10 different crime scenes in Malaysia. The molecular identification method involved the sequencing of a total length of 2.2 kilo base pairs encompassing the 'barcode' fragments of the mitochondrial cytochrome oxidase I (COI), cytochrome oxidase II (COII) and t-RNA leucine genes. Phylogenetic analyses confirmed the presence of Chrysomya megacephala, Chrysomya rufifacies and Chrysomya nigripes. In addition, one unidentified blow fly species was found based on phylogenetic tree analysis.

  13. Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

    Science.gov (United States)

    Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

    2018-03-13

    Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

  14. Characterizing the binding interaction between antimalarial artemether (AMT) and bovine serum albumin (BSA): Spectroscopic and molecular docking methods.

    Science.gov (United States)

    Shi, Jie-Hua; Pan, Dong-Qi; Wang, Xiou-Xiou; Liu, Ting-Ting; Jiang, Min; Wang, Qi

    2016-09-01

    Artemether (AMT), a peroxide sesquiterpenoides, has been widely used as an antimalarial for the treatment of multiple drug-resistant strains of plasmodium falciparum malaria. In this work, the binding interaction of AMT with bovine serum albumin (BSA) under the imitated physiological conditions (pH7.4) was investigated by UV spectroscopy, fluorescence emission spectroscopy, synchronous fluorescence spectroscopy, Fourier transform infrared spectroscopy (FT-IR), circular dichroism (CD), three-dimensional fluorescence spectroscopy and molecular docking methods. The experimental results indicated that there was a change in UV absorption of BSA along with a slight red shift of absorption wavelength, indicating that the interaction of AMT with BSA occurred. The intrinsic fluorescence of BSA was quenched by AMT due to the formation of AMT-BSA complex. The number of binding sites (n) and binding constant of AMT-BSA complex were about 1 and 2.63×10(3)M(-1) at 298K, respectively, suggesting that there was stronger binding interaction of AMT with BSA. Based on the analysis of the signs and magnitudes of the free energy change (ΔG(0)), enthalpic change (ΔH(0)) and entropic change (ΔS(0)) in the binding process, it can be concluded that the binding of AMT with BSA was enthalpy-driven process due to |ΔH°|>|TΔS°|. The results of experiment and molecular docking confirmed the main interaction forces between AMT and BSA were van der Waals force. And, there was a slight change in the BSA conformation after binding AMT but BSA still retains its secondary structure α-helicity. However, it had been confirmed that AMT binds on the interface between sub-domain IIA and IIB of BSA. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Interaction of anticancer drug clofarabine with human serum albumin and human α-1 acid glycoprotein. Spectroscopic and molecular docking approach.

    Science.gov (United States)

    Ajmal, Mohammad Rehan; Nusrat, Saima; Alam, Parvez; Zaidi, Nida; Khan, Mohsin Vahid; Zaman, Masihuz; Shahein, Yasser E; Mahmoud, Mohamed H; Badr, Gamal; Khan, Rizwan Hasan

    2017-02-20

    The binding interaction between clofarabine, an important anticancer drug and two important carrier proteins found abundantly in human plasma, Human Serum Albumin (HSA) and α-1 acid glycoprotein (AAG) was investigated by spectroscopic and molecular modeling methods. The results obtained from fluorescence quenching experiments demonstrated that the fluorescence intensity of HSA and AAG is quenched by clofarabine and the static mode of fluorescence quenching is operative. UV-vis spectroscopy deciphered the formation of ground state complex between anticancer drug and the two studied proteins. Clofarabine was found to bind at 298K with both AAG and HSA with the binding constant of 8.128×10 3 and 4.120×10 3 for AAG and HSA, respectively. There is stronger interaction of clofarabine with AAG as compared to HSA. The Gibbs free energy change was found to be negative for the interaction of clofarabine with AAG and HSA indicating that the binding process is spontaneous. Binding of clofarabine with HSA and AAG induced ordered structures in both proteins and lead to molecular compaction. Clofarabine binds to HSA near to drug site II. Hydrogen bonding and hydrophobic interactions were the main bonding forces between HSA-clofarabine and AAG-clofarabine as revealed by docking results. This study suggests the importance of binding of anticancer drug to AAG spatially in the diseases like cancers where the plasma concentration of AAG increases many folds. Design of drug dosage can be adjusted accordingly to achieve optimal treatment outcome. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Building KCNQ1/KCNE1 channel models and probing their interactions by molecular-dynamics simulations.

    Science.gov (United States)

    Xu, Yu; Wang, Yuhong; Meng, Xuan-Yu; Zhang, Mei; Jiang, Min; Cui, Meng; Tseng, Gea-Ny

    2013-12-03

    The slow delayed rectifier (I(KS)) channel is composed of KCNQ1 (pore-forming) and KCNE1 (auxiliary) subunits, and functions as a repolarization reserve in the human heart. Design of I(KS)-targeting anti-arrhythmic drugs requires detailed three-dimensional structures of the KCNQ1/KCNE1 complex, a task made possible by Kv channel crystal structures (templates for KCNQ1 homology-modeling) and KCNE1 NMR structures. Our goal was to build KCNQ1/KCNE1 models and extract mechanistic information about their interactions by molecular-dynamics simulations in an explicit lipid/solvent environment. We validated our models by confirming two sets of model-generated predictions that were independent from the spatial restraints used in model-building. Detailed analysis of the molecular-dynamics trajectories revealed previously unrecognized KCNQ1/KCNE1 interactions, whose relevance in I(KS) channel function was confirmed by voltage-clamp experiments. Our models and analyses suggest three mechanisms by which KCNE1 slows KCNQ1 activation: by promoting S6 bending at the Pro hinge that closes the activation gate; by promoting a downward movement of gating charge on S4; and by establishing a network of electrostatic interactions with KCNQ1 on the extracellular surface that stabilizes the channel in a pre-open activated state. Our data also suggest how KCNE1 may affect the KCNQ1 pore conductance. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Study on the interaction of tussilagone with human serum albumin (HSA) by spectroscopic and molecular docking techniques

    Science.gov (United States)

    Xu, Liang; Hu, Yan-Xi; Li, Yan-Cheng; Zhang, Li; Ai, Hai-Xin; Liu, Hong-Sheng; Liu, Yu-Feng; Sang, Yu-Li

    2017-12-01

    Tussilagone is a sesquiterpenoid which exhibits a variety of pharmacological activities. The interaction of tussilagone with human serum albumin (HSA) was investigated using fluorescence spectroscopy, UV-vis absorption, fluorescence probe experiments, synchronous fluorescence, circular dichroism (CD) spectra, three-dimensional spectra and molecular docking techniques under simulative physiological conditions. The results clarified that the fluorescence quenching of HSA by tussilagone was a static quenching process as a result of HSA-tussilagone (1:1) complex. Tussilagone spontaneously bound to HSA in site I (subdomain IIA), which was primarily driven by hydrophobic forces and hydrogen bonds (ΔH° = -13.89 kJ mol-1, ΔS° = 16.39 J mol-1 K-1). The binding constant was calculated to be 2.182 × 103 L mol-1 and the binding distance was estimated to be 2.07 nm at 291 K, showing the occurrence of fluorescence energy transfer. The results of CD, synchronous and three-dimensional fluorescence spectra all revealed that tussilagone induced the conformational changes of HSA. Meanwhile, the study of molecular docking also indicated that tussilagone could bind to the site I of HSA mainly by hydrophobic and hydrogen bond interactions.

  18. Synthesis and structure of interaction products of quinoline-2(1H)-thione with molecular iodine.

    Science.gov (United States)

    Chernov'yants, Margarita S; Starikova, Zoya A; Kolesnikova, Tatiana S; Karginova, Anastasia O; Lyanguzov, Nikolay V

    2015-03-15

    The behavior of quinoline-2(1H)-thione, which is a potential antithyroid drug toward molecular iodine, was investigated. The ability of quinoline-2(1H)-thione to form the outer-sphere charge-transfer complex C9H7NS·I2 with iodine molecular in dilute chloroform solution has been studied by UV-vis spectroscopy (lgβ=3.85). The crystal structure of the new salt 2-(quinoline-2-yldisulfanyl)quinolinium triiodide - product of irreversible oxidation of quinoline-2(1H)-thione was determined by X-ray diffraction. The 2-(quinoline-2-yldisulfanyl)quinolinium cations form dimers through π-π-stacking interaction between quinoline rings. Strong intramolecular interactions are observed between iodine - sulfur atoms and iodine - hydrogen atoms with shortened contacts (less of sum of van der Waals contacts). It is noteworthy that two perfectly centrosymmetrical anions I3(-) form a very short contact I(3)⋯I(3') 3.7550(5) so we can state the formation of the dianion I(6)(2-). Therefore the formation and topology of polyiodide species depend on the characteristics, such as shape, size and charge, etc., of the counter cation, 2-(quinoline-2-yldisulfanyl)quinolinium, which is considered as templating agent. Copyright © 2015. Published by Elsevier B.V.

  19. In vitro assays of molecular motors--impact of motor-surface interactions.

    Science.gov (United States)

    Mansson, Alf; Balaz, Martina; Albet-Torres, Nuria; Rosengren, K Johan

    2008-05-01

    In many types of biophysical studies of both single molecules and ensembles of molecular motors the motors are adsorbed to artificial surfaces. Some of the most important assay systems of this type (in vitro motility assays and related single molecule techniques) will be briefly described together with an account of breakthroughs in the understanding of actomyosin function that have resulted from their use. A poorly characterized, but potentially important, entity in these studies is the mechanism of motor adsorption to surfaces and the effects of motor surface interactions on experimental results. A better understanding of these phenomena is also important for the development of commercially viable nanotechnological applications powered by molecular motors. Here, we will consider several aspects of motor surface interactions with a particular focus on heavy meromyosin (HMM) from skeletal muscle. These aspects will be related to heavy meromyosin structure and relevant parts of the vast literature on protein-surface interactions for non-motor proteins. An overview of methods for studying motor-surface interactions will also be given. The information is used as a basis for further development of a model for HMM-surface interactions and is discussed in relation to experiments where nanopatterning has been employed for in vitro reconstruction of actomyosin order. The challenges and potentials of this approach in biophysical studies, compared to the use of self-assembly of biological components into supramolecular protein aggregates (e.g. myosin filaments) will be considered. Finally, this review will consider the implications for further developments of motor-powered lab-on-a-chip devices.

  20. Interaction of C2H with molecular hydrogen: Ab initio potential energy surface and scattering calculations

    Science.gov (United States)

    Dagdigian, Paul J.

    2018-01-01

    The potential energy surface (PES) describing the interaction of the ethynyl (C2H) radical in its ground X˜ 2Σ+ electronic state with molecular hydrogen has been computed through restricted coupled cluster calculations including single, double, and (perturbative) triple excitations [RCCSD(T)], with the assumption of fixed molecular geometries. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants. A representative set of energy dependent state-to-state cross sections is presented and discussed. The PES and cross sections for collisions of H2(j = 0) are compared with a previous study [F. Najar et al., Chem. Phys. Lett. 614, 251 (2014)] of collisions of C2H with H2 treated as a spherical collision partner. Good agreement is found between the two sets of calculations when the H2 molecule in the present calculation is spherically averaged.

  1. Molecular interactions between general anesthetics and the 5HT2B receptor.

    Science.gov (United States)

    Matsunaga, Felipe; Gao, Lu; Huang, Xi-Ping; Saven, Jeffery G; Roth, Bryan L; Liu, Renyu

    2015-01-01

    Serotonin modulates many processes through a family of seven serotonin receptors. However, no studies have screened for interactions between general anesthetics currently in clinical use and serotonergic G-protein-coupled receptors (GPCRs). Given that both intravenous and inhalational anesthetics have been shown to target other classes of GPCRs, we hypothesized that general anesthetics might interact directly with some serotonin receptors and thus modify their function. Radioligand binding assays were performed to screen serotonin receptors for interactions with propofol and isoflurane as well as for affinity determinations. Docking calculations using the crystal structure of 5-HT2B were performed to computationally confirm the binding assay results and locate anesthetic binding sites. The 5-HT2B class of receptors interacted significantly with both propofol and isoflurane in the primary screen. The affinities for isoflurane and propofol were determined to be 7.78 and .95 μM, respectively, which were at or below the clinical concentrations for both anesthetics. The estimated free energy derived from docking calculations for propofol (-6.70 kcal/mol) and isoflurane (-5.10 kcal/mol) correlated with affinities from the binding assay. The anesthetics were predicted to dock at a pharmacologically relevant binding site of 5HT2B. The molecular interactions between propofol and isoflurane with the 5-HT2B class of receptors were discovered and characterized. This finding implicates the serotonergic GPCRs as potential anesthetic targets.

  2. Molecular determinants of the interaction between Doa1 and Hse1 involved in endosomal sorting.

    Science.gov (United States)

    Han, Seungsu; Shin, Donghyuk; Choi, Hoon; Lee, Sangho

    2014-03-28

    Yeast Doa1/Ufd3 is an adaptor protein for Cdc48 (p97 in mammal), an AAA type ATPase associated with endoplasmic reticulum-associated protein degradation pathway and endosomal sorting into multivesicular bodies. Doa1 functions in the endosomal sorting by its association with Hse1, a component of endosomal sorting complex required for transport (ESCRT) system. The association of Doa1 with Hse1 was previously reported to be mediated between PFU domain of Doa1 and SH3 of Hse1. However, it remains unclear which residues are specifically involved in the interaction. Here we report that Doa1/PFU interacts with Hse1/SH3 with a moderate affinity of 5 μM. Asn-438 of Doa1/PFU and Trp-254 of Hse1/SH3 are found to be critical in the interaction while Phe-434, implicated in ubiquitin binding via a hydrophobic interaction, is not. Small-angle X-ray scattering measurements combined with molecular docking and biochemical analysis yield the solution structure of the Doa1/PFU:Hse1/SH3 complex. Taken together, our results suggest that hydrogen bonding is a major determinant in the interaction of Doa1/PFU with Hse1/SH3. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Source-sink interaction: a century old concept under the light of modern molecular systems biology.

    Science.gov (United States)

    Chang, Tian-Gen; Zhu, Xin-Guang; Raines, Christine

    2017-07-20

    Many approaches to engineer source strength have been proposed to enhance crop yield potential. However, a well-co-ordinated source-sink relationship is required finally to realize the promised increase in crop yield potential in the farmer's field. Source-sink interaction has been intensively studied for decades, and a vast amount of knowledge about the interaction in different crops and under different environments has been accumulated. In this review, we first introduce the basic concepts of source, sink and their interactions, then summarize current understanding of how source and sink can be manipulated through both environmental control and genetic manipulations. We show that the source-sink interaction underlies the diverse responses of crops to the same perturbations and argue that development of a molecular systems model of source-sink interaction is required towards a rational manipulation of the source-sink relationship for increased yield. We finally discuss both bottom-up and top-down routes to develop such a model and emphasize that a community effort is needed for development of this model. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  4. Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction.

    Science.gov (United States)

    Harrison, Ellie; Hall, James P J; Paterson, Steve; Spiers, Andrew J; Brockhurst, Michael A

    2017-05-01

    Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities, bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here, we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage, SBW25φ2, and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions. © 2017 John Wiley & Sons Ltd.

  5. Towards a molecular level understanding of the sulfanilamide-soil organic matter-interaction.

    Science.gov (United States)

    Ahmed, Ashour A; Thiele-Bruhn, Sören; Leinweber, Peter; Kühn, Oliver

    2016-07-15

    Sorption experiments of sulfanilamide (SAA) on well-characterized samples of soil size-fractions were combined with the modeling of SAA-soil-interaction via quantum chemical calculations. Freundlich unit capacities were determined in batch experiments and it was found that they increase with the soil organic matter (SOM) content according to the order fine silt > medium silt > clay > whole soil > coarse silt > sand. The calculated binding energies for mass-spectrometrically quantified sorption sites followed the order ionic species > peptides > carbohydrates > phenols and lignin monomers > lignin dimers > heterocyclic compounds > fatty acids > sterols > aromatic compounds > lipids, alkanes, and alkenes. SAA forms H-bonds through its polar centers with the polar SOM sorption sites. In contrast dispersion and π-π-interactions predominate the interaction of the SAA aromatic ring with the non-polar moieties of SOM. Moreover, the dipole moment, partial atomic charges, and molecular volume of the SOM sorption sites are the main physical properties controlling the SAA-SOM-interaction. Further, reasonable estimates of the Freundlich unit capacities from the calculated binding energies have been established. Consequently, we suggest using this approach in forthcoming studies to disclose the interactions of a wide range of organic pollutants with SOM. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Molecular property investigations of an ortho-hydroxy Schiff base type compound with the first-principle molecular dynamics approach.

    Science.gov (United States)

    Jezierska-Mazzarello, Aneta; Vuilleumier, Rodolphe; Panek, Jarosław J; Ciccotti, Giovanni

    2010-01-14

    The structure, proton transfer, and vibrational dynamics under ambient conditions of a selected ortho-hydroxy Schiff base type compound, 2-(N-methyl-alpha-iminoethyl)-4-chlorophenol, containing a very short intramolecular hydrogen bond, were investigated computationally in the gas phase and in the crystal by density functional theory (DFT) based first-principle molecular dynamics (FPMD). It is found that the proton is well localized on the nitrogen side of the O...H...N bridge in the crystal phase, in agreement with X-ray diffraction experiments, while a more labile proton is located most of the time on the oxygen side in a vacuum. Environmental effects on this very strong hydrogen bond thus appear crucial and lead to drastic changes of the infrared (IR) spectrum: The computed gas-phase IR spectrum shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1) assigned to the labile proton. In mere contrast, a much more localized absorption band around 2600-2700 cm(-1) is predicted in the crystal phase. Finally, effects of the quantization of the proton motion on the hydrogen bond structure were estimated in two ways. First, we constructed the one-dimensional (1D) potential energy surface (PES) for the proton along the O...H...N bridge in a vacuum. The 1D Schrodinger equation was then solved. Next, path integral molecular dynamics (PIMD) was performed in the solid state. Inclusion of quantum effects does not affect the observed change of the most probable tautomer, upon going from the gas phase to the crystal.

  7. Molecular interactions and thermal transport in ionic liquids with carbon nanomaterials.

    Science.gov (United States)

    França, João M P; Nieto de Castro, Carlos A; Pádua, Agílio A H

    2017-07-05

    We used molecular dynamics simulation to study the effect of suspended carbon nanomaterials, nanotubes and graphene sheets, on the thermal conductivity of ionic liquids, an issue related to understanding the properties of nanofluids. One important aspect that we developed is an atomistic model of the interactions between the organic ions and carbon nanomaterials, so we did not rely on existing force fields for small organic molecules or assume simple combining rules to describe the interactions at the liquid/material interface. Instead, we used quantum calculations with a density functional suitable for non-covalent interactions to parameterize an interaction model, including van der Waals terms and also atomic partial charges on the materials. We fitted a n-m interaction potential function with n values of 9 or 10 and m values between 5 and 8, so a 12-6 Lennard-Jones function would not fit the quantum calculations. For the atoms of ionic liquids and carbon nanomaterials interacting among themselves, we adopted existing models from the literature. We studied the imidazolium ionic liquids [C 4 C 1 im][SCN], [C 4 C 1 im][N(CN) 2 ], [C 4 C 1 im][C(CN) 3 ] and [C 4 C 1 im][(CF 3 SO 2 ) 2 N]. Attraction is stronger for cations (than for anions) above and below the π-system of the nanomaterials, whereas anions show stronger attraction for the hydrogenated edges. The ordering of ions around and inside (7,7) and (10,10) single-walled nanotubes, and near a stack of graphene sheets, was analysed in terms of density distribution functions. We verified that anions are found, as well as cations, in the first interfacial layer interacting with the materials, which is surprising given the interaction potential surfaces. The thermal conductivity of the ionic liquids and of composite systems containing one nanotube or one graphene stack in suspension was calculated using non-equilibrium molecular dynamics. Thermal conductivity was calculated along the axis of the nanotube and

  8. Molecular level investigation of CH4 and CO2 adsorption in hydrated Ca-Montmorillonite

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Mal Soon; McGrail, Bernard P.; Rousseau, Roger J.; Glezakou, Vassiliki-Alexandra

    2018-01-18

    We have studied the mechanism of intercalation and methane adsorption from a H2O/CH4/CO2 mixture on a prototypical shale component, Ca-montmorillonite. We employed ab initio molecular dynamics simulations at 323 K and 90 bar to obtain molecular level information of adsorption energetics, speciation, and structural and thermodynamic properties. Interaction of CH4 with surface Lewis acidic sites (Ca2+, surface OH) results in large induced dipoles (~1 D) that lead to relatively strong adsorption energies that level off once a full CH4 layer is formed. Intercalated CH4, also exhibits induced dipoles at low hydration levels, when the interaction with Ca2+ cations are less hindered. CO2 displaces CH4 in the coordination sphere of the cations (in the interlayer) or in the surface, thereby driving CH4 extraction. Our simulations indicate that there is a Goldilocks pressure range (~60-100 bar) where scCO2 –facilitated CH4 extraction will be maximized.

  9. Molecular-Scale Investigation of Heavy Metal Ions at a Charged Langmuir Monolayer

    Science.gov (United States)

    Rock, William; Qiao, Baofu; Uysal, Ahmet; Bu, Wei; Lin, Binhua

    Solvent extraction - the surfactant-aided preferential transfer of a species from an aqueous to an organic phase - is an important technique used in heavy and precious metal refining and reprocessing. Solvent extraction requires transfer through an oil/water interface, and interfacial interactions are expected to control transfer kinetics and phase stability, yet these key interactions are poorly understood. Langmuir monolayers with charged headgroups atop concentrated salt solutions containing heavy metal ions act as a model of solvent extraction interfaces; studies of ions at a charged surface are also fundamentally important to many other phenomena including protein solvation, mineral surface chemistry, and electrochemistry. We probe these charged interfaces using a variety of surface-sensitive techniques - vibrational sum frequency generation (VSFG) spectroscopy, x-ray reflectivity (XRR), x-ray fluorescence near total reflection (XFNTR), and grazing incidence diffraction (GID). We integrate experiments with Molecular Dynamics (MD) simulations to uncover the molecular-level interfacial structure. This work is supported by the U.S. DOE, BES, Contract DE-AC02-06CH11357. ChemMatCARS is supported by NSF/CHE-1346572.

  10. Ultraviolet-Visible (UV-Vis) and Fluorescence Spectroscopic Investigation of the Interactions of Ionic Liquids and Catalase.

    Science.gov (United States)

    Dong, Xing; Fan, Yunchang; Yang, Peng; Kong, Jichuan; Li, Dandan; Miao, Juan; Hua, Shaofeng; Hu, Chaobing

    2016-11-01

    The inhibitory effects of nine ionic liquids (ILs) on the catalase activity were investigated using fluorescence, absorption ultraviolet-visible spectroscopy. The interactions of ILs and catalase on the molecular level were studied. The experimental results indicated that ILs could inhibit the catalase activity and their inhibitory abilities depended on their chemical structures. Fluorescence experiments showed that hydrogen bonding played an important role in the interaction process. The inhibitory abilities of ILs on catalase activity could be simply described by their hydrophobicity and hydrogen bonding abilities. Unexpected less inhibitory effects of trifluoromethanesulfonate (TfO - ) might be ascribed to its larger size, which makes it difficult to go through the substrate channel of catalase to the active site. © The Author(s) 2016.

  11. Microstructural Investigation and MolecularWeight Determination of 1, 2-Polybutadiene by Nuclear Magnetic Resonance Spectroscopy

    Directory of Open Access Journals (Sweden)

    Farshid Ziaee

    2013-01-01

    Full Text Available In this research, the microstructural of low molecular weight 1,2-polybutadiene (1,2-PBD was conducted by 1H and 13C nuclear magnetic resonance spectroscopy (NMR to determine the isomeric contents of 1,4-cis, 1,4-trans and 1,2-vinyl in 1,2-PBD polymer structures. Number average molecular weight for low molecular weight 1,2-PBD was measured by NMR techniques and the results were compared with gel permeation chromatography. Due to the presence of methyl end group and its comparison with repeating units in 1,2-PBD microstructure, the number average molecular weight was calculated by NMR techniques. For calculation of surface areas, carbon and protons of methyl groups were characterized using distortion enhancement by polarization transfer (DEPT methods. For proton assignment of methyl end groups in 1H NMR spectral analysis the heteronuclear multiple quantum coherence (HMQC method was employed. Finally, stereoregularity and tacticity of 1,2-PBD were investigated through pentad and heptad sequences splitting of olefinic methylene and methine carbons pendant groups with various NMR acquisition temperatures from 20 to 50oC. 13C NMR spectra showed that with increasing of NMR acquisition temperature, the number of split peaks of two olefinic carbons increased.

  12. Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.; Nico, Peter; Keiluweit, Marco; Ahmed, Musahid

    2013-04-01

    Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.

  13. Plane-Wave Density Functional Theory Meets Molecular Crystals: Thermal Ellipsoids and Intermolecular Interactions.

    Science.gov (United States)

    Deringer, Volker L; George, Janine; Dronskowski, Richard; Englert, Ulli

    2017-05-16

    Molecular compounds, organic and inorganic, crystallize in diverse and complex structures. They continue to inspire synthetic efforts and "crystal engineering", with implications ranging from fundamental questions to pharmaceutical research. The structural complexity of molecular solids is linked with diverse intermolecular interactions: hydrogen bonding with all its facets, halogen bonding, and other secondary bonding mechanisms of recent interest (and debate). Today, high-resolution diffraction experiments allow unprecedented insight into the structures of molecular crystals. Despite their usefulness, however, these experiments also face problems: hydrogen atoms are challenging to locate, and thermal effects may complicate matters. Moreover, even if the structure of a crystal is precisely known, this does not yet reveal the nature and strength of the intermolecular forces that hold it together. In this Account, we show that periodic plane-wave-based density functional theory (DFT) can be a useful, and sometimes unexpected, complement to molecular crystallography. Initially developed in the solid-state physics communities to treat inorganic solids, periodic DFT can be applied to molecular crystals just as well: theoretical structural optimizations "help out" by accurately localizing the elusive hydrogen atoms, reaching neutron-diffraction quality with much less expensive measurement equipment. In addition, phonon computations, again developed by physicists, can quantify the thermal motion of atoms and thus predict anisotropic displacement parameters and ORTEP ellipsoids "from scratch". But the synergy between experiment and theory goes much further than that. Once a structure has been accurately determined, computations give new and detailed insights into the aforementioned intermolecular interactions. For example, it has been debated whether short hydrogen bonds in solids have covalent character, and we have added a new twist to this discussion using an orbital

  14. Assessing the Effectiveness of Parent-Child Interaction Therapy with Language Delayed Children: A Clinical Investigation

    Science.gov (United States)

    Falkus, Gila; Tilley, Ciara; Thomas, Catherine; Hockey, Hannah; Kennedy, Anna; Arnold, Tina; Thorburn, Blair; Jones, Katie; Patel, Bhavika; Pimenta, Claire; Shah, Rena; Tweedie, Fiona; O'Brien, Felicity; Leahy, Ruth; Pring, Tim

    2016-01-01

    Parent-child interaction therapy (PCIT) is widely used by speech and language therapists to improve the interactions between children with delayed language development and their parents/carers. Despite favourable reports of the therapy from clinicians, little evidence of its effectiveness is available. We investigated the effects of PCIT as…

  15. An Investigation of Human-Computer Interaction Approaches Beneficial to Weak Learners in Complex Animation Learning

    Science.gov (United States)

    Yeh, Yu-Fang

    2016-01-01

    Animation is one of the useful contemporary educational technologies in teaching complex subjects. There is a growing interest in proper use of learner-technology interaction to promote learning quality for different groups of learner needs. The purpose of this study is to investigate if an interaction approach supports weak learners, who have…

  16. Investigating Pedagogical Techniques in Classroom Interactions at a CELTA Training Programme

    Science.gov (United States)

    Rahman, Md Shidur

    2016-01-01

    The study investigated the similarities and dissimilarities of using pedagogical techniques in classroom interactions, taken place whilst teaching a known language and an unknown language in a CELTA training classroom context. For this purpose, the classroom interactions in unknown and known languages were analysed according to the qualitative…

  17. A differential vapor-pressure equipment for investigations of biopolymer interactions

    DEFF Research Database (Denmark)

    Andersen, Kim B; Koga, Y.; Westh, Peter

    2002-01-01

    , particularly a "gas-phase titration" routine for changing the cell composition, makes it effective for the investigations of several types of biopolymer interactions. These include isothermal studies of net affinities such as the adsorption of water to proteins or membranes, the preferential interaction...

  18. Investigating Cross-Device Interaction between a Handheld Device and a Large Display

    DEFF Research Database (Denmark)

    Paay, Jeni; Raptis, Dimitrios; Kjeldskov, Jesper

    2017-01-01

    There is a growing interest in HCI research to explore cross-device interaction, giving rise to an interest in different approaches facilitating interaction between handheld devices and large displays. Contributing to this, we have investigated the use of four existing approaches combining touch...

  19. FTIR and dielectric studies of molecular interaction between alkyl methacrylates and primary alcohols

    International Nuclear Information System (INIS)

    Dharmalingam, K.; Ramachandran, K.; Sivagurunathan, P.

    2007-01-01

    The molecular interaction between alkyl methacrylates (methyl methacrylate, ethyl methacrylate and butyl methacrylate) and primary alcohols (1-propanol, 1-butanol, 1-pentanol, 1-heptanol, 1-octanol and 1-decanol) has been studied in carbon tetrachloride by FTIR spectroscopic and dielectric methods. The results show that the most likely association between alcohol and ester is 1:1 complex through the free hydroxyl group of the alcohol and the carbonyl group of ester, and the alkyl chain length of both the alcohols and esters plays an important role in the determination of the strength of hydrogen bond (O-H:O=C) formed

  20. Conductance switching in a molecular device: The role of side groups and intermolecular interactions

    DEFF Research Database (Denmark)

    Taylor, Jeremy Philip; Brandbyge, Mads; Stokbro, Kurt

    2003-01-01

    flow through the monolayer. However, functionalization has a significant effect on the interactions within the monolayer, so that monolayers with NO2 side groups exhibit local minima associated with twisted conformations of the molecules. We use our results to interpret observations of negative......We report first-principles studies of electronic transport in monolayers of Tour wires functionalized with different side groups. An analysis of the scattering states and transmission eigenchannels suggests that the functionalization does not strongly affect the resonances responsible for current...... differential resistance and molecular memory in monolayers of NO2 functionalized molecules in terms of a twisting of the central ring induced by an applied bias potential....

  1. Quantum molecular modeling of the interaction between guanine and alkylating agents--1--sulfur mustard.

    Science.gov (United States)

    Broch, H; Hamza, A; Vasilescu, D

    1996-06-01

    Interaction between Guanine and the episulfonium form of Sulfur mustard (HD) was studied using the ab initio LCAO-MO method at the HF/6-31G level. The alkylation mechanism on guanine-N7 was analyzed by using a supermolecular modeling. Our stereostructural results associated with the molecular electrostatic potentials and HOMO-LUMO properties, show that in vacuum the alkylation of the N7 of guanine by HD in the aggressive episulfonium form is a direct process without transition state and of which the pathway is determined.

  2. Interactivity effects in social media marketing on brand engagement: an investigation of underlying mechanisms

    NARCIS (Netherlands)

    Antheunis, M.L.; van Noort, G.; Eisend, M.; Langner, T.

    2011-01-01

    Although, SNS advertising spending increases, research on SNS campaigning is still underexposed. First, this study aims to investigate the effect of SNS campaign interactivity on the receivers brand engagement, taking four underlying mechanisms into account (brand identification, campaign

  3. Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2007-01-01

    -18 to extend perpendicular to the beta-hairpin plane. This bend was driven by a highly persistent hydrogen-bond between the polar peptide side-chain of TYR7 and the unshielded backbone carbonyl oxygen atom of GLY17. The H-bond formation relieves the unfavorable free energy of insertion of polar groups......All atom molecular dynamics simulations of the 18-residue beta-hairpin antimicrobial peptide protegrin-1 (PG-1, RGGRLCYCRRRFCVCVGR-NH(2)) in a fully hydrated dilauroylphosphatidylcholine (DLPC) lipid bilayer have been implemented. The goal of the reported work is to investigate the structure......-550]), and to delineate specific peptide-membrane interactions which are responsible for the peptide's membrane binding properties. A novel, previously unknown, "kick" shaped conformation of the peptide was detected, where a bend at the C-terminal beta-strand of the peptide caused the peptide backbone at residues 16...

  4. Spectroscopic and molecular docking approaches for investigating conformation and binding characteristics of clonazepam with bovine serum albumin (BSA).

    Science.gov (United States)

    Lou, Yan-Yue; Zhou, Kai-Li; Pan, Dong-Qi; Shen, Jia-Le; Shi, Jie-Hua

    2017-02-01

    Clonazepam, a type of benzodiazepine, is a classical drug used to prevent and treat seizures, panic disorder, movement disorder, among others. For further clarifying the distribution of clonazepam in vivo and the pharmacodynamic and pharmacokinetic mechanisms, the binding interaction between clonazepam and bovine serum albumin (BSA) was investigated using ultraviolet spectroscopy (UV), steady-state fluorescence spectroscopy, synchronous fluorescence spectroscopy, three-dimensional (3D) fluorescence spectroscopy, Fourier transform infrared spectroscopy (FT-IR) and molecular docking methods. The results well confirmed that clonazepam bound on the subdomain III A (Site II) of BSA through van der Waals force and hydrogen bonding interaction, and quenched the intrinsic fluorescence of BSA through a static quenching process. The number of binding sites (n) and binding constant (K b ) of clonazepam-BSA complex were about 1 and 7.94×10 4 M -1 at 308K, respectively. The binding process of clonazepam with BSA was spontaneous and enthalpy-driven process due to ΔG 0 T|ΔS 0 | over the studied temperature range. Meanwhile, the binding interaction of clonazepam with BSA resulted in the slight change in the conformation of BSA and the obvious change in the conformation of clonazepam, implying that the flexibility of clonazepam also played an important role in increasing the stability of the clonazepam-BSA complex. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Molecular dynamics approaches to the design and synthesis of PCB targeting molecularly imprinted polymers: interference to monomer-template interactions in imprinting of 1,2,3-trichlorobenzene.

    Science.gov (United States)

    Cleland, Dougal; Olsson, Gustaf D; Karlsson, Björn C G; Nicholls, Ian A; McCluskey, Adam

    2014-02-07

    The interactions between each component of the pre-polymerisation mixtures used in the synthesis of molecularly imprinted polymers (MIP) specific for 1,2,3,4,5-pentachlorobenzene (1) and 1,2,3-trichlorobenzene (2) were examined in four molecular dynamics simulations. These simulations revealed that the relative frequency of functional monomer-template (FM-T) interactions was consistent with results obtained by the synthesis and evaluation of the actual MIPs. The higher frequency of 1 interaction with trimethylstyrene (TMS; 54.7%) than 1 interaction with pentafluorostyrene (PFS; 44.7%) correlated with a higher imprinting factor (IF) of 2.1 vs. 1.7 for each functional monomer respectively. The higher frequency of PFS interactions with 2 (29.6%) than TMS interactions with 2 (1.9%) also correlated well with the observed differences in IF (3.7) of 2 MIPs imprinted using PFS as the FM than the IF (2.8) of 2 MIPs imprinted using TMS as the FM. The TMS-1 interaction dominated the molecular simulation due to high interaction energies, but the weaker TMS-2 resulted in low interaction maintenance, and thus lower IF values. Examination of the other pre-polymerisation mixture components revealed that the low levels of TMS-2 interaction was, in part, due to interference caused by the cross linker (CL) ethyleneglycol dimethylacrylate (EGDMA) interactions with TMS. The main reason was, however, attributed to MeOH interactions with TMS in both a hydrogen bond and perpendicular configuration. This positioned a MeOH directly above the π-orbital of all TMS for an average of 63.8% of MD2 creating significant interference to π-π stacking interactions between 2 and TMS. These findings are consistent with the deviation from the 'normal' molecularly imprinted polymer synthesis ratio of 1 : 4 : 20 (T : FM : CL) of 20 : 1 : 29 and 15 : 6 : 29 observed with 2 and TMS and PFS respectively. Our molecular dynamics simulations correctly predicted the high level

  6. Electrochemical and calorimetric investigation of interaction of novel biscationic anticancer agents with DNA

    OpenAIRE

    Silva, Láuris Lucia da; Donnici, Claudio Luis; Lopes, Júlio César Dias; Goulart, Marília Oliveira Fonseca; Abreu, Fabiane Caxico de; Paula, Francine Santos de; Bravo, Carlos E. Salas; Santoro, Marcelo Matos; Denadai, Ângelo Márcio Leite; Santos, Alexandre Martins Costa; Montanari, Carlos Alberto

    2012-01-01

    ELECTROCHEMICAL AND CALORIMETRIC INVESTIGATION OF INTERACTION OF NOVEL BISCATIONIC ANTICANCER AGENTS WITH DNA. Biscationic amidines bind in the DNA minor groove and present biological activity against a range of infectious diseases. Two new biscationic compounds (bis-alpha,omega-S-thioureido, amino and sulfide analogues) were synthesized in good yields and fully characterized, and their interaction with DNA was also investigated. Isothermal titration calorimetry (ITC) was used to measure the ...

  7. Molecular modeling of interactions in electronic nose sensors for environmental monitoring

    Science.gov (United States)

    Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Yen, S. -P. S.; Zhou, H.; Manatt, K.

    2002-01-01

    We report a study aimed at understanding analyte interactions with sensors made from polymer-carbon black composite films. The sensors are used in an Electronic Nose (ENose) which is used for monitoring the breathing air quality in human habitats. The model mimics the experimental conditions of the composite film deposition and formation and was developed using molecular modeling and simulation tools. The Dreiding 2.21 Force Field was used for the polymer and analyte molecules while graphite parameters were assigned to the carbon black atoms. The polymer considered for this work is methyl vinyl ether / maleic acid copolymer. The target analytes include both inorganic (NH3) and organic (methanol) types of compound. Results indicate different composite-analyte interaction behavior.

  8. A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data.

    Science.gov (United States)

    Broom, Bradley M; Ryan, Michael C; Brown, Robert E; Ikeda, Futa; Stucky, Mark; Kane, David W; Melott, James; Wakefield, Chris; Casasent, Tod D; Akbani, Rehan; Weinstein, John N

    2017-11-01

    Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in web technologies to produce interactive "next-generation" clustered heatmaps (NG-CHM) that enable extreme zooming and navigation without loss of resolution. NG-CHMs also provide link-outs to additional information sources and include other features that facilitate deep exploration of the biology behind the image. Here, we describe an implementation of the NG-CHM system in the Galaxy bioinformatics platform. We illustrate the algorithm and available computational tool using RNA-seq data from The Cancer Genome Atlas program's Kidney Clear Cell Carcinoma project. Cancer Res; 77(21); e23-26. ©2017 AACR . ©2017 American Association for Cancer Research.

  9. Inelastic Neutron Scattering and Molecular Dynamics Determination of the Interaction Potential in Liquid CD4

    International Nuclear Information System (INIS)

    Guarini, E.; Barocchi, F.; Sampoli, M.; Venturi, G.; Bafile, U.

    2007-01-01

    Anisotropic interactions of liquid CD 4 are studied in detail by comparison of inelastic neutron Brillouin scattering data with molecular dynamics simulations using up to four different models of the methane site-site potential. We demonstrate that the experimental dynamic structure factor S(Q,ω) acts as a highly discriminating quantity for possible interaction schemes. In particular, the Q evolution of the spectra enables a selective probing of the short- and medium-range features of the anisotropic potentials. We show that the preferential configuration of methane dimers at liquid densities can thus be discerned by analyzing the orientation-dependent model potential curves, in light of the experimental and simulation results

  10. Investigating the interaction between the neonatal Fc receptor and monoclonal antibody variants by hydrogen/deuterium exchange mass spectrometry.

    Science.gov (United States)

    Jensen, Pernille Foged; Larraillet, Vincent; Schlothauer, Tilman; Kettenberger, Hubert; Hilger, Maximiliane; Rand, Kasper D

    2015-01-01

    The recycling of immunoglobulins by the neonatal Fc receptor (FcRn) is of crucial importance in the maintenance of antibody levels in plasma and is responsible for the long half-lives of endogenous and recombinant monoclonal antibodies. From a therapeutic point of view there is great interest in understanding and modulating the IgG-FcRn interaction to optimize antibody pharmacokinetics and ultimately improve efficacy and safety. Here we studied the interaction between a full-length human IgG(1) and human FcRn via hydrogen/deuterium exchange mass spectrometry and targeted electron transfer dissociation to map sites perturbed by binding on both partners of the IgG-FcRn complex. Several regions in the antibody Fc region and the FcRn were protected from exchange upon complex formation, in good agreement with previous crystallographic studies of FcRn in complex with the Fc fragment. Interestingly, we found that several regions in the IgG Fab region also showed reduced deuterium uptake. Our findings indicate the presence of hitherto unknown FcRn interaction sites in the Fab region or a possible conformational link between the IgG Fc and Fab regions upon FcRn binding. Further, we investigated the role of IgG glycosylation in the conformational response of the IgG-FcRn interaction. Removal of antibody glycans increased the flexibility of the FcRn binding site in the Fc region. Consequently, FcRn binding did not induce a similar conformational stabilization of deglycosylated IgG as observed for the wild-type glycosylated IgG. Our results provide new molecular insight into the IgG-FcRn interaction and illustrate the capability of hydrogen/deuterium exchange mass spectrometry to advance structural proteomics by providing detailed information on the conformation and dynamics of large protein complexes in solution. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  11. Molecular mechanisms underlying the interaction of protein phosphatase-1c with ASPP proteins.

    Science.gov (United States)

    Skene-Arnold, Tamara D; Luu, Hue Anh; Uhrig, R Glen; De Wever, Veerle; Nimick, Mhairi; Maynes, Jason; Fong, Andrea; James, Michael N G; Trinkle-Mulcahy, Laura; Moorhead, Greg B; Holmes, Charles F B

    2013-02-01

    The serine/threonine PP-1c (protein phosphatase-1 catalytic subunit) is regulated by association with multiple regulatory subunits. Human ASPPs (apoptosis-stimulating proteins of p53) comprise three family members: ASPP1, ASPP2 and iASPP (inhibitory ASPP), which is uniquely overexpressed in many cancers. While ASPP2 and iASPP are known to bind PP-1c, we now identify novel and distinct molecular interactions that allow all three ASPPs to bind differentially to PP-1c isoforms and p53. iASPP lacks a PP-1c-binding RVXF motif; however, we show it interacts with PP-1c via a RARL sequence with a Kd value of 26 nM. Molecular modelling and mutagenesis of PP-1c-ASPP protein complexes identified two additional modes of interaction. First, two positively charged residues, Lys260 and Arg261 on PP-1c, interact with all ASPP family members. Secondly, the C-terminus of the PP-1c α, β and γ isoforms contain a type-2 SH3 (Src homology 3) poly-proline motif (PxxPxR), which binds directly to the SH3 domains of ASPP1, ASPP2 and iASPP. In PP-1cγ this comprises residues 309-314 (PVTPPR). When the Px(T)PxR motif is deleted or mutated via insertion of a phosphorylation site mimic (T311D), PP-1c fails to bind to all three ASPP proteins. Overall, we provide the first direct evidence for PP-1c binding via its C-terminus to an SH3 protein domain.

  12. Binding analysis for interaction of diacetylcurcumin with β-casein nanoparticles by using fluorescence spectroscopy and molecular docking calculations

    Science.gov (United States)

    Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Fani, Najme; Keyhanfar, Mehrnaz

    2013-11-01

    The interaction of diacetylcurcumin (DAC), as a novel synthetic derivative of curcumin, with bovine β-casein (an abundant milk protein that is highly amphiphilic and self assembles into stable micellar nanoparticles in aqueous solution) was investigated using fluorescence quenching experiments, Forster energy transfer measurements and molecular docking calculations. The fluorescence quenching measurements revealed the presence of a single binding site on β-casein for DAC with the binding constant value equals to (4.40 ± 0.03) × 104 M-1. Forster energy transfer measurements suggested that the distance between bound DAC and Trp143 residue is higher than the respective critical distance, hence, the static quenching is more likely responsible for fluorescence quenching other than the mechanism of non-radiative energy transfer. Our results from molecular docking calculations indicated that binding of DAC to β-casein predominantly occurred through hydrophobic contacts in the hydrophobic core of protein. Additionally, in vitro investigation of the cytotoxicity of free DAC and DAC-β-casein complex in human breast cancer cell line MCF7 revealed the higher cytotoxic effect of DAC-β-casein complex.

  13. Investigating direct interaction between Escherichia coli topoisomerase I and RecA

    Science.gov (United States)

    Darici, Yesim; Tse-Dinh, Yuk-Ching

    2016-01-01

    Protein-protein interactions are of special importance in cellular processes, including replication, transcription, recombination, and repair. Escherichia coli topoisomerase I (EcTOP1) is primarily involved in the relaxation of negative DNA supercoiling. E. coli RecA, the key protein for homologous recombination and SOS DNA-damage response, has been shown to stimulate the relaxation activity of EcTOP1. The evidence for their direct protein-protein interaction has not been previously established. We report here the direct physical interaction between E. coli RecA and topoisomerase I. We demonstrated the RecA-topoisomerase I interaction via pull-down assays, and surface plasmon resonance measurements. Molecular docking supports the observation that the interaction involves the topoisomerase I N-terminal domains that form the active site. Our results from pull-down assays showed that ATP, although not required, enhances the RecA-EcTOP1 interaction. We propose that E. coli RecA physically interacts with topoisomerase I to modulate the chromosomal DNA supercoiling. PMID:27001450

  14. Yield and Failure Behavior Investigated for Cross-Linked Phenolic Resins Using Molecular Dynamics

    Science.gov (United States)

    Monk, Joshua D.; Lawson, John W.

    2016-01-01

    Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

  15. Utility of checklist to describe experimental methods for investigating molecular biomarkers.

    Science.gov (United States)

    Chiarella, Pieranna; Carbonari, Damiano; Iavicoli, Sergio

    2015-01-01

    In research articles, detailed description of experimental methods and reagents is fundamental for correct reproducibility of the published data. This becomes even more important when such data contribute to identify molecular targets and toxicity biomarkers whose role is crucial in the physiology and pathology of human health. Methods & Objectives: To achieve good reproducibility of data we took advantage of others' experiences and analyzed molecular biology and immunodetection techniques in 32 journal articles investigating the human NRF2 and Keap1 genes involved in the cell response to oxidative stress. In conclusion of the analysis, we assessed deficiency of information in the published methods, making it difficult to select appropriate protocols. Underlining the importance of assay reproducibility, this paper proposes the utility of a minimum information checklist of methods for biomarker detection.

  16. Investigating conversational dynamics: Interactive alignment, Interpersonal synergy, and collective task performance

    DEFF Research Database (Denmark)

    Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    This study investigates interpersonal processes underlying dialog by comparing two approaches, interactive alignment and interpersonal synergy, and assesses how they predict collective performance in a joint task. While the interactive alignment approach highlights imitative patterns between...... interlocutors, the synergy approach points to structural organization at the level of the interaction - such as complementary patterns straddling speech-turns and interlocutors. We develop a general, quantitative method to assess lexical, prosodic and speech/pause patterns related to the two approaches...... does not improve the model. This suggests that structural organization at the level of the interaction plays a crucial role in task-oriented conversations, possibly constraining and integrating processes related to alignment....

  17. Molecular interactions in the complexes of toluene with butyronitrile: A DFT approach

    Science.gov (United States)

    Karthick, N. K.; Arivazhagan, G.

    2018-04-01

    Density Functional Theory (DFT) has been employed to investigate the self association of butyronitrile and the heterointeractions in the 1:2 (toluene: butyronitrile) and 1:1 complexes of toluene with butyronitrile. For this investigation the B3LYP functional with Grimme's dispersion correction (D3) term and ωB97XD functionals were used. The theoretical frequency analysis shows the unsuitability of B3LYP with D3 for the present investigation. Therefore, Natural Bonding Orbital analysis was done at the functional ωB97XD. It is found through this work that only the methylene hydrogens of butyronitrile are responsible for the self association among the butyronitrile molecules. In 1:1 complex, the red shift in the butyronitrile methyl asymmetric stretching mode is not due to the active participation of this group in heterointeractions and it is solely due to the other interactions happening in its vicinity. Only the interaction (TOL) C - H ⋯ N(BN) is present in the complex. In 1:2 complex the butyronitrile methyl/methylene hydrogens interact with the delocalized electron cloud of toluene and the toluene hydrogens interact with the butyronitrile nitrogen. Comparison of interaction energies shows that the stability of 1:2 complex is more than that of butyronitrile dimer and 1:1 complex.

  18. Non-autonomous matter-wave solitons in hybrid atomic-molecular Bose-Einstein condensates with tunable interactions and harmonic potential

    Science.gov (United States)

    Wang, Deng-Shan; Liu, Jiang; Wang, Lizhen

    2018-03-01

    In this paper, we investigate matter-wave solitons in hybrid atomic-molecular Bose-Einstein condensates with tunable interactions and external potentials. Three types of time-modulated harmonic potentials are considered and, for each of them, two groups of exact non-autonomous matter-wave soliton solutions of the coupled Gross-Pitaevskii equation are presented. Novel nonlinear structures of these non-autonomous matter-wave solitons are analyzed by displaying their density distributions. It is shown that the time-modulated nonlinearities and external potentials can support exact non-autonomous atomic-molecular matter-wave solitons.

  19. Elucidating the interaction of clofazimine with bovine liver catalase; a comprehensive spectroscopic and molecular docking approach.

    Science.gov (United States)

    Zaman, Masihuz; Nusrat, Saima; Zakariya, Syed Mohammad; Khan, Mohsin Vahid; Ajmal, Mohammad Rehan; Khan, Rizwan Hasan

    2017-08-01

    Nowadays, understanding of interface between protein and drugs has become an active research area of interest. These types of interactions provide structural guidelines in drug design with greater clinical efficacy. Thus, structural changes in catalase induced by clofazimine were monitored by various biophysical techniques including UV-visible spectrometer, fluorescence spectroscopy, circular dichroism, and dynamic light scattering techniques. Increase in absorption spectra (UV-visible spectrum) confers the complex formation between drug and protein. Fluorescence quenching with a binding constants of 2.47 × 10 4  M -1 revealed that clofazimine binds with protein. Using fluorescence resonance energy transfer, the distance (r) between the protein (donor) and drug (acceptor) was found to be 2.89 nm. Negative Gibbs free energy change (ΔG°) revealed that binding process is spontaneous. In addition, an increase in α-helicity was observed by far-UV circular dichroism spectra by adding clofazimine to protein. Dynamic light scattering results indicate that topology of bovine liver catalase was slightly altered in the presence of clofazimine. Hydrophobic interactions are the main forces between clofazimine and catalase interaction as depicted by molecular docking studies. Apart from hydrophobic interactions, some hydrogen bonding was also observed during docking method. The results obtained from the present study may establish abundant in optimizing the properties of ligand-protein mixtures relevant for numerous formulations. Copyright © 2017 John Wiley & Sons, Ltd.

  20. 2008 Atomic and Molecular Interactions GRC-July 6-11, 2008

    Energy Technology Data Exchange (ETDEWEB)

    Arthur Suits

    2009-06-03

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2008 conference continues these traditions. At the 2008 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Spectroscopy; (2) Molecules in Strong Fields; (3) Photodissociation Dynamics; (4) Astrochemistry; and (5) Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed. Limited funds are available to support attendance for students and post-docs. Advisors should email the conference chair requesting such support, and the students should apply online as usual.

  1. Interactions between fibronectin and chondroitin sulfate are modulated by molecular context.

    Science.gov (United States)

    Barkalow, F J; Schwarzbauer, J E

    1994-02-11

    Interactions between fibronectin (FN) and glycosaminoglycans are essential for extracellular matrix morphology and cell adhesion. One of the most abundant glycosaminoglycans is chondroitin sulfate, and here we show that recombinant FNs (deminectins (DN)) containing the carboxyl-terminal cell, heparin, and fibrin domains bind specifically to chondroitin sulfate in affinity chromatography assays. Using a panel of mutant DNs, important determinants for chondroitin sulfate binding have been localized to repeats III13 and III14 within the heparin domain. In particular, mutation of an arginine pair in repeat III13 to neutral residues ablated binding to chondroitin sulfate as we previously reported for heparin (Barkalow, F.J.B., and Schwarzbauer, J.E. (1991) J. Biol. Chem. 266, 7812-7818). These results, in combination with the ability of heparin and chondroitin sulfate to compete for binding to DNs, demonstrate that these two glycosaminoglycans interact with similar or overlapping sites in FN. One important difference between FN interactions with heparin and chondroitin sulfate is that, while FN and DNs bound equally to heparin, FN bound less efficiently than DNs to chondroitin sulfate. Reduced binding to chondroitin sulfate was also observed with a larger recombinant FN lacking internal repeats III1-7 indicating that the amino-terminal region acts to limit binding to the carboxyl-terminal domain. Our results demonstrate that interactions between FN and chondroitin sulfate are modulated by molecular context.

  2. Molecular tweezers modulate 14-3-3 protein-protein interactions

    Science.gov (United States)

    Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian

    2013-03-01

    Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins—a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)—in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.

  3. New aspects of π–d interactions in magnetic molecular conductors

    Directory of Open Access Journals (Sweden)

    Toyonari Sugimoto, Hideki Fujiwara, Satoru Noguchi and Keizo Murata

    2009-01-01

    Full Text Available The 2 : 1 cation radical salts of bent donor molecules of ethylenedithio-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDT-TTFVO, ethylenedithio-diselenadithiafulvalenoquinone-1,3-dithiolemethide (EDT-DSDTFVO, ethylenedithio-diselenadithiafulvalenothioquinone-1,3-diselenolemethide (EDT-DSDTFVSDS, ethylenedioxy-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDO-TTFVO and ethylenedioxy-tetrathiafulvalenoquinone-1,3-diselenolemethide (EDO-TTFVODS with FeX4− (X = Cl, Br ions are prepared by electrocrystallization. The crystal structures of these salts are composed of alternately stacked donor molecule and magnetic anion layers. The band structures of the donor molecule layers are calculated using the overlap integrals between neighboring donor molecules and are compared with the observed electronic transport properties. The magnetic ordering of the Fe(III d spins of FeX4− ions is determined from magnetization and heat capacity measurements. The magnetic ordering temperatures are estimated by considering a combination of a direct d–d interaction between the d spins and an indirect π–d interaction between the conduction π electron and the d spins, whose magnitudes are separately calculated from the crystal structures with an extended Hückel molecular orbital method. The occurrence of a π–d interaction is proved by the negative magnetoresistance, and the magnitude of magnetoresistance reflects the strength of the π–d interaction. The effect of pressure on the magnetoresistance is studied, and the result indicates that the magnitude of magnetoresistance increases, namely, the π–d interaction is enhanced with increasing pressure. From these experimental results it is shown that (EDT-TTFVO2•FeBr4 is a ferromagnetic semiconductor, (EDT-DSDTFVO2•FeX4 (X = Cl, Br and (EDT-DSDTFVSDS2•FeBr4 are metals exhibiting antiferromagnetic ordering of the d spins, and (EDO-TTFVO2•FeCl4 and (EDO-TTFVODS2•FeBr4•(DCE0.5 (DCE

  4. TOPICAL REVIEW: New aspects of π-d interactions in magnetic molecular conductors

    Science.gov (United States)

    Sugimoto, Toyonari; Fujiwara, Hideki; Noguchi, Satoru; Murata, Keizo

    2009-04-01

    The 2 : 1 cation radical salts of bent donor molecules of ethylenedithio-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDT-TTFVO), ethylenedithio-diselenadithiafulvalenoquinone-1,3-dithiolemethide (EDT-DSDTFVO), ethylenedithio-diselenadithiafulvalenothioquinone-1,3-diselenolemethide (EDT-DSDTFVSDS), ethylenedioxy-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDO-TTFVO) and ethylenedioxy-tetrathiafulvalenoquinone-1,3-diselenolemethide (EDO-TTFVODS) with FeX4- (X = Cl, Br) ions are prepared by electrocrystallization. The crystal structures of these salts are composed of alternately stacked donor molecule and magnetic anion layers. The band structures of the donor molecule layers are calculated using the overlap integrals between neighboring donor molecules and are compared with the observed electronic transport properties. The magnetic ordering of the Fe(III) d spins of FeX4- ions is determined from magnetization and heat capacity measurements. The magnetic ordering temperatures are estimated by considering a combination of a direct d-d interaction between the d spins and an indirect π-d interaction between the conduction π electron and the d spins, whose magnitudes are separately calculated from the crystal structures with an extended Hückel molecular orbital method. The occurrence of a π-d interaction is proved by the negative magnetoresistance, and the magnitude of magnetoresistance reflects the strength of the π-d interaction. The effect of pressure on the magnetoresistance is studied, and the result indicates that the magnitude of magnetoresistance increases, namely, the π-d interaction is enhanced with increasing pressure. From these experimental results it is shown that (EDT-TTFVO)2•FeBr4 is a ferromagnetic semiconductor, (EDT-DSDTFVO)2•FeX4 (X = Cl, Br) and (EDT-DSDTFVSDS)2•FeBr4 are metals exhibiting antiferromagnetic ordering of the d spins, and (EDO-TTFVO)2•FeCl4 and (EDO-TTFVODS)2•FeBr4•(DCE)0.5 (DCE =-dichloroethane) are genuine

  5. New aspects of π-d interactions in magnetic molecular conductors.

    Science.gov (United States)

    Sugimoto, Toyonari; Fujiwara, Hideki; Noguchi, Satoru; Murata, Keizo

    2009-04-01

    The 2 : 1 cation radical salts of bent donor molecules of ethylenedithio-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDT-TTFVO), ethylenedithio-diselenadithiafulvalenoquinone-1,3-dithiolemethide (EDT-DSDTFVO), ethylenedithio-diselenadithiafulvalenothioquinone-1,3-diselenolemethide (EDT-DSDTFVSDS), ethylenedioxy-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDO-TTFVO) and ethylenedioxy-tetrathiafulvalenoquinone-1,3-diselenolemethide (EDO-TTFVODS) with FeX 4 - (X = Cl, Br) ions are prepared by electrocrystallization. The crystal structures of these salts are composed of alternately stacked donor molecule and magnetic anion layers. The band structures of the donor molecule layers are calculated using the overlap integrals between neighboring donor molecules and are compared with the observed electronic transport properties. The magnetic ordering of the Fe(III) d spins of FeX 4 - ions is determined from magnetization and heat capacity measurements. The magnetic ordering temperatures are estimated by considering a combination of a direct d-d interaction between the d spins and an indirect π-d interaction between the conduction π electron and the d spins, whose magnitudes are separately calculated from the crystal structures with an extended Hückel molecular orbital method. The occurrence of a π-d interaction is proved by the negative magnetoresistance, and the magnitude of magnetoresistance reflects the strength of the π-d interaction. The effect of pressure on the magnetoresistance is studied, and the result indicates that the magnitude of magnetoresistance increases, namely, the π-d interaction is enhanced with increasing pressure. From these experimental results it is shown that (EDT-TTFVO) 2 •FeBr 4 is a ferromagnetic semiconductor, (EDT-DSDTFVO) 2 •FeX 4 (X = Cl, Br) and (EDT-DSDTFVSDS) 2 •FeBr 4 are metals exhibiting antiferromagnetic ordering of the d spins, and (EDO-TTFVO) 2 •FeCl 4 and (EDO-TTFVODS) 2 •FeBr 4 •(DCE) 0.5 (DCE

  6. New aspects of π–d interactions in magnetic molecular conductors

    Science.gov (United States)

    Sugimoto, Toyonari; Fujiwara, Hideki; Noguchi, Satoru; Murata, Keizo

    2009-01-01

    The 2 : 1 cation radical salts of bent donor molecules of ethylenedithio-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDT-TTFVO), ethylenedithio-diselenadithiafulvalenoquinone-1,3-dithiolemethide (EDT-DSDTFVO), ethylenedithio-diselenadithiafulvalenothioquinone-1,3-diselenolemethide (EDT-DSDTFVSDS), ethylenedioxy-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDO-TTFVO) and ethylenedioxy-tetrathiafulvalenoquinone-1,3-diselenolemethide (EDO-TTFVODS) with FeX4− (X = Cl, Br) ions are prepared by electrocrystallization. The crystal structures of these salts are composed of alternately stacked donor molecule and magnetic anion layers. The band structures of the donor molecule layers are calculated using the overlap integrals between neighboring donor molecules and are compared with the observed electronic transport properties. The magnetic ordering of the Fe(III) d spins of FeX4− ions is determined from magnetization and heat capacity measurements. The magnetic ordering temperatures are estimated by considering a combination of a direct d–d interaction between the d spins and an indirect π–d interaction between the conduction π electron and the d spins, whose magnitudes are separately calculated from the crystal structures with an extended Hückel molecular orbital method. The occurrence of a π–d interaction is proved by the negative magnetoresistance, and the magnitude of magnetoresistance reflects the strength of the π–d interaction. The effect of pressure on the magnetoresistance is studied, and the result indicates that the magnitude of magnetoresistance increases, namely, the π–d interaction is enhanced with increasing pressure. From these experimental results it is shown that (EDT-TTFVO)2•FeBr4 is a ferromagnetic semiconductor, (EDT-DSDTFVO)2•FeX4 (X = Cl, Br) and (EDT-DSDTFVSDS)2•FeBr4 are metals exhibiting antiferromagnetic ordering of the d spins, and (EDO-TTFVO)2•FeCl4 and (EDO-TTFVODS)2•FeBr4•(DCE)0.5 (DCE =-dichloroethane) are

  7. Interaction of polar and nonpolar organic pollutants with soil organic matter: sorption experiments and molecular dynamics simulation.

    Science.gov (United States)

    Ahmed, Ashour A; Thiele-Bruhn, Sören; Aziz, Saadullah G; Hilal, Rifaat H; Elroby, Shaaban A; Al-Youbi, Abdulrahman O; Leinweber, Peter; Kühn, Oliver

    2015-03-01

    The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question "How organic pollutants interact with SOM?" is still lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model and carried out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), simulating the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and theoretical investigations explored four major points regarding sorption of SAA and HCB on soil, yielding the following results. 1--The interaction depends on the SOM chemical composition more than the SOM content. 2--The interaction causes a site-specific adsorption on the soil surfaces. 3--Sorption hysteresis occurs, which can be explained by inclusion of these pollutants inside soil voids. 4--The hydrophobic HCB is adsorbed on soil stronger than the hydrophilic SAA. Moreover, the theoretical results showed that HCB forms stable complexes with all SOM models in the aqueous solution, while most of SAA-SOM complexes are accompanied by dissociation into SAA and the free SOM models. The SOM-cavity modeling had a significant effect on binding of organic pollutants to SOM. Both HCB and SAA bind to the SOM models in the order of models with a small cavity>a large cavity>no cavity. Although HCB binds to all SOM models stronger than SAA, the latter is more affected by the presence of the cavity. Finally, HCB and SAA bind to the hydrophobic functional group (naphthalene) stronger than to the hydrophilic one (carboxylic acid

  8. On the molecular interaction between albumin and ibuprofen: An AFM and QCM-D study.

    Science.gov (United States)

    Eleta-Lopez, Aitziber; Etxebarria, Juan; Reichardt, Niels-Christian; Georgieva, Radostina; Bäumler, Hans; Toca-Herrera, José L

    2015-10-01

    The adsorption of proteins on surfaces often results in a change of their structural behavior and consequently, a loss of bioactivity. One experimental method to study interactions on a molecular level is single molecular force spectroscopy that permits to measure forces down to the pico-newton range. In this work, the binding force between human serum albumin (HSA), covalently immobilized on glutaraldehyde modified gold substrates, and ibuprofen sodium salt was studied by means of single molecular force spectroscopy. First of all, a protocol was established to functionalize atomic force microscopy (AFM) tips with ibuprofen. The immobilization protocol was additionally tested by quartz crystal microbalance with dissipation (QCM-D) and contact angle measurements. AFM was used to characterize the adsorption of HSA on gold substrates, which lead to a packed monolayer of thickness slightly lower than the reported value in solution. Finally, single molecule spectroscopy results were used to characterize the binding force between albumin and ibuprofen and calculate the distance of the transition state (0.6 nm) and the dissociation rate constant (0.055 s(-1)). The results might indicate that part of the adsorbed protein still preserves its functionality upon adsorption. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. The molecular understanding of interfacial interactions of functionalized graphene and chitosan

    International Nuclear Information System (INIS)

    Zhang, Hong-ping; Luo, Xue-gang; Lin, Xiao-yan; Lu, Xiong; Tang, Youhong

    2016-01-01

    Graphical abstract: The type of the functional groups can be used to modulating interactions between graphene sheet and chitosan. - Highlights: • Investigate interfacial interactions between chitosan and functionalized graphene by DFT. • Observe covalent linkages between COOH-modified graphene and chitosan units. • Multi-functionalized graphene regulates the interfacial interactions with chitosan. • It is useful for guiding the preparation of graphene/chitosan composites. - Abstract: Graphene-reinforced chitosan scaffolds have been extensively studied for several years as promising hard tissue replacements. However, the interfacial interactions between graphene and chitosan are strongly related to the solubility, processability, and mechanical properties of graphene-reinforced chitosan (G–C) composites. The functionalization of graphene is regarded as the most effective way to improve the abovementioned properties of the G–C composite. In this study, the interfacial interactions between chitosan and functionalized graphene sheets with carboxylization (COOH-), amination (NH 2 -), and hydroxylation (OH-) groups were systematically studied at the electronic level using the method of ab initio simulations based on quantum mechanics theory and the observations were compared with reported experimental results. The covalent linkages between COOH-modified graphene and the chitosan units were demonstrated and the combination of multi-functionalization on graphene could regulate the interfacial interactions between graphene and the chitosan. The interfacial interactions between chitosan and properly functionalized graphene are critical for the preparation of G–C-based composites for tissue engineering scaffolds and other applications.

  10. Investigation of adsorption of polymers on metallic nanowires: A molecular dynamics study

    Science.gov (United States)

    Mirabbaszadeh, Kavoos; Zaminpayma, Esmaeil

    2012-11-01

    Composite of polymer with a small content of strong material, such as carbon nanotube (CNT) and metallic nanowire (NW) has interesting mechanical, thermal, optical and electrical properties. For the first time, we used molecular dynamics simulations (MD) with polymer consistent force field (PCFF) to study adsorption of polymers involving Poly(3-hexythiophene) (P3HT) and Poly[[[(2ethylhexyl)oxy]methoxy-1,4-phenylene]-1,2-ethenediyl] (MEH-PPV) on metallic NW including silver and gold. The influence of main factors such as NW radius and temperature on the interfacial adhesion of NW-polymer and radius of gyration of polymers (Rg) were studied. We showed that the interaction energy decreases slowly with increasing temperature, thus the temperature influence is very weak. Our results showed that P3HT-Au has the strongest interaction energy, then MEH-PPV-Au, P3HT-Ag, and finally MEH-PPV-Ag. In addition, the interaction energy increased with increasing NW radius, thus the NW with large radius is the best type for reinforcement. We studied the influence of NW radius and temperature on the radius of gyration (Rg). We found that Rg oscillated slowly and no obvious trend was seen. In other words, NW radius and temperature had no influence on Rg value. We showed that the Rg value for P3HT was higher than MEH-PPV, thus P3HT expanded more than MEH-PPV on NW surface.

  11. Molecular Docking and 3D-Pharmacophore Modeling to Study the Interactions of Chalcone Derivatives with Estrogen Receptor Alpha

    Directory of Open Access Journals (Sweden)

    Muchtaridi Muchtaridi

    2017-10-01

    Full Text Available Tamoxifen is the most frequently used anti-estrogen adjuvant treatment for estrogen receptor-positive breast cancer. However, it is associated with an increased risk of several serious side–effects, such as uterine cancer, stroke, and pulmonary embolism. The 2′,4′-dihydroxy-6-methoxy-3,5-dimethylchalcone (ChalcEA from plant leaves of Eugenia aquea, has been found to inhibit the proliferation of MCF-7 human breast cancer cells in a dose-dependent manner, with an IC50 of 74.5 μg/mL (250 μM. The aim of this work was to study the molecular interactions of new ChalcEA derivatives formed with the Estrogen Receptor α (ERα using computer aided drug design approaches. Molecular docking using Autodock 4.2 was employed to explore the modes of binding of ChalcEA derivatives with ERα. The 3D structure-based pharmacophore model was derived using LigandScout 4.1 Advanced to investigate the important chemical interactions of the ERα-tamoxifen complex structure. The binding energy and the tamoxifen-pharmacophore fit score of the best ChalcEA derivative (HNS10 were −12.33 kcal/mol and 67.07 kcal/mol, respectively. The HNS10 interacted with Leu346, Thr347, Leu349, Ala350, Glu353, Leu387, Met388, Leu391, Arg394, Met421, and Leu525. These results suggest that the new ChalcEA derivatives could serve as the lead compound for potent ERα inhibitor in the fight against breast cancer.

  12. Molecular Docking and 3D-Pharmacophore Modeling to Study the Interactions of Chalcone Derivatives with Estrogen Receptor Alpha.

    Science.gov (United States)

    Muchtaridi, Muchtaridi; Syahidah, Hasna Nur; Subarnas, Anas; Yusuf, Muhammad; Bryant, Sharon D; Langer, Thierry

    2017-10-16

    Tamoxifen is the most frequently used anti-estrogen adjuvant treatment for estrogen receptor-positive breast cancer. However, it is associated with an increased risk of several serious side-effects, such as uterine cancer, stroke, and pulmonary embolism. The 2',4'-dihydroxy-6-methoxy-3,5-dimethylchalcone (ChalcEA) from plant leaves of Eugenia aquea , has been found to inhibit the proliferation of MCF-7 human breast cancer cells in a dose-dependent manner, with an IC 50 of 74.5 μg/mL (250 μM). The aim of this work was to study the molecular interactions of new ChalcEA derivatives formed with the Estrogen Receptor α (ERα) using computer aided drug design approaches. Molecular docking using Autodock 4.2 was employed to explore the modes of binding of ChalcEA derivatives with ERα. The 3D structure-based pharmacophore model was derived using LigandScout 4.1 Advanced to investigate the important chemical interactions of the ERα-tamoxifen complex structure. The binding energy and the tamoxifen-pharmacophore fit score of the best ChalcEA derivative (HNS10) were -12.33 kcal/mol and 67.07 kcal/mol, respectively. The HNS10 interacted with Leu346, Thr347, Leu349, Ala350, Glu353, Leu387, Met388, Leu391, Arg394, Met421, and Leu525. These results suggest that the new ChalcEA derivatives could serve as the lead compound for potent ERα inhibitor in the fight against breast cancer.

  13. Interaction mechanisms between organic UV filters and bovine serum albumin as determined by comprehensive spectroscopy exploration and molecular docking.

    Science.gov (United States)

    Ao, Junjie; Gao, Li; Yuan, Tao; Jiang, Gaofeng

    2015-01-01

    Organic UV filters are a group of emerging PPCP (pharmaceuticals and personal care products) contaminants. Current information is insufficient to understand the in vivo processes and health risks of organic UV filters in humans. The interaction mechanism of UV filters with serum albumin provides critical information for the health risk assessment of these active ingredients in sunscreen products. This study investigates the interaction mechanisms of five commonly used UV filters (2-hydroxy-4-methoxybenzophenone, BP-3; 2-ethylhexyl 4-methoxycinnamate, EHMC; 4-methylbenzylidene camphor, 4-MBC; methoxydibenzoylmethane, BDM; homosalate, HMS) with bovine serum albumin (BSA) by spectroscopic measurements of fluorescence, circular dichroism (CD), competitive binding experiments and molecular docking. Our results indicated that the fluorescence of BSA was quenched by these UV filters through a static quenching mechanism. The values of the binding constant (Ka) ranged from (0.78±0.02)×10(3) to (1.29±0.01)×10(5) L mol(-1). Further exploration by synchronous fluorescence and CD showed that the conformation of BSA was demonstrably changed in the presence of these organic UV filters. It was confirmed that the UV filters can disrupt the α-helical stability of BSA. Moreover, the results of molecular docking revealed that the UV filter molecule is located in site II (sub-domain IIIA) of BSA, which was further confirmed by the results of competitive binding experiments. In addition, binding occurred mainly through hydrogen bonding and hydrophobic interaction. This study raises critical concerns regarding the transportation, distribution and toxicity effects of organic UV filters in human body. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Caffeine and sulfadiazine interact differently with human serum albumin: A combined fluorescence and molecular docking study

    Science.gov (United States)

    Islam, Mullah Muhaiminul; Sonu, Vikash K.; Gashnga, Pynsakhiat Miki; Moyon, N. Shaemningwar; Mitra, Sivaprasad

    2016-01-01

    The interaction and binding behavior of the well-known drug sulfadiazine (SDZ) and psychoactive stimulant caffeine (CAF) with human serum albumin (HSA) was monitored by in vitro fluorescence titration and molecular docking calculations under physiological condition. The quenching of protein fluorescence on addition of CAF is due to the formation of protein-drug complex in the ground state; whereas in case of SDZ, the experimental results were explained on the basis of sphere of action model. Although both these compounds bind preferentially in Sudlow's site 1 of the protein, the association constant is approximately two fold higher in case of SDZ (∼4.0 × 104 M-1) in comparison with CAF (∼9.3 × 102 M-1) and correlates well with physico-chemical properties like pKa and lipophilicity of the drugs. Temperature dependent fluorescence study reveals that both SDZ and CAF bind spontaneously with HSA. However, the binding of SDZ with the protein is mainly governed by the hydrophobic forces in contrast with that of CAF; where, the interaction is best explained in terms of electrostatic mechanism. Molecular docking calculation predicts the binding of these drugs in different location of sub-domain IIA in the protein structure.

  15. Molecular players involved in the interaction between beneficial bacteria and the immune system

    Directory of Open Access Journals (Sweden)

    Arancha eHevia

    2015-11-01

    Full Text Available The human gastrointestinal tract is a very complex ecosystem, in which there is a continuous interaction between nutrients, host cells, and microorganisms. The gut microbiota comprises trillions of microbes that have been selected during evolution on the basis of their functionality and capacity to survive in, and adapt to, the intestinal environment. Host bacteria and our immune system constantly sense and react to one another. In this regard, commensal microbes contribute to gut homeostasis, whereas the necessary responses are triggered against enteropathogens. Some representatives of our gut microbiota have beneficial effects on human health. Some of the most important roles of these microbes are to help to maintain the integrity of the mucosal barrier, to provide nutrients such as vitamins, or to protect against pathogens. In addition, the interaction between commensal microbiota and the mucosal immune system is crucial for proper immune function. This process is mainly performed via the pattern recognition receptors of epithelial cells, such as Toll-like or Nod-like receptors, which are able to recognize the molecular effectors that are produced by intestinal microbes. These effectors mediate processes that can ameliorate certain inflammatory gut disorders, discriminate between beneficial and pathogenic bacteria, or increase the number of immune cells or their pattern recognition receptors. This review intends to summarize the molecular players produced by probiotic bacteria, notably Lactobacillus and Bifidobacterium strains, but also other very promising potential probiotics, which affect the human immune system.

  16. Interaction of VUV-photons with molecules. Spectroscopy and dynamics of molecular superexcited states

    International Nuclear Information System (INIS)

    Hatano, Y.

    2002-01-01

    Complete text of publication follows. A survey is given of recent progress in experimental studies of the interaction of VUV-photons with molecules, i.e., those of photoabsorption, photoionization, and photodissociation of molecules in the excitation photon energy range of 10-50 eV, with a particular emphasis placed on current understanding of the spectroscopy and dynamics of formed molecular superexcited states. These studies are of great importance in understanding the interaction of ionizing radiation with matter. Molecules studied are ranged from simple diatomic and triatomic molecules to polyatomic molecules such as hydrocarbons. Most of the observed molecular superexcited states are assigned to high Rydber states which are vibrationally, doubly, or inner-core excited and converge to each of ion states. Non-Rydberg superexcited states are also observed. Dissociation into neutral fragments in comparison with ionization is of unexpectedly great importance in the observed decay of each of these state-assigned superexcited molecules. Dissociation dynamics as well as its products of superexcited states are remarkably different from those of lower excited states below about ionization thresholds. Some remarks are also presented of molecules in the condensed phase

  17. TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.

    Science.gov (United States)

    Newton, Yulia; Novak, Adam M; Swatloski, Teresa; McColl, Duncan C; Chopra, Sahil; Graim, Kiley; Weinstein, Alana S; Baertsch, Robert; Salama, Sofie R; Ellrott, Kyle; Chopra, Manu; Goldstein, Theodore C; Haussler, David; Morozova, Olena; Stuart, Joshua M

    2017-11-01

    Vast amounts of molecular data are being collected on tumor samples, which provide unique opportunities for discovering trends within and between cancer subtypes. Such cross-cancer analyses require computational methods that enable intuitive and interactive browsing of thousands of samples based on their molecular similarity. We created a portal called TumorMap to assist in exploration and statistical interrogation of high-dimensional complex "omics" data in an interactive and easily interpretable way. In the TumorMap, samples are arranged on a hexagonal grid based on their similarity to one another in the original genomic space and are rendered with Google's Map technology. While the important feature of this public portal is the ability for the users to build maps from their own data, we pre-built genomic maps from several previously published projects. We demonstrate the utility of this portal by presenting results obtained from The Cancer Genome Atlas project data. Cancer Res; 77(21); e111-4. ©2017 AACR . ©2017 American Association for Cancer Research.

  18. Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials.

    Science.gov (United States)

    Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D

    2017-08-14

    Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

  19. Molecular Players Involved in the Interaction Between Beneficial Bacteria and the Immune System.

    Science.gov (United States)

    Hevia, Arancha; Delgado, Susana; Sánchez, Borja; Margolles, Abelardo

    2015-01-01

    The human gastrointestinal tract is a very complex ecosystem, in which there is a continuous interaction between nutrients, host cells, and microorganisms. The gut microbiota comprises trillions of microbes that have been selected during evolution on the basis of their functionality and capacity to survive in, and adapt to, the intestinal environment. Host bacteria and our immune system constantly sense and react to one another. In this regard, commensal microbes contribute to gut homeostasis, whereas the necessary responses are triggered against enteropathogens. Some representatives of our gut microbiota have beneficial effects on human health. Some of the most important roles of these microbes are to help to maintain the integrity of the mucosal barrier, to provide nutrients such as vitamins, or to protect against pathogens. In addition, the interaction between commensal microbiota and the mucosal immune system is crucial for proper immune function. This process is mainly performed via the pattern recognition receptors of epithelial cells, such as Toll-like or Nod-like receptors, which are able to recognize the molecular effectors that are produced by intestinal microbes. These effectors mediate processes that can ameliorate certain inflammatory gut disorders, discriminate between beneficial and pathogenic bacteria, or increase the number of immune cells or their pattern recognition receptors (PRRs). This review intends to summarize the molecular players produced by probiotic bacteria, notably Lactobacillus and Bifidobacterium strains, but also other very promising potential probiotics, which affect the human immune system.

  20. Binding and discerning interactions of PTP1B allosteric inhibitors: novel insights from molecular dynamics simulations.

    Science.gov (United States)

    Shinde, Ranajit Nivrutti; Sobhia, M Elizabeth

    2013-09-01

    The α7 helix is either disordered or missing in the three co-crystal structures of allosteric inhibitors with protein tyrosine phosphatase 1B (PTP1B). It was modeled in each complex using the open form of PTP1B structure and studied using molecular dynamics (MD) simulations for 25 ns. B-factor analysis of the residues sheds light on its disordered nature in the co-crystal structures. Further, the ability of inhibitors to act as allosteric inhibitor was studied and established using novel hydrogen bond criteria. The MD simulations were utilized to determine the relative importance of electrostatic and hydrophobic component in to the binding of inhibitors. It was revealed that the hydrophobic interactions predominantly drive the molecular recognition of these inhibitors. Per residue energy decomposition analysis attributed dissimilar affinities of three inhibitors to the several hydrogen bonds and non-bonded interactions. Among the secondary structure elements that surround the allosteric site, helices α6, α7 and loop α6-α7 were notorious in providing variable affinities to the inhibitors. A novel hydrophobic pocket lined by the α7 helix residues Val287, Asn289 and Trp291 was identified in the allosteric site. This study provides useful insights for the rational design of high affinity PTP1B allosteric inhibitors. Copyright © 2013 Elsevier Inc. All rights reserved.