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Sample records for gas-phase protein structure

  1. Probing Protein Structure and Folding in the Gas Phase by Electron Capture Dissociation

    Science.gov (United States)

    Schennach, Moritz; Breuker, Kathrin

    2015-07-01

    The established methods for the study of atom-detailed protein structure in the condensed phases, X-ray crystallography and nuclear magnetic resonance spectroscopy, have recently been complemented by new techniques by which nearly or fully desolvated protein structures are probed in gas-phase experiments. Electron capture dissociation (ECD) is unique among these as it provides residue-specific, although indirect, structural information. In this Critical Insight article, we discuss the development of ECD for the structural probing of gaseous protein ions, its potential, and limitations.

  2. Protein and Peptide Gas-phase Structure Investigation Using Collision Cross Section Measurements and Hydrogen Deuterium Exchange

    Science.gov (United States)

    Khakinejad, Mahdiar

    Protein and peptide gas-phase structure analysis provides the opportunity to study these species outside of their explicit environment where the interaction network with surrounding molecules makes the analysis difficult [1]. Although gas-phase structure analysis offers a unique opportunity to study the intrinsic behavior of these biomolecules [2-4], proteins and peptides exhibit very low vapor pressures [2]. Peptide and protein ions can be rendered in the gas-phase using electrospray ionization (ESI) [5]. There is a growing body of literature that shows proteins and peptides can maintain solution structures during the process of ESI and these structures can persist for a few hundred milliseconds [6-9]. Techniques for monitoring gas-phase protein and peptide ion structures are categorized as physical probes and chemical probes. Collision cross section (CCS) measurement, being a physical probe, is a powerful method to investigate gas-phase structure size [3, 7, 10-15]; however, CCS values alone do not establish a one to one relation with structure(i.e., the CCS value is an orientationally averaged value [15-18]. Here we propose the utility of gas-phase hydrogen deuterium exchange (HDX) as a second criterion of structure elucidation. The proposed approach incudes extensive MD simulations to sample biomolecular ion conformation space with the production of numerous, random in-silico structures. Subsequently a CCS can be calculated for these structures and theoretical CCS values are compared with experimental values to produce a pool of candidate structures. Utilizing a chemical reaction model based on the gas-phase HDX mechanism, the HDX kinetics behavior of these candidate structures are predicted and compared to experimental results to nominate the best in-silico structures which match (chemically and physically) with experimental observations. For the predictive approach to succeed, an extensive technique and method development is essential. To combine CCS

  3. Charge Mediated Compaction and Rearrangement of Gas-Phase Proteins: A Case Study Considering Two Proteins at Opposing Ends of the Structure-Disorder Continuum

    Science.gov (United States)

    Jhingree, Jacquelyn R.; Bellina, Bruno; Pacholarz, Kamila J.; Barran, Perdita E.

    2017-07-01

    Charge reduction in the gas phase provides a direct means of manipulating protein charge state, and when coupled to ion mobility mass spectrometry (IM-MS), it is possible to monitor the effect of charge on protein conformation in the absence of solution. Use of the electron transfer reagent 1,3-dicyanobenzene, coupled with IM-MS, allows us to monitor the effect of charge reduction on the conformation of two proteins deliberately chosen from opposite sides of the order to disorder continuum: bovine pancreatic trypsin inhibitor (BPTI) and beta casein. The ordered BPTI presents compact conformers for each of three charge states accompanied by narrow collision cross-section distributions (TWCCSDN2→He). Upon reduction of BPTI, irrespective of precursor charge state, the TWCCSN2→He decreases to a similar distribution as found for the nESI generated ion of identical charge. The behavior of beta casein upon charge reduction is more complex. It presents over a wide charge state range (9-28), and intermediate charge states (13-18) have broad TWCCSDN2→He with multiple conformations, where both compaction and rearrangement are seen. Further, we see that the TWCCSDN2→He of the latter charge states are even affected by the presence of radical anions. Overall, we conclude that the flexible nature of some proteins result in broad conformational distributions comprised of many families, even for single charge states, and the barrier between different states can be easily overcome by an alteration of the net charge.

  4. Gas phase structure of transition metal dihydrides

    International Nuclear Information System (INIS)

    Demuynck, J.; Schaefer, H.F. III

    1980-01-01

    ESR and infrared spectroscopic measurements on matrix isolated MnH 2 and CrH 2 have recently suggested that these simple molecules may be bent. This result would be the opposite of that found experimentally for the transition metal dihalides MX 2 , known to be linear. Here the geometrical structure of MnH 2 has been investigated by molecular electronic structure theory. A large contracted Gaussian basis set [Mn(14s11p6p/9s8p3d), H(5s1p/3s1p)] was used in conjunction with self-consistent field and configuration interaction methods. These suggest that the 6 A 1 ground state of MnH 2 is linear. Further studies of the 3 A 1 state (one of several low-lying states) of TiH 2 also favor linearity, although this potential energy surface is extremely flat with respect to bending. Thus it appears probable that most MH 2 molecules, like the related MX 2 family, are linear

  5. Probing the Binding Interfaces of Protein Complexes Using Gas-Phase H/D Exchange Mass Spectrometry

    DEFF Research Database (Denmark)

    Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F

    2016-01-01

    Fast gas-phase hydrogen/deuterium exchange mediated by ND3 gas and measured by mass spectrometry (gas-phase HDX-MS) is a largely unharnessed, fast, and sensitive method for probing primary- and higher-order polypeptide structure. Labeling of heteroatom-bound non-amide hydrogens in a sub-milliseco......Fast gas-phase hydrogen/deuterium exchange mediated by ND3 gas and measured by mass spectrometry (gas-phase HDX-MS) is a largely unharnessed, fast, and sensitive method for probing primary- and higher-order polypeptide structure. Labeling of heteroatom-bound non-amide hydrogens in a sub......-millisecond time span after electrospray ionization by ND3 gas can provide structural insights into protein conformers present in solution. Here, we have explored the use of gas-phase HDX-MS for probing the higher-order structure and binding interfaces of protein complexes originating from native solution...

  6. Gas phase absorption studies of photoactive yellow protein chromophore derivatives.

    Science.gov (United States)

    Rocha-Rinza, Toms; Christiansen, Ove; Rajput, Jyoti; Gopalan, Aravind; Rahbek, Dennis B; Andersen, Lars H; Bochenkova, Anastasia V; Granovsky, Alexander A; Bravaya, Ksenia B; Nemukhin, Alexander V; Christiansen, Kasper Lincke; Nielsen, Mogens Brøndsted

    2009-08-27

    Photoabsorption spectra of deprotonated trans p-coumaric acid and two of its methyl substituted derivatives have been studied in gas phase both experimentally and theoretically. We have focused on the spectroscopic effect of the location of the two possible deprotonation sites on the trans p-coumaric acid which originate to either a phenoxide or a carboxylate. Surprisingly, the three chromophores were found to have the same absorption maximum at 430 nm, in spite of having different deprotonation positions. However, the absorption of the chromophore in polar solution is substantially different for the distinct deprotonation locations. We also report on the time scales and pathways of relaxation after photoexcitation for the three photoactive yellow protein chromophore derivatives. As a result of these experiments, we could detect the phenoxide isomer within the deprotonated trans p-coumaric acid in gas phase; however, the occurrence of the carboxylate is uncertain. Several computational methods were used simultaneously to provide insights and assistance in the interpretation of our experimental results. The calculated excitation energies S(0)-S(1) are in good agreement with experiment for those systems having a negative charge on a phenoxide moiety. Although our augmented multiconfigurational quasidegenerate perturbation theory calculations agree with experiment in the description of the absorption spectrum of anions with a carboxylate functional group, there are some puzzling disagreements between experiment and some calculational methods in the description of these systems.

  7. Determination of gas phase protein ion densities via ion mobility analysis with charge reduction.

    Science.gov (United States)

    Maisser, Anne; Premnath, Vinay; Ghosh, Abhimanyu; Nguyen, Tuan Anh; Attoui, Michel; Hogan, Christopher J

    2011-12-28

    We use a charge reduction electrospray (ESI) source and subsequent ion mobility analysis with a differential mobility analyzer (DMA, with detection via both a Faraday cage electrometer and a condensation particle counter) to infer the densities of single and multiprotein ions of cytochrome C, lysozyme, myoglobin, ovalbumin, and bovine serum albumin produced from non-denaturing (20 mM aqueous ammonium acetate) and denaturing (1 : 49.5 : 49.5, formic acid : methanol : water) ESI. Charge reduction is achieved through use of a Po-210 radioactive source, which generates roughly equal concentrations of positive and negative ions. Ions produced by the source collide with and reduce the charge on ESI generated drops, preventing Coulombic fissions, and unlike typical protein ESI, leading to gas-phase protein ions with +1 to +3 excess charges. Therefore, charge reduction serves to effectively mitigate any role that Coulombic stretching may play on the structure of the gas phase ions. Density inference is made via determination of the mobility diameter, and correspondingly the spherical equivalent protein volume. Through this approach it is found that for both non-denaturing and denaturing ESI-generated ions, gas-phase protein ions are relatively compact, with average densities of 0.97 g cm(-3) and 0.86 g cm(-3), respectively. Ions from non-denaturing ESI are found to be slightly more compact than predicted from the protein crystal structures, suggesting that low charge state protein ions in the gas phase are slightly denser than their solution conformations. While a slight difference is detected between the ions produced with non-denaturing and denaturing ESI, the denatured ions are found to be much more dense than those examined previously by drift tube mobility analysis, in which charge reduction was not employed. This indicates that Coulombic stretching is typically what leads to non-compact ions in the gas-phase, and suggests that for gas phase

  8. Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

    OpenAIRE

    De Almeida, Wagner B.

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can ma...

  9. The gas phase structure of α -pinene, a main biogenic volatile organic compound

    Science.gov (United States)

    Neeman, Elias M.; Avilés Moreno, Juan Ramón; Huet, Thérèse R.

    2017-12-01

    The gas phase structure of the bicyclic atmospheric aerosol precursor α-pinene was investigated employing a combination of quantum chemical calculation and Fourier transform microwave spectroscopy coupled to a supersonic jet expansion. The very weak rotational spectra of the parent species and all singly substituted 13C in natural abundance have been identified, from 2 to 20 GHz, and fitted to Watson's Hamiltonian model. The rotational constants were used together with geometrical parameters from density functional theory and ab initio calculations to determine the rs, r0, and rm(1 ) structures of the skeleton, without any structural assumption in the fit concerning the heavy atoms. The double C=C bond was found to belong to a quasiplanar skeleton structure containing 6 carbon atoms. Comparison with solid phase structure is reported. The significant differences of α-pinene in gas phase and other gas phase bicyclic monoterpene structures (β-pinene, nopinone, myrtenal, and bicyclo[3.1.1]heptane) are discussed.

  10. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase

    International Nuclear Information System (INIS)

    Almeida, Wagner B. de

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  11. Origin of Asymmetric Charge Partitioning in the Dissociation of Gas-Phase Protein Homodimers

    OpenAIRE

    Jurchen, John C.; Williams, Evan R.

    2003-01-01

    The origin of asymmetric charge and mass partitioning observed for gas-phase dissociation of multiply charged macromolecular complexes has been hotly debated. These experiments hold the potential to provide detailed information about the interactions between the macromolecules within the complex. Here, this unusual phenomenon of asymmetric charge partitioning is investigated for several protein homodimers. Asymmetric charge partitioning in these ions depends on a number of factors, including ...

  12. Probing the glycosidic linkage: secondary structures in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Simons, John P; Cristina Stanca-Kaposta, E; Cocinero, Emilio J; Liu, B [Chemistry Department, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (United Kingdom); Davis, Benjamin G; Gamblin, David P [Chemistry Department, Chemical Research Laboratory, 12 Mansfield Road, Oxford OX1 4TA (United Kingdom); Kroemer, Romano T [Sanofi-Aventis, CRVA, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine (France)], E-mail: John.Simons@chem.ox.ac.uk

    2008-10-15

    The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition, is immense. Characterizing the three-dimensional (3D) structures of carbohydrates and glycoproteins, and their interactions with other molecules, not least the ubiquitous solvent, water, is a key starting point for understanding these processes. The combination of laser-based electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is providing a uniquely powerful means of characterizing 3D carbohydrate conformations; the structures of their hydrated complexes, the hydrogen-bonded networks they support (or which support them); and the factors that determine their conformational and structural preferences.

  13. Probing the glycosidic linkage: secondary structures in the gas phase

    International Nuclear Information System (INIS)

    Simons, John P; Cristina Stanca-Kaposta, E; Cocinero, Emilio J; Liu, B; Davis, Benjamin G; Gamblin, David P; Kroemer, Romano T

    2008-01-01

    The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition, is immense. Characterizing the three-dimensional (3D) structures of carbohydrates and glycoproteins, and their interactions with other molecules, not least the ubiquitous solvent, water, is a key starting point for understanding these processes. The combination of laser-based electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is providing a uniquely powerful means of characterizing 3D carbohydrate conformations; the structures of their hydrated complexes, the hydrogen-bonded networks they support (or which support them); and the factors that determine their conformational and structural preferences.

  14. Gas Phase Structure of Amino Acids: La-Mb Studies

    Science.gov (United States)

    Mata, I. Pena S.; Sanz, M. E.; Vaquero, V.; Cabezas, C.; Perez, C.; Blanco, S.; López, J. C.; Alonso, J. L.

    2009-06-01

    Recent improvements in our laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectrometer such as using Laval-type nozzles and picoseconds Nd:YAG lasers (30 to 150 ps) have allowed a major step forward in the capabilities of this experimental technique as demonstrated by the last results in serine cysteine and threonine^a for which seven, six and seven conformers have been respectively identified. Taking advantage of these improvements we have investigated the natural amino acids metionine, aspartic and glutamic acids and the γ-aminobutyric acid (GABA) with the aim of identify and characterize their lower energy conformers. Searches in the rotational spectra have lead to the identification of seven conformers of metionine, six and five of aspartic and glutamic acids, respectively, and seven for the γ-aminobutyric. These conformers have been unambiguously identified by their spectroscopic constants. In particular the ^{14}N nuclear quadrupole coupling constants, that depend heavily on the orientation of the amino group with respect to the principal inertial axes of the molecule, prove to be a unique tool to distinguish unambigously between conformations with similar rotational constants. For the γ-aminobutyric acid two of the seven observed structures are stablized by an intramolecular interaction n-π*. Two new conformers of proline have been identified together with the two previously observed. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys.Chem.Chem.Phys., 2009, 11, 617. D. B. Atkinson, M. A. Smith, Rev. Sci. Instrum. 1995, 66, 4434 S. Blanco, M. E. Sanz, J. C. López, J. L. Alonso, Proc. Natl. Acad. Sci. USA2007, 104, 20183. M. E. Sanz, S. Blanco, J. C. López, J. L. Alonso, Angew. Chem. Int. Ed.,2008, 120, 6312. A. Lesarri, S. Mata, E. J. Cocinero, S. Blanco, J.C. López, J. L. Alonso, Angew. Chem. Int. Ed. , 2002, 41, 4673

  15. Biofilm structure and mass transfer in a gas phase trickle-bed biofilter.

    Science.gov (United States)

    Zhu, X; Suidan, M T; Alonso, C; Yu, T; Kim, B J; Kim, B R

    2001-01-01

    Mass transport phenomena occurring in the biofilms of gas phase trickle-bed biofilters are investigated in this study. The effect of biofilm structure on mass transfer mechanisms is examined using experimental observation from the operating of biofilters, microelectrode techniques and microscopic examination. Since the biofilms of biofilters used for waste gas treatment are not completely saturated with water, there is not a distinguishable liquid layer outside the biofilm. Results suggest that due to this characteristic, gas phase substrates (such as oxygen or volatile organic compounds) may not be limited by the aqueous phase because transport of the compound into the biofilm can occur directly through non-wetted areas. On the other hand, for substrates that are present only in the liquid phase, such as nitrate, the mass transfer limitation is more serious because of the limited liquid supply. Microscopic observations show that a layered structure with void spaces exists within the biofilm. Oxygen concentration distributions along the depth of the biofilms are examined using an oxygen microelectrode. Results indicate that there are some high dissolved oxygen zones inside the biofilm, which suggests the existence of passages for oxygen transfer into the deeper sections of the biofilm in a gas phase trickle-bed biofilter. Both the low gas-liquid mass transfer resistance and the resulting internal structure contribute to the high oxygen penetration within the biofilms in gas phase trickle-bed biofilters.

  16. Gas-phase ion/ion reactions of peptides and proteins: acid/base, redox, and covalent chemistries.

    Science.gov (United States)

    Prentice, Boone M; McLuckey, Scott A

    2013-02-01

    Gas-phase ion/ion reactions are emerging as useful and flexible means for the manipulation and characterization of peptide and protein biopolymers. Acid/base-like chemical reactions (i.e., proton transfer reactions) and reduction/oxidation (redox) reactions (i.e., electron transfer reactions) represent relatively mature classes of gas-phase chemical reactions. Even so, especially in regards to redox chemistry, the widespread utility of these two types of chemistries is undergoing rapid growth and development. Additionally, a relatively new class of gas-phase ion/ion transformations is emerging which involves the selective formation of functional-group-specific covalent bonds. This feature details our current work and perspective on the developments and current capabilities of these three areas of ion/ion chemistry with an eye towards possible future directions of the field.

  17. Structure and dynamics of gas phase ions: Interplay between experiments and computations in IRMPD spectroscopy

    Science.gov (United States)

    Coletti, Cecilia; Corinti, Davide; Paciotti, Roberto; Re, Nazzareno; Crestoni, Maria Elisa; Fornarini, Simonetta

    2017-11-01

    The investigation of the molecular structure and dynamics of ions in gas phase is an item of increasing interest, due the role such species play in many areas of chemistry and physics, not to mention that they often represent elusive intermediates in more complex reaction mechanisms. Infrared Multiple Photon Dissociation spectroscopy is today one of the most advanced technique to this purpose, because of its high sensitivity to even small structure changes. The interpretation of IRMPD spectra strongly relies on high level quantum mechanical computations, so that a close interplay is needed for a detailed understanding of structure and kinetics properties which can be gathered from the many applications of this powerful technique. Recent advances in experiment and theory in this field are here illustrated, with emphasis on recent progresses for the elucidation of the mechanism of action of cisplatin, one of the most widely used anticancer drugs.

  18. UPS and DFT investigation of the electronic structure of gas-phase trimesic acid

    Energy Technology Data Exchange (ETDEWEB)

    Reisberg, L., E-mail: rebban@ut.ee [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); Pärna, R. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); MAX IV Laboratory, Lund University, Fotongatan 2, 225 94 Lund (Sweden); Kikas, A.; Kuusik, I.; Kisand, V. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia); Hirsimäki, M.; Valden, M. [Surface Science Laboratory, Optoelectronics Research Centre, Tampere University of Technology, FIN-33101 Tampere (Finland); Nõmmiste, E. [Institute of Physics, University of Tartu, W. Oswaldi 1, EE-50411 Tartu (Estonia)

    2016-11-15

    Highlights: • In the current study outer valence band electronic structure of benzene-1,3,5-tricarboxylic acid was interpreted. • Experimental and calculated trimesic acid (TMA) spectrum were compared to ones of benzene and benzoic acid. • It is shown that similarities between MO energies and shapes for benzene and TMA exists. • Addition of carboxyl groups to the benzene ring clearly correlates with increasing binding energy of HOMO. - Abstract: Benzene-1,3,5-tricarboxylic acid (trimesic acid, TMA) molecules in gas-phase have been investigated by using valence band photoemission. The photoelectron spectrum in the binding energy region from 9 to 22 eV is interpreted by using density functional theory calculations. The electronic structure of TMA is compared with benzene and benzoic acid in order to demonstrate changes in molecular orbital energies induced by addition of carboxyl groups to benzene ring.

  19. Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.

    Science.gov (United States)

    Bythell, Benjamin J; Csonka, István P; Suhai, Sándor; Barofsky, Douglas F; Paizs, Béla

    2010-11-25

    The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.

  20. The structure optimization of gas-phase surface discharge and its application for dye degradation

    Science.gov (United States)

    Ying, CAO; Jie, LI; Nan, JIANG; Yan, WU; Kefeng, SHANG; Na, LU

    2018-05-01

    A gas-phase surface discharge (GSD) was employed to optimize the discharge reactor structure and investigate the dye degradation. A dye mixture of methylene blue, acid orange and methyl orange was used as a model pollutant. The results indicated that the reactor structure of the GSD system with the ratio of tube inner surface area and volume of 2.48, screw pitch between a high-voltage electrode of 9.7 mm, high-voltage electrode wire diameter of 0.8 mm, dielectric tube thickness of 2.0 mm and tube inner diameter of 16.13 mm presented a better ozone (O3) generation efficiency. Furthermore, a larger screw pitch and smaller wire diameter enhanced the O3 generation. After the dye mixture degradation by the optimized GSD system, 73.21% and 50.74% of the chemical oxygen demand (COD) and total organic carbon removal rate were achieved within 20 min, respectively, and the biochemical oxygen demand (BOD) and biodegradability (BOD/COD) improved.

  1. Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

    Science.gov (United States)

    Mawhorter, Richard J., Jr.

    A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

  2. Ground-State Gas-Phase Structures of Inorganic Molecules Predicted by Density Functional Theory Methods

    KAUST Repository

    Minenkov, Yury

    2017-11-29

    We tested a battery of density functional theory (DFT) methods ranging from generalized gradient approximation (GGA) via meta-GGA to hybrid meta-GGA schemes as well as Møller–Plesset perturbation theory of the second order and a single and double excitation coupled-cluster (CCSD) theory for their ability to reproduce accurate gas-phase structures of di- and triatomic molecules derived from microwave spectroscopy. We obtained the most accurate molecular structures using the hybrid and hybrid meta-GGA approximations with B3PW91, APF, TPSSh, mPW1PW91, PBE0, mPW1PBE, B972, and B98 functionals, resulting in lowest errors. We recommend using these methods to predict accurate three-dimensional structures of inorganic molecules when intramolecular dispersion interactions play an insignificant role. The structures that the CCSD method predicts are of similar quality although at considerably larger computational cost. The structures that GGA and meta-GGA schemes predict are less accurate with the largest absolute errors detected with BLYP and M11-L, suggesting that these methods should not be used if accurate three-dimensional molecular structures are required. Because of numerical problems related to the integration of the exchange–correlation part of the functional and large scattering of errors, most of the Minnesota models tested, particularly MN12-L, M11, M06-L, SOGGA11, and VSXC, are also not recommended for geometry optimization. When maintaining a low computational budget is essential, the nonseparable gradient functional N12 might work within an acceptable range of error. As expected, the DFT-D3 dispersion correction had a negligible effect on the internuclear distances when combined with the functionals tested on nonweakly bonded di- and triatomic inorganic molecules. By contrast, the dispersion correction for the APF-D functional has been found to shorten the bonds significantly, up to 0.064 Å (AgI), in Ag halides, BaO, BaS, BaF, BaCl, Cu halides, and Li and

  3. Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: overcoming gas-phase hydrogen/deuterium scrambling.

    Science.gov (United States)

    Rand, Kasper D; Zehl, Martin; Jørgensen, Thomas J D

    2014-10-21

    acidic conditions where the amide hydrogen exchange rate is slowed by many orders of magnitude). The ability to localize the individual deuterated residues (the spatial resolution) is determined by the size (typically ∼7-15 residues) and the number of peptic peptides. These peptides provide a relatively coarse-grained picture of the protein dynamics. A fundamental understanding of the relationship between protein function/dysfunction and conformational dynamics requires in many cases higher resolution and ultimately single-residue resolution. In this Account, we summarize our efforts to achieve single-residue deuterium levels in proteins by electron-based or laser-induced gas-phase fragmentation methods. A crucial analytical requirement for this approach is that the pattern of deuterium labeling from solution is retained in the gas-phase fragment ions. It is therefore essential to control and minimize any occurrence of gas-phase randomization of the solution deuterium label (H/D scrambling) during the MS experiment. For this purpose, we have developed model peptide probes to accurately measure the onset and extent of H/D scrambling. Our analytical procedures to control the occurrence of H/D scrambling are detailed along with the physical parameters that induce it during MS analysis. In light of the growing use of gas-phase dissociation experiments to measure the HDX of proteins in order to obtain a detailed characterization and understanding of the dynamic conformations and interactions of proteins at the molecular level, we discuss the perspectives and challenges of future high-resolution HDX-MS methodology.

  4. Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 3. Relating Solution-Phase to Gas-Phase Structures.

    Science.gov (United States)

    Kondalaji, Samaneh Ghassabi; Khakinejad, Mahdiar; Valentine, Stephen J

    2018-06-01

    Molecular dynamics (MD) simulations have been utilized to study peptide ion conformer establishment during the electrospray process. An explicit water model is used for nanodroplets containing a model peptide and hydronium ions. Simulations are conducted at 300 K for two different peptide ion charge configurations and for droplets containing varying numbers of hydronium ions. For all conditions, modeling has been performed until production of the gas-phase ions and the resultant conformers have been compared to proposed gas-phase structures. The latter species were obtained from previous studies in which in silico candidate structures were filtered according to ion mobility and hydrogen-deuterium exchange (HDX) reactivity matches. Results from the present study present three key findings namely (1) the evidence from ion production modeling supports previous structure refinement studies based on mobility and HDX reactivity matching, (2) the modeling of the electrospray process is significantly improved by utilizing initial droplets existing below but close to the calculated Rayleigh limit, and (3) peptide ions in the nanodroplets sample significantly different conformers than those in the bulk solution due to altered physicochemical properties of the solvent. Graphical Abstract ᅟ.

  5. Structure Elucidation of Dimethylformamide-Solvated Alkylzinc Cations in the Gas Phase

    NARCIS (Netherlands)

    Dreiocker, F.; Oomens, J.; Meijer, Ajhm; Pickup, B. T.; Jackson, R. F. W.; Schafer, M.

    2010-01-01

    Organozinc iodides, useful for the synthesis of nonproteinogenic amino acids, are investigated in the gas phase by a combination of electrospray (ESI)-MS/MS, accurate ion mass measurements, and infrared multiphoton dissociation (IRMPD) spectroscopy employing a free electron laser. ESI allowed the

  6. Structure elucidation of dimethylformamide-solvated alkylzinc cations in the gas phase

    NARCIS (Netherlands)

    Dreiocker, F.; Oomens, J.; Meijer, A.J.H.M.; Pickup, B.T.; Jackson, R.F.W.; Schäfer, M.

    2010-01-01

    Organozinc iodides, useful for the synthesis of nonproteinogenic amino acids, are investigated in the gas phase by a combination of electrospray (ESI)-MS/MS, accurate ion mass measurements, and infrared multiphoton dissociation (IRMPD) spectroscopy employing a free electron laser. ESI allowed the

  7. Imaging Molecular Structure through Femtosecond Photoelectron Diffraction on Aligned and Oriented Gas-Phase Molecules

    DEFF Research Database (Denmark)

    Boll, Rebecca; Rouzee, Arnaud; Adolph, Marcus

    2014-01-01

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray Free-Electron Laser. We present results of two experiments aimed at measuring photoelectron angular...

  8. Activation of methane by zinc: gas-phase synthesis, structure, and bonding of HZnCH3.

    Science.gov (United States)

    Flory, Michael A; Apponi, Aldo J; Zack, Lindsay N; Ziurys, Lucy M

    2010-12-08

    The methylzinc hydride molecule, HZnCH3, has been observed in the gas phase for the first time in the monomeric form using high-resolution spectroscopic techniques. The molecule was synthesized by two methods: the reaction of dimethylzinc with hydrogen gas and methane in an AC discharge and the reaction of zinc vapor produced in a Broida-type oven with methane in a DC discharge. HZnCH3 was identified on the basis of its pure rotational spectrum, which was recorded using millimeter/submillimeter direct-absorption and Fourier transform microwave techniques over the frequency ranges 332-516 GHz and 18-41 GHz, respectively. Multiple rotational transitions were measured for this molecule in seven isotopic variants. K-ladder structure was clearly present in all of the spectra, indicating a molecule with C3v symmetry and a (1)A1 ground electronic state. Extensive quadrupole hyperfine structure arising from the (67)Zn nucleus was observed for the H(67)ZnCH3 species, suggesting covalent bonding to the zinc atom. From the multiple isotopic substitutions, a precise structure for HZnCH3 has been determined. The influence of the axial hydrogen atom slightly distorts the methyl group but stabilizes the Zn-C bond. This study suggests that HZnCH3 can be formed through the oxidative addition of zinc to methane in the gas phase under certain conditions. HZnCH3 is the first metal-methane insertion complex to be structurally characterized.

  9. Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale.

    Science.gov (United States)

    Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D

    2014-12-02

    Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.

  10. Analyte induced water adsorbability in gas phase biosensors: the influence of ethinylestradiol on the water binding protein capacity.

    Science.gov (United States)

    Snopok, Borys; Kruglenko, Ivanna

    2015-05-07

    An ultra-sensitive gas phase biosensor/tracer/bio-sniffer is an emerging technology platform designed to provide real-time information on air-borne analytes, or those in liquids, through classical headspace analysis. The desired bio-sniffer measures gaseous 17α- ethinylestradiol (ETED) as frequency changes on a quartz crystal microbalance (QCM), which is a result of the interactions of liquid sample components in the headspace (ETED and water) with a biorecognition layer. The latter was constructed by immobilization of polyclonal antiserum against a phenolic A-ring of estrogenic receptors through protein A. The QCM response exhibited stretched exponential kinetics of negative frequency shifts with reversible and "irreversible" components of mass uptake onto the sensor surface in static headspace conditions when exposed to water solutions of ETED over the sensor working range, from 10(-10) to 10(-17) g L(-1). It was shown that the variations in the QCM response characteristics are due to the change of the water-binding capacity of the sensing layer induced by protein transformations initiated by the binding of ETED molecules. This result is well correlated with the natural physiological function of estrogens in controlling the homeostasis of body fluids in living beings.

  11. An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase.

    Science.gov (United States)

    Bravaya, Ksenia; Bochenkova, Anastasia; Granovsky, Alexander; Nemukhin, Alexander

    2007-10-31

    We considered a series of model systems for treating the photoabsorption of the 11-cis retinal chromophore in the protonated Schiff-base form in vacuum, solutions, and the protein environment. A high computational level, including the quantum mechanical-molecular mechanical (QM/MM) approach for solution and protein was utilized in simulations. The S0-S1 excitation energies in quantum subsystems were evaluated by means of an augmented version of the multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) with the ground-state geometry parameters optimized in the density functional theory PBE0/cc-pVDZ approximation. The computed positions of absorption bands lambdamax, 599(g), 448(s), and 515(p) nm for the gas phase, solution, and protein, respectively, are in excellent agreement with the corresponding experimental data, 610(g), 445(s), and 500(p) nm. Such consistency provides a support for the formulated qualitative conclusions on the role of the chromophore geometry, environmental electrostatic field, and the counterion in different media. An essentially nonplanar geometry conformation of the chromophore group in the region of the C14-C15 bond was obtained for the protein, in particular, owing to the presence of the neighboring charged amino acid residue Glu181. Nonplanarity of the C14-C15 bond region along with the influence of the negatively charged counterions Glu181 and Glu113 are found to be important to reproduce the spectroscopic features of retinal chromophore inside the Rh cavity. Furthermore, the protein field is responsible for the largest bond-order decrease at the C11-C12 double bond upon excitation, which may be the reason for the 11-cis photoisomerization specificity.

  12. Gas phase ion chemistry

    CERN Document Server

    Bowers, Michael T

    1979-01-01

    Gas Phase Ion Chemistry, Volume 2 covers the advances in gas phase ion chemistry. The book discusses the stabilities of positive ions from equilibrium gas-phase basicity measurements; the experimental methods used to determine molecular electron affinities, specifically photoelectron spectroscopy, photodetachment spectroscopy, charge transfer, and collisional ionization; and the gas-phase acidity scale. The text also describes the basis of the technique of chemical ionization mass spectrometry; the energetics and mechanisms of unimolecular reactions of positive ions; and the photodissociation

  13. Application of structured illumination to gas phase thermometry using thermographic phosphor particles: a study for averaged imaging

    Science.gov (United States)

    Zentgraf, Florian; Stephan, Michael; Berrocal, Edouard; Albert, Barbara; Böhm, Benjamin; Dreizler, Andreas

    2017-07-01

    Structured laser illumination planar imaging (SLIPI) is combined with gas phase thermometry measurements using thermographic phosphor (TGP) particles. The technique is applied to a heated jet surrounded by a coflow which is operated at ambient temperature. The respective air flows are seeded with a powder of BaMgAl10O17:Eu2+ (BAM) which is used as temperature-sensitive gas phase tracer. Upon pulsed excitation in the ultraviolet spectral range, the temperature is extracted based on the two-color ratio method combined with SLIPI. The main advantage of applying the SLIPI approach to phosphor thermometry is the reduction of particle-to-particle multiple light scattering and diffuse wall reflections, yielding a more robust calibration procedure as well as improving the measurement accuracy, precision, and sensitivity. For demonstration, this paper focuses on sample-averaged measurements of temperature fields in a jet-in-coflow configuration. Using the conventional approach, which in contrast to SLIPI is based on imaging with an unmodulated laser light sheet, we show that for the present setup typically 40% of the recorded signal is affected by the contribution of multiply scattered photons. At locations close to walls even up to 75% of the apparent signal is due to diffuse reflection and wall luminescence of BAM sticking at the surface. Those contributions lead to erroneous temperature fields. Using SLIPI, an unbiased two-color ratio field is recovered allowing for two-dimensional mean temperature reconstructions which exhibit a more realistic physical behavior. This is in contrast to results deduced by the conventional approach. Furthermore, using the SLIPI approach it is shown that the temperature sensitivity is enhanced by a factor of up to 2 at 270 °C. Finally, an outlook towards instantaneous SLIPI phosphorescence thermometry is provided.

  14. Tuning structural motifs and alloying of bulk immiscible Mo-Cu bimetallic nanoparticles by gas-phase synthesis

    Science.gov (United States)

    Krishnan, Gopi; Verheijen, Marcel A.; Ten Brink, Gert H.; Palasantzas, George; Kooi, Bart J.

    2013-05-01

    Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still remains a formidable challenge. Hence, we present here a general methodology for gas phase synthesis of bimetallic NPs with distinctively different structural motifs ranging at a single particle level from a fully mixed alloy to core-shell, to onion (multi-shell), and finally to a Janus/dumbbell, with the same overall particle composition. These concepts are illustrated for Mo-Cu NPs, where the precise control of the bimetallic NPs with various degrees of chemical ordering, including different shapes from spherical to cube, is achieved by tailoring the energy and thermal environment that the NPs experience during their production. The initial state of NP growth, either in the liquid or in the solid state phase, has important implications for the different structural motifs and shapes of synthesized NPs. Finally we demonstrate that we are able to tune the alloying regime, for the otherwise bulk immiscible Mo-Cu, by achieving an increase of the critical size, below which alloying occurs, closely up to an order of magnitude. It is discovered that the critical size of the NP alloy is not only affected by controlled tuning of the alloying temperature but also by the particle shape.Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still

  15. PIV Measurement of Transient 3-D (Liquid and Gas Phases) Flow Structures Created by a Spreading Flame over 1-Propanol

    Science.gov (United States)

    Hassan, M. I.; Kuwana, K.; Saito, K.

    2001-01-01

    In the past, we measured three-D flow structure in the liquid and gas phases that were created by a spreading flame over liquid fuels. In that effort, we employed several different techniques including our original laser sheet particle tracking (LSPT) technique, which is capable of measuring transient 2-D flow structures. Recently we obtained a state-of-the-art integrated particle image velocimetry (IPIV), whose function is similar to LSPT, but it has an integrated data recording and processing system. To evaluate the accuracy of our IPIV system, we conducted a series of flame spread tests using the same experimental apparatus that we used in our previous flame spread studies and obtained a series of 2-D flow profiles corresponding to our previous LSPT measurements. We confirmed that both LSPT and IPIV techniques produced similar data, but IPIV data contains more detailed flow structures than LSPT data. Here we present some of newly obtained IPIV flow structure data, and discuss the role of gravity in the flame-induced flow structures. Note that the application of IPIV to our flame spread problems is not straightforward, and it required several preliminary tests for its accuracy including this IPIV comparison to LSPT.

  16. Ground-State Gas-Phase Structures of Inorganic Molecules Predicted by Density Functional Theory Methods

    KAUST Repository

    Minenkov, Yury; Cavallo, Luigi

    2017-01-01

    -GGA approximations with B3PW91, APF, TPSSh, mPW1PW91, PBE0, mPW1PBE, B972, and B98 functionals, resulting in lowest errors. We recommend using these methods to predict accurate three-dimensional structures of inorganic molecules when intramolecular dispersion

  17. Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments.

    Science.gov (United States)

    Somogyi, Arpád

    2008-12-01

    The usefulness of gas-phase H/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly and multiply protonated peptides/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The fragments and the surviving precursor ions then all undergo H/D exchange in the gas-phase with either D(2)O or CD(3)OD under the same experimental conditions. Usually, 10 to 60 s of reaction time is adequate to monitor characteristic differences in the H/D exchange kinetic rates. These differences are then correlated to isomeric ion structures. The SORI-HDX method can be used to rapidly test fragment ion structures and provides useful insights into peptide fragmentation mechanisms.

  18. Structure and reactivity of molybdenum oxide cluster ions in the gas phase

    International Nuclear Information System (INIS)

    Goncharov, V.B.; Fialko, E.F.

    2002-01-01

    A set of cluster ions of molybdenum oxides Mo x O y + (x = 1-5, y = 1-15) was prepared using a combination of the ionic cyclotron resonance method and Knudsen effusion source. Dependence of concentration of different molybdenum oxide ions on the time of retention and their interaction with carbon monoxide was studied. It is shown that Mo x O y + ions with x>3 contain cyclic fragment Mo 3 O 9 in their structure. Oxygen binding energies within ionic clusters Mo x O y + were estimated [ru

  19. Gas-phase synthesis and structure of monomeric ZnOH: a model species for metalloenzymes and catalytic surfaces.

    Science.gov (United States)

    Zack, Lindsay N; Sun, Ming; Bucchino, Matthew P; Clouthier, Dennis J; Ziurys, Lucy M

    2012-02-16

    Monomeric ZnOH has been studied for the first time using millimeter and microwave gas-phase spectroscopy. ZnOH is important in surface processes and at the active site of the enzyme carbonic anhydrase. In the millimeter-wave direct-absorption experiments, ZnOH was synthesized by reacting zinc vapor, produced in a Broida-type oven, with water. In the Fourier-transform microwave measurements, ZnOH was produced in a supersonic jet expansion of CH(3)OH and zinc vapor, created by laser ablation. Multiple rotational transitions of six ZnOH isotopologues in their X(2)A' ground states were measured over the frequency range of 22-482 GHz, and splittings due to fine and hyperfine structure were resolved. An asymmetric top pattern was observed in the spectra, showing that ZnOH is bent, indicative of covalent bonding. From these data, spectroscopic constants and an accurate structure were determined. The Zn-O bond length was found to be similar to that in carbonic anhydrase and other model enzyme systems.

  20. Discriminating Properties of Alkali Metal Ions Towards the Constituents of Proteins and Nucleic Acids. Conclusions from Gas-Phase and Theoretical Studies.

    Science.gov (United States)

    Rodgers, Mary T; Armentrout, Peter B

    2016-01-01

    Quantitative insight into the structures and thermodynamics of alkali metal cations interacting with biological molecules can be obtained from studies in the gas phase combined with theoretical work. In this chapter, the fundamentals of the experimental and theoretical techniques are first summarized and results for such work on complexes of alkali metal cations with amino acids, small peptides, and nucleobases are reviewed. Periodic trends in how these interactions vary as the alkali metal cations get heavier are highlighted.

  1. The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations

    Science.gov (United States)

    Belova, Natalya V.; Girichev, Georgiy V.; Kotova, Vitaliya E.; Korolkova, Kseniya A.; Trang, Nguyen Hoang

    2018-03-01

    The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in CS molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed.

  2. Using Gas-Phase Guest-Host Chemistry to Probe the Structures of b Ions of Peptides

    Science.gov (United States)

    Somogyi, Árpád; Harrison, Alex G.; Paizs, Béla

    2012-12-01

    Middle-sized b n ( n ≥ 5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen-deuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b n ( n ≤ 4) fragments do not form stable ammonia adducts. We propose that complex formation of b n ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b n ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b 4 , b 5 , and b 7 ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N+-H…O H-bonds; this stabilization is much stronger for macrocyclic b n isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest-host chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b 9 , b 9 -A, and b 9 -2A of A8YA, and b 13 of A20YVFL are observed indicating that even these large b-type ions form macrocyclic structures.

  3. Gas Phase Nanoparticle Synthesis

    Science.gov (United States)

    Granqvist, Claes; Kish, Laszlo; Marlow, William

    This book deals with gas-phase nanoparticle synthesis and is intended for researchers and research students in nanomaterials science and engineering, condensed matter physics and chemistry, and aerosol science. Gas-phase nanoparticle synthesis is instrumental to nanotechnology - a field in current focus that raises hopes for environmentally benign, resource-lean manufacturing. Nanoparticles can be produced by many physical, chemical, and even biological routes. Gas-phase synthesis is particularly interesting since one can achieve accurate manufacturing control and hence industrial viability.

  4. GAS PHASE STRUCTURE AND STABILITY OF COMPLEX FORMED BY H2O, NH3, H2S AND THEIR METHYL DERIVATIVES WITH THE CATION CO2+

    Directory of Open Access Journals (Sweden)

    Cahyorini Kusumawardani

    2010-06-01

    Full Text Available Ab initio molecular orbital calculations at the Hartree-Fock-Self Consistent Field (HF-SCF have been performed in order to determine the structure and gas phase energies of complex formed by the Lewis bases of H2O, NH3, H2S and their methyl derivatives with the cation Co2+. The relative basicities of the base studied depend on both the substituent. The gas-phase interaction energies computed by the SCF method including electron correlation Møller-Plesset 2 (MP2 dan Configuration Iteration (CI were comparable in accuracy. The binding energies computed by these two methods reach the targeted chemical accuracy.   Keywords: ab initio calculation, cobalt complex, structure stability

  5. The structure and conformations of piracetam (2-oxo-1-pyrrolidineacetamide): Gas-phase electron diffraction and quantum chemical calculations

    Science.gov (United States)

    Ksenafontov, Denis N.; Moiseeva, Natalia F.; Khristenko, Lyudmila V.; Karasev, Nikolai M.; Shishkov, Igor F.; Vilkov, Lev V.

    2010-12-01

    The geometric structure of piracetam was studied by quantum chemical calculations (DFT and ab initio), gas electron diffraction (GED), and FTIR spectroscopy. Two stable mirror symmetric isomers of piracetam were found. The conformation of pyrrolidine ring is an envelope in which the C4 atom deviates from the ring plane, the angle between the planes (C3 sbnd C4 sbnd C5) and (C2 sbnd C3 sbnd C5) is 154.1°. The direction of the deviation is the same as that of the side acetamide group. The piracetam molecule is stabilized in the gas phase by an intramolecular hydrogen bond between the N9H 2 group and the oxygen O6, bonded to C2. The principal structural parameters ( re, Å and ∠e, degrees; uncertainties are 3 σLS values) were found to be: r(С3 sbnd С4) = 1.533(1), r(C4 sbnd C5) = 1.540(1), r(N1 sbnd C5) = 1.456(1), r(C2 sbnd C3) = 1.520(1), r(N1 sbnd C7) = 1.452(1), r(C7 sbnd C8) = 1.537(1), r(N1 sbnd C2) = 1.365(2), r(C8 sbnd N9) = 1.360(2), r(C2 dbnd O6) = 1.229(1), r(C8 dbnd O10) = 1.221(1), ∠C2 sbnd N1 sbnd C5 = 113.4(6), ∠N1 sbnd C2 sbnd C3 = 106.9(6), ∠N1 sbnd C7 sbnd C8 = 111.9(6), ∠C7 sbnd C8 sbnd N9 = 112.5(6), ∠N1 sbnd C2 sbnd O6 = 123.0(4), ∠C3 sbnd N1 sbnd C7 = 120.4(4), ∠C7 sbnd C8 sbnd O10 = 120.2(4), ∠C5 sbnd N1 sbnd C2 sbnd O6 = 170(6), ∠C3 sbnd C2 sbnd N1 sbnd C7 = 178(6), ∠C2 sbnd N1 sbnd C7 sbnd C8 = 84.2, ∠N1 sbnd C7 sbnd C8 sbnd O10 = 111.9.

  6. Gas phase ion chemistry

    CERN Document Server

    Bowers, Michael T

    1979-01-01

    Gas Phase Ion Chemistry, Volume 1 covers papers on the advances of gas phase ion chemistry. The book discusses the advances in flow tubes and the measurement of ion-molecule rate coefficients and product distributions; the ion chemistry of the earth's atmosphere; and the classical ion-molecule collision theory. The text also describes statistical methods in reaction dynamics; the state selection by photoion-photoelectron coincidence; and the effects of temperature and pressure in the kinetics of ion-molecule reactions. The energy distribution in the unimolecular decomposition of ions, as well

  7. Gas phase pulse radiolysis

    International Nuclear Information System (INIS)

    Jonah, C.D.; Andong Liu; Mulac, W.A.

    1987-01-01

    Gas phase pulse radiolysis, a technique which can be used to study many different phenomena in chemistry and physics, is discussed. As a source of small radicals, pulse radiolysis is important to the field of chemistry, particularly to combustion and atmospheric kinetics. The reactions of 1,3-butadiene, allene, ethylene and acetylene with OH are presented. 52 refs., 1 fig., 1 tab

  8. Gas-Phase Thermolyses

    DEFF Research Database (Denmark)

    Carlsen, Lars; Egsgaard, Helge

    1982-01-01

    The unimolecular gas-phase thermolyses of 1,2,3-oxadithiolan 2-oxide and thiiran 1-oxide have been studied by the flash vacuum thermolysis–field ionization mass spectrometry (f.v.t.–f.i.m.s.) technique in the temperature range from 1 043 to 1 404 K. The reactions are rationalized in terms of sulp...

  9. Gas-Phase Thermolyses

    DEFF Research Database (Denmark)

    Carlsen, Lars; Egsgaard, Helge

    1982-01-01

    The unimolecular gas-phase thermolyses of the four methyl and ethyl monothioacetates (5)–(8) have been studied by the flash vacuum thermolysis–field ionization mass spectrometry technique in the temperature range 883–1 404 K. The types of reactions verified were keten formation, thiono–thiolo rea...

  10. Gas-Phase Thermolysis

    DEFF Research Database (Denmark)

    Carlsen, Lars; Egsgaard, Helge; Schaumann, Ernst

    1980-01-01

    The unimolecular gas-phase thermolytic decomposition of three silylated thionocarboxylic acid derivatives (2b), (3), and (8) have been studied by the flash vacuum thermolysis–field ionization mass spectrometry technique in the temperature range from 783 to 1 404 K in order to elucidate its possible...... applicability as a route to thioketens. Only very minor amounts of the expected thioketens were found, whereas the corresponding ketens were obtained as the major products. A possible mechanism for keten formation is discussed....

  11. Gas phase structures and charge localization in small aluminum oxide anions: Infrared photodissociation spectroscopy and electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Song, Xiaowei; Fagiani, Matias R. [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Germany); Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103 Leipzig (Germany); Gewinner, Sandy; Schöllkopf, Wieland [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin (Germany); Asmis, Knut R., E-mail: knut.asmis@uni-leipzig.de, E-mail: js@chemie.hu-berlin.de [Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, D-04103 Leipzig (Germany); Bischoff, Florian A.; Berger, Fabian; Sauer, Joachim, E-mail: knut.asmis@uni-leipzig.de, E-mail: js@chemie.hu-berlin.de [Institut für Chemie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin (Germany)

    2016-06-28

    We use cryogenic ion trap vibrational spectroscopy in combination with quantum chemical calculations to study the structure of mono- and dialuminum oxide anions. The infrared photodissociation spectra of D{sub 2}-tagged AlO{sub 1-4}{sup −} and Al{sub 2}O{sub 3-6}{sup −} are measured in the region from 400 to 1200 cm{sup −1}. Structures are assigned based on a comparison to simulated harmonic and anharmonic IR spectra derived from electronic structure calculations. The monoaluminum anions contain an even number of electrons and exhibit an electronic closed-shell ground state. The Al{sub 2}O{sub 3-6}{sup −} anions are oxygen-centered radicals. As a result of a delicate balance between localization and delocalization of the unpaired electron, only the BHLYP functional is able to qualitatively describe the observed IR spectra of all species with the exception of AlO{sub 3}{sup −}. Terminal Al–O stretching modes are found between 1140 and 960 cm{sup −1}. Superoxo and peroxo stretching modes are found at higher (1120-1010 cm{sup −1}) and lower energies (850-570 cm{sup −1}), respectively. Four modes in-between 910 and 530 cm{sup −1} represent the IR fingerprint of the common structural motif of dialuminum oxide anions, an asymmetric four-member Al–(O){sub 2}–Al ring.

  12. Identification of isomers in the gas phase and as adsorbates by near-edge X-ray absorption fine structure spectroscopy: Cis- and trans-stilbene

    International Nuclear Information System (INIS)

    Püttner, Ralph; Schmidt-Weber, Philipp; Kampen, Thorsten; Kolczewski, Christine; Hermann, Klaus; Horn, Karsten

    2017-01-01

    Highlights: • NEXAFS spectra of the cis- and trans-isomer of stilbene reveal distinct differences by which the isomers can be distinguished. • DFT calculations using the transition potential approach assign specific transitions that are different in the two isomers. • On Si(100), these differences in NEXAFS are also observed, suggesting that their conformations survive in the bonding situation. • NEXAFS is thus shown to be a sensitive tool to distinguish isomers in adsorbed species. - Abstract: Near-edge x-ray absorption fine structure spectra of the cis- and trans-isomers of stilbene in the gas phase reveal clear differences, which are analyzed by results from density-functional theory calculations using the transition potential approach. The differences between the two species also occur in stilbene adsorbed on Si(100), opening the way towards studying structural changes in molecules in different surface environments, and configurational switching in organic molecules on surfaces in particular.

  13. Identification of isomers in the gas phase and as adsorbates by near-edge X-ray absorption fine structure spectroscopy: Cis- and trans-stilbene

    Energy Technology Data Exchange (ETDEWEB)

    Püttner, Ralph [Department of Physics, Freie Universität Berlin, 14195 Berlin (Germany); Schmidt-Weber, Philipp [Fritz Haber Institute of the Max Planck Society, 14195 Berlin (Germany); Kampen, Thorsten [SPECS Surface Nano Analysis GmbH, 13355 Berlin (Germany); Kolczewski, Christine [Deutsches Museum München, 80538 Munich (Germany); Hermann, Klaus [Fritz Haber Institute of the Max Planck Society, 14195 Berlin (Germany); Horn, Karsten, E-mail: horn@fhi-berlin.mpg.de [Fritz Haber Institute of the Max Planck Society, 14195 Berlin (Germany)

    2017-02-15

    Highlights: • NEXAFS spectra of the cis- and trans-isomer of stilbene reveal distinct differences by which the isomers can be distinguished. • DFT calculations using the transition potential approach assign specific transitions that are different in the two isomers. • On Si(100), these differences in NEXAFS are also observed, suggesting that their conformations survive in the bonding situation. • NEXAFS is thus shown to be a sensitive tool to distinguish isomers in adsorbed species. - Abstract: Near-edge x-ray absorption fine structure spectra of the cis- and trans-isomers of stilbene in the gas phase reveal clear differences, which are analyzed by results from density-functional theory calculations using the transition potential approach. The differences between the two species also occur in stilbene adsorbed on Si(100), opening the way towards studying structural changes in molecules in different surface environments, and configurational switching in organic molecules on surfaces in particular.

  14. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase; Determinacao da estrutura molecular do ciclooctano por metodos Ab Initio e difracao de eletrons na fase gasosa

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Wagner B. de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Quimica

    2000-10-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  15. Gas-phase spectroscopy of ferric heme-NO complexes

    DEFF Research Database (Denmark)

    Wyer, J.A.; Jørgensen, Anders; Pedersen, Bjarke

    2013-01-01

    and significantly blue-shifted compared to ferric heme nitrosyl proteins (maxima between 408 and 422 nm). This is in stark contrast to the Q-band absorption where the protein microenvironment is nearly innocent in perturbing the electronic structure of the porphyrin macrocycle. Photodissociation is primarily...... maxima of heme and its complexes with amino acids and NO. Not so innocent: Weakly bound complexes between ferric heme and NO were synthesised in the gas phase, and their absorption measured from photodissociation yields. Opposite absorption trends in the Soret-band are seen upon NO addition to heme ions...

  16. Soil-gas phase transport and structure parameters for soils under different management regimes and at two moisture levels

    DEFF Research Database (Denmark)

    Eden, Marie; Møldrup, Per; Schjønning, Per

    2012-01-01

    Measurements of diffusive and convective gas transport parameters can be used to describe soil functional architecture and reveal key factors for soil structure development. Undisturbed 100-cm(3) soil samples were sampled at the Long-term Research on Agricultural Systems experiment located...... displayed markedly lower D-P/D-0 values at similar air-filled porosity, illustrating soil structure effects on D-P/D-0. The Currie tortuosity-connectivity parameter, X=Log(D-P/D-0)/Log(epsilon), decreased with increasing bulk density in the intact samples at both moisture conditions, suggesting less...

  17. Electronic structures and reactivities of iodinating agents in the gas phase and in solutions: a density functional study

    International Nuclear Information System (INIS)

    Filimonov, V.D.; Krasnokutskaya, E.L.; Lesina, Yu.A.; Chajkovskij, V.K.; Poleshchuk, O.X.

    2006-01-01

    The electronic and spatial structures of a broad spectrum of neutral compounds with X-Hal (X = N, O, Cl; Hal = Cl, Br, I) bonds and their protonated forms and of different electronic states of triiodide cation, I 3 + , were determined from density functional B3LYP/6-311G* quantum-chemical calculations. The effects of the structure of these compounds on the parameters of electrophilic reactivity were revealed and the thermochemical characteristics of homolytic and heterolytic X-Hal bond dissociation and of iodine transfer in hydroxyl-containing solvents were calculated. Due to low homolytic bond dissociation energies of X-I, the formation of molecular iodine and triiodide cation I 3 + becomes thermodynamically favorable and the cation should act as iodinating agent alternative to acylhypoiodites and N-iodoimides. The solvation effects of MeOH and CH 2 Cl 2 on the X-Hal bond homolysis and heterolysis were determined using the PCM model [ru

  18. Structures and electrochemical properties of pyrolytic carbon films infiltrated from gas phase into electro-conductive substrates derived from wood

    International Nuclear Information System (INIS)

    Ohzawa, Yoshimi; Mitani, Masami; Li, Jianling; Nakajima, Tsuyoshi

    2004-01-01

    Using the pressure-pulsed chemical vapor infiltration technique, pyrolytic carbon (pyrocarbon) films were deposited into two sorts of conductive porous substrates, that is, the carbonized wood (A) and the TiN-coated wood (B). Structures and electrochemical properties were investigated as the negative electrodes of lithium-ion secondary battery. The electrodes had the three-dimensionally continuous current paths in the pyrocarbon-based anodes without the organic binders and the additional conductive fillers. The pyrocarbon films adhered tightly to the carbonized wood or TiN as current collector. These macro-structures of electrodes were effective in improving the high rate property. The sort of substrates affected the nano-structure of pyrocarbon. The pyrocarbon in sample (A) had the relatively high crystallinity, whereas the pyrocarbon in sample (B) was disordered. The capacity of pyrocarbon in sample (B) was higher than that of sample (A), reflecting the disordered microstructure of pyrocarbon film (B). However, sample (A) showed higher Coulombic efficiency at first cycle (i.e. 87%) than that of sample (B), which would result from the high crystallinity, laminar microstructure and low surface area of pyrocarbon in sample (A)

  19. Determination of molecular structure of succinic acid in a very complex conformational landscape: Gas-phase electron diffraction (GED) and ab initio studies

    Science.gov (United States)

    Vogt, Natalja; Abaev, Maxim A.; Rykov, Anatolii N.; Shishkov, Igor F.

    2011-06-01

    The molecular structure of succinic acid has been investigated by the gas-phase electron diffraction (GED) method for the first time. According to predictions of MP2/cc-pVTZ calculations, the molecule has 18 stable conformers with the C sbnd C sbnd C sbnd C chain in the gauche ( G) or anti ( A) configuration, and four of them, I ( G), II ( A), III ( G) and IV ( A) belonging to the C 2, C 2h, C 1 and C 1 point groups, respectively, with relative energies ΔE ZPE within 2.2 kcal/mol can be present at the experimental temperature of 445 K in noticeable amounts. The ratio of the conformers I:II:III:IV = 45(15):20(15):10(assumed):25(15) (in %) has been determined in the GED analysis guided by theoretical predictions. To take into account vibrational effects, the corrections Δ( r e - r a) to the experimental r a bond lengths were calculated from the MP2/cc-pVTZ quadratic and cubic force constants. The obtained equilibrium structural parameters of the dominant conformer I are the following (bond lengths in Å, angles in degrees): r e(C sp3sbnd C sp3) = 1.508(3), r e(C sp3sbnd C sp2) = 1.499(2), r e(C sbnd O) = 1.343(2), r e(C dbnd O) = 1.202(1), e(C sbnd C sbnd C) = 111.8(4), e(C sbnd C sbnd O) = 112.0(4), e(O sbnd C dbnd O) = 123.0(1), τ(C sbnd C sbnd C sbnd C) = 69.9(11). Yielding the best agreement with the GED structure, the MP2/cc-pVQZ approximation overestimates the C sbnd O and C dbnd O bond lengths by ca. 0.005(2) Å.

  20. The gas-phase bis-uranyl nitrate complex ((UO2)2(NO3)5)-: infrared spectrum and structure

    International Nuclear Information System (INIS)

    Groenewold, Gary S.; van Stipdonk, Michael J.; Oomens, Jos; de Jong, Wibe; McIlwain, Michael E.

    2011-01-01

    The infrared spectrum of the bis-uranyl nitrate complex ((UO 2 ) 2 (NO 3 ) 5 ) - was measured in the gas phase using multiple photon dissociation (IRMPD). Intense absorptions corresponding to the nitrate symmetric and asymmetric vibrations, and the uranyl asymmetric vibration were observed. The nitrate nu3 vibrations indicate the presence of nitrate in a bridging configuration bound to both uranyl cations, and probably two distinct pendant nitrates in the complex. The coordination environment of the nitrate ligands and the uranyl cations were compared to those in the mono-uranyl complex. Overall, the uranyl cation is more loosely coordinated in the bis-uranyl complex ((UO 2 ) 2 (NO 3 ) 5 ) - compared to the mono-complex (UO 2 (NO 3 ) 3 ) - , as indicated by a higher O-U-O asymmetric stretching (nu3) frequency. However, the pendant nitrate ligands are more strongly bound in the bis-complex than they are in the mono-uranyl complex, as indicated by the ν 3 frequencies of the pendant nitrate, which are split into nitrosyl and O-N-O vibrations as a result of bidentate coordination. These phenomena are consistent with lower electron density donation per uranyl by the nitrate bridging two uranyl centers compared to that of a pendant nitrate in the mono-uranyl complex. The structure was calculated using density functional theory (B3LYP functional), which produced a structure in which the two uranyl molecules bridged by a single nitrate coordinated in a bis-bidentate fashion. Each uranyl molecule was coordinated by two pendant nitrate ligands. The corresponding vibrational spectrum was in excellent agreement with the IRMPD measurement, confirming the structural assignment.

  1. Experiment and theory at the convergence limit: accurate equilibrium structure of picolinic acid by gas-phase electron diffraction and coupled-cluster computations.

    Science.gov (United States)

    Vogt, Natalja; Marochkin, Ilya I; Rykov, Anatolii N

    2018-04-18

    The accurate molecular structure of picolinic acid has been determined from experimental data and computed at the coupled cluster level of theory. Only one conformer with the O[double bond, length as m-dash]C-C-N and H-O-C[double bond, length as m-dash]O fragments in antiperiplanar (ap) positions, ap-ap, has been detected under conditions of the gas-phase electron diffraction (GED) experiment (Tnozzle = 375(3) K). The semiexperimental equilibrium structure, rsee, of this conformer has been derived from the GED data taking into account the anharmonic vibrational effects estimated from the ab initio force field. The equilibrium structures of the two lowest-energy conformers, ap-ap and ap-sp (with the synperiplanar H-O-C[double bond, length as m-dash]O fragment), have been fully optimized at the CCSD(T)_ae level of theory in conjunction with the triple-ζ basis set (cc-pwCVTZ). The quality of the optimized structures has been improved due to extrapolation to the quadruple-ζ basis set. The high accuracy of both GED determination and CCSD(T) computations has been disclosed by a correct comparison of structures having the same physical meaning. The ap-ap conformer has been found to be stabilized by the relatively strong NH-O hydrogen bond of 1.973(27) Å (GED) and predicted to be lower in energy by 16 kJ mol-1 with respect to the ap-sp conformer without a hydrogen bond. The influence of this bond on the structure of picolinic acid has been analyzed within the Natural Bond Orbital model. The possibility of the decarboxylation of picolinic acid has been considered in the GED analysis, but no significant amounts of pyridine and carbon dioxide could be detected. To reveal the structural changes reflecting the mesomeric and inductive effects due to the carboxylic substituent, the accurate structure of pyridine has been also computed at the CCSD(T)_ae level with basis sets from triple- to 5-ζ quality. The comprehensive structure computations for pyridine as well as for

  2. The gas-phase bis-uranyl nitrate complex ((UO2)2(NO3)5)-: infrared spectrum and structure

    International Nuclear Information System (INIS)

    Groenewold, G.S.; van Stipdonk, Michael J.; Oomens, Jos; De Jong, Wibe A.; McIlwain, Michael E.

    2011-01-01

    The infrared spectrum of the bis-uranyl nitrate complex ((UO 2 ) 2 (NO 3 ) 5 ) - was measured in the gas phase using multiple photon dissociation (IRMPD). Intense absorptions corresponding to the nitrate symmetric and asymmetric vibrations, and the uranyl asymmetric vibration were observed. The nitrate v 3 vibrations indicate the presence of nitrate in a bridging configuration bound to both uranyl cations, and probably two distinct pendant nitrates in the complex. The coordination environment of the nitrate ligands and the uranyl cations were compared to those in the mono-uranyl complex. Overall, the uranyl cation is more loosely coordinated in the bis-uranyl complex ((UO 2 ) 2 (NO 3 ) 5 ) - compared to the mono-complex (UO 2 (NO 3 ) 3 ) - , as indicated by a higher O-U-O asymmetric stretching (v 3 ) frequency. However, the pendant nitrate ligands are more strongly bound in the bis-complex than they are in the mono-uranyl complex, as indicated by the v 3 frequencies of the pendant nitrate, which are split into nitrosyl and O-N-O vibrations as a result of bidentate coordination. These phenomena are consistent with lower electron density donation per uranyl by the nitrate bridging two uranyl centers compared to that of a pendant nitrate in the mono-uranyl complex. The lowest energy structure predicted by density functional theory (B3LYP functional) calculations was one in which the two uranyl molecules bridged by a single nitrate coordinated in a bis-bidentate fashion. Each uranyl molecule was coordinated by two pendant nitrate ligands. The corresponding vibrational spectrum was in excellent agreement with the IRMPD measurement, confirming the structural assignment.

  3. Heterometallic molecular precursors for a lithium-iron oxide material: synthesis, solid state structure, solution and gas-phase behaviour, and thermal decomposition.

    Science.gov (United States)

    Han, Haixiang; Wei, Zheng; Barry, Matthew C; Filatov, Alexander S; Dikarev, Evgeny V

    2017-05-02

    Three heterometallic single-source precursors with a Li : Fe = 1 : 1 ratio for a LiFeO 2 oxide material are reported. Heterometallic compounds LiFeL 3 (L = tbaoac (1), ptac (2), and acac(3)) have been obtained on a large scale, in nearly quantitative yields by one-step reactions that employ readily available reagents. The heterometallic precursor LiFe(acac) 3 (3) with small, symmetric substituents on the ligand (acac = pentane-2,4-dionate), maintains a 1D polymeric structure in the solid state that limits its volatility and prevents solubility in non-coordinating solvents. The application of the unsymmetrical ligands, tbaoac (tert-butyl acetoacetate) and ptac (1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedionate), that exhibit different bridging properties at the two ends of the ligand, allowed us to change the connectivity pattern within the heterometallic assembly. The latter was demonstrated by structural characterization of heterometallic complexes LiFe(tbaoac) 3 (1) and LiFe(ptac) 3 (2) that consist of discrete heterocyclic tetranuclear molecules Li 2 Fe 2 L 6 . The compounds are highly volatile and exhibit a congruent sublimation character. DART mass spectrometric investigation revealed the presence of heterometallic molecules in the gas phase. The positive mode spectra are dominated by the presence of [M - L] + peaks (M = Li 2 Fe 2 L 6 ). In accord with their discrete molecular structure, complexes 1 and 2 are highly soluble in nearly all common solvents. In order to test the retention of the heterometallic structure in solution, the diamagnetic analog of 1, LiMg(tbaoac) 3 (4), has been isolated. Its tetranuclear molecular structure was found to be isomorphous to that of the iron counterpart. 1 H and 7 Li NMR spectroscopy unambiguously confirmed the presence of heterometallic molecules in solutions of non-coordinating solvents. The heterometallic precursor 1 was shown to exhibit clean thermal decomposition in air that results in phase-pure

  4. Gas Phase Molecular Dynamics

    International Nuclear Information System (INIS)

    Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.

    1999-01-01

    The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wave packet calculations that provide insights into energy flow between the vibrational modes of the molecule

  5. Gas-Phase Reactivity of Microsolvated Anions

    DEFF Research Database (Denmark)

    Thomsen, Ditte Linde

    the gas-phase α-effect. The experimental studies are performed by means of the flowing after glow selected ion flow tube technique, and these are supplemented by electronic structure calculations. The α-nucleophile employed is the microsolvated hydrogen peroxide anion whose reactivity is compared......Gas-phase studies of ion-molecule reactions shed light on the intrinsic factors that govern reactivity; and even solvent effects can be examined in the gasphase environment by employing microsolvated ions. An area that has received considerable attention with regard to the interplay between...... to that of a series of microsolvated oxygen centered anions. The association of the nucleophiles with a single water or methanol molecule allows the α-effect to be observed in the SN2 reaction with methyl chloride; this effect was not apparent in the reactions of the unsolvated anions. The results suggest...

  6. GAS PHASE ION CHEMISTRY OF COUMARINS: AB INITIO ...

    African Journals Online (AJOL)

    B. S. Chandravanshi

    The gas phase ion chemistry of coumarins using electron ionization (EI), positive chemical ionization (PCI) and ... Figure 1. Generic chemical structures of the coumarins in this study. ..... Part of this work was conducted using the resources of ...

  7. Noncovalent Halogen Bonding as a Mechanism for Gas-Phase Clustering

    DEFF Research Database (Denmark)

    Wegeberg, Christina; Donald, William A.; McKenzie, Christine

    2017-01-01

    in the crystalline phases of PhIO2 and its derivatives serve as models for the structures of larger gas-phase clusters, and calculations on simple model gas-phase dimer and trimer clusters result in similar motifs. This is the first account of halogen bonding playing an extensive role in gas-phase associations....

  8. Studies of matrix diffusion in gas phase

    International Nuclear Information System (INIS)

    Hartikainen, K.; Timonen, J.; Vaeaetaeinen, K.; Pietarila, H.

    1994-03-01

    The diffusion of solutes from fractures into rock matrix is an important factor in the safety analysis of disposal of radioactive waste. Laboratory measurements are needed to complement field investigations for a reliable determination of the necessary transport parameters. Measurements of diffusion coefficients in tight rock samples are usually time consuming because the diffusion processes are slow. On the other hand it is well known that diffusion coefficients in the gas phase are roughly four orders of magnitude larger than those in the liquid phase. Therefore, for samples whose structures do not change much upon drying, it is possible to estimate the diffusion properties of the liquid phase when the properties of the gas phase are known. Advantages of the gas method are quick and easy measurements. In the measurements nitrogen was used as the carrier gas and helium as the tracer gas, and standard techniques have been used for helium detection. Techniques have been developed for both channel flow and through-diffusion measurements. The breakthrough curves have been measured in every experiment and all measurements have been modelled by using appropriate analytical models. As a result matrix porosities and effective diffusion coefficients in the gas phase have been determined. (12 refs., 21 figs., 6 tabs.)

  9. Liquid phase separation of proteins based on electrophoretic effects in an electrospray setup during sample introduction into a gas-phase electrophoretic mobility molecular analyzer (CE–GEMMA/CE–ES–DMA)

    Science.gov (United States)

    Weiss, Victor U.; Kerul, Lukas; Kallinger, Peter; Szymanski, Wladyslaw W.; Marchetti-Deschmann, Martina; Allmaier, Günter

    2014-01-01

    Nanoparticle characterization is gaining importance in food technology, biotechnology, medicine, and pharmaceutical industry. An instrument to determine particle electrophoretic mobility (EM) diameters in the single-digit to double-digit nanometer range receiving increased attention is the gas-phase electrophoretic mobility molecular analyzer (GEMMA) separating electrophoretically single charged analytes in the gas-phase at ambient pressure. A fused-silica capillary is used for analyte transfer to the gas-phase by means of a nano electrospray (ES) unit. The potential of this capillary to separate analytes electrophoretically in the liquid phase due to different mobilities is, at measurement conditions recommended by the manufacturer, eliminated due to elevated pressure applied for sample introduction. Measurements are carried out upon constant feeding of analytes to the system. Under these conditions, aggregate formation is observed for samples including high amounts of non-volatile components or complex samples. This makes the EM determination of individual species sometimes difficult, if not impossible. With the current study we demonstrate that liquid phase electrophoretic separation of proteins (as exemplary analytes) occurs in the capillary (capillary zone electrophoresis, CE) of the nano ES unit of the GEMMA. This finding was consecutively applied for on-line desalting allowing EM diameter determination of analytes despite a high salt concentration within samples. The present study is to our knowledge the first report on the use of the GEMMA to determine EM diameters of analytes solubilized in the ES incompatible electrolyte solutions by the intended use of electrophoresis (in the liquid phase) during sample delivery. Results demonstrate the proof of concept of such an approach and additionally illustrate the high potential of a future on-line coupling of a capillary electrophoresis to a GEMMA instrument. PMID:25109866

  10. Iodine removal from a gas phase

    International Nuclear Information System (INIS)

    Vikis, A. Ch.

    1982-01-01

    Iodine, e.g. radioactive iodine, present as one or more organic iodides, optionally with elemental iodine, in a gas phase (e.g. air) are removed by photochemically decomposing the organic iodides to elemental iodine, reacting the iodine produced, and any initially present with excess ozone, preferably photochemically produced in situ in the gas phase to produce solid iodine oxides, and removing the solid oxides from the gas phase. (author)

  11. Iodine removal from a gas phase

    International Nuclear Information System (INIS)

    Vikis, A.C.

    1984-01-01

    Iodine, e.g. radioactive iodine, present as one or more organic iodides, optionally with elemental iodine, in a gas phase (e.g. air) are removed by photochemically decomposing the organic iodides to elemental iodine, reacting the iodine produced, and any initially present with excess ozone, preferably photochemically produced in situ in the gas phase to produce solid iodine oxides, and removing the solid oxides from the gas phase

  12. A direct comparison of protein structure in the gas and solution phase: the Trp-cage

    DEFF Research Database (Denmark)

    Patriksson, Alexandra; Adams, Christopher M; Kjeldsen, Frank

    2007-01-01

    Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location...

  13. Evidence for α-helices in the gas phase: a case study using Melittin from honey bee venom.

    Science.gov (United States)

    Florance, Hannah V; Stopford, Andrew P; Kalapothakis, Jason M; McCullough, Bryan J; Bretherick, Andrew; Barran, Perdita E

    2011-09-07

    Gas phase methodologies are increasingly used to study the structure of proteins and peptides. A challenge to the mass spectrometrist is to preserve the structure of the system of interest intact and unaltered from solution into the gas phase. Small peptides are very flexible and can present a number of conformations in solution. In this work we examine Melittin a 26 amino acid peptide that forms the active component of honey bee venom. Melittin is haemolytic and has been shown to form an α-helical tetrameric structure by X-ray crystallography [M. Gribskov et al., The RCSB Protein Data Bank, 1990] and to be helical in high concentrations of methanol. Here we use ion mobility mass spectrometry, molecular dynamics and gas-phase HDX to probe its structure in the gas phase and specifically interrogate whether the helical form can be preserved. All low energy calculated structures possess some helicity. In our experiments we examine the peptide following nano-ESI from solutions with varying methanol content. Ion mobility gives collision cross sections (CCS) that compare well with values found from molecular modelling and from other reported structures, but with inconclusive results regarding the effect of solvent. There is only a slight increase in CCS with charge, showing minimal coloumbically driven unfolding. HDX supports preservation of some helical content into the gas phase and again shows little difference in the exchange rates of species sprayed from different solvents. The [M + 3H](3+) species has two exchanging populations both of which exhibit faster exchange rates than observed for the [M + 2H](2+) species. One interpretation for these results is that the time spent being analysed is sufficient for this peptide to form a helix in the 'ultimate' hydrophobic environment of a vacuum.

  14. Gas Phase Sulfur, Chlorine and Potassium Chemistry in Biomass Combustion

    DEFF Research Database (Denmark)

    Løj, Lusi Hindiyarti

    2007-01-01

    Gas Phase Sulfur, Chlorine and Alkali Metal Chemistry in Biomass Combustion Concern about aerosols formation, deposits, corrosion, and gaseous emissions during biomass combustion, especially straw, continues to be a driving force for investigation on S, Cl, K-containing species under combustions...... conditions. These trace species contained in the biomass structure will be released to the gas phase during combustion and contribute to the problems generated during the process. The investigation during this PhD project is done to stepwise improve the understanding in the chemistry and reduce...... the uncertainties. In the present work, the detailed kinetic model for gas phase sulfur, chlorine, alkali metal, and their interaction has been updated. The K/O/H/Cl chemistry, S chemistry, and their interaction can reasonably predict a range of experimental data. In general, understanding of the interaction...

  15. Structures composing protein domains.

    Science.gov (United States)

    Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

    2013-08-01

    This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  16. An Introduction to the Gas Phase

    Science.gov (United States)

    Vallance, Claire

    2017-11-01

    'An Introduction to the Gas Phase' is adapted from a set of lecture notes for a core first year lecture course in physical chemistry taught at the University of Oxford. The book is intended to give a relatively concise introduction to the gas phase at a level suitable for any undergraduate scientist. After defining the gas phase, properties of gases such as temperature, pressure, and volume are discussed. The relationships between these properties are explained at a molecular level, and simple models are introduced that allow the various gas laws to be derived from first principles. Finally, the collisional behaviour of gases is used to explain a number of gas-phase phenomena, such as effusion, diffusion, and thermal conductivity.

  17. Molecular Structure of 3,3-Diethylpenthane (Tetraethylmethane) in the Gas Phase As Determined by Electron Diffraction and ab Initio Calculations

    Czech Academy of Sciences Publication Activity Database

    Adler, R. W.; Allen, P. R.; Hnyk, Drahomír; Rankin, D. W. H.; Robertson, H. E.; Smart, B. A.; Gillespie, R. J.; Bytheway, I.

    1999-01-01

    Roč. 64, č. 12 (1999), s. 4226-4232 ISSN 0022-3263 Institutional research plan: CEZ:AV0Z4032918 Keywords : structure * initio calculations * 3,3-Diethylpentane Subject RIV: CC - Organic Chemistry Impact factor: 3.440, year: 1999

  18. Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization

    Czech Academy of Sciences Publication Activity Database

    Pepin, R.; Laszlo, K. J.; Marek, Aleš; Peng, B.; Bush, M. F.; Lavanant, H.; Afonso, C.; Tureček, F.

    2016-01-01

    Roč. 27, č. 10 (2016), s. 1647-1660 ISSN 1044-0305 Institutional support: RVO:61388963 Keywords : peptide ions * ion mobility * collisional cross sections * density functional theory calculations * ion structures * polar effects Subject RIV: CC - Organic Chemistry Impact factor: 2.786, year: 2016

  19. Structural and magnetic properties of FePt nanoparticles from the gas phase; Strukturelle und magnetische Eigenschaften von FePt-Nanopartikeln aus der Gasphase

    Energy Technology Data Exchange (ETDEWEB)

    Dmitrieva, O.

    2007-09-21

    In this work, we present the structural and magnetic characterization of FePt nanoparticles. The nanoparticles with mean size of about 6 nm were prepared by sputtering in the gas and subsequent inert gas condensation. The particles are annealed in the furnace during their flight prior to deposition on a substrate. The aim of this work is to prepare magnetically hard FePt nanoparticles in the L1{sub 0}-ordered phase. The structure of the particles was investigated by high-resolution transmission electron microscopy, and the investigations were supported by contrast simulations. The morphology of the particles varies with the sputter-gas pressure and with the annealing temperature. At a pressure of 0.5 mbar, the FePt-nanoparticles are multiply-twinned with an icosahedral structure and exhibit no formation of the L1{sub 0}-ordered phase. At a higher pressure of 1 mbar and an annealing temperature of 1000 C, the particles are partially single-crystalline. About 36 % of the particles are found to be in the L1{sub 0}-ordered state as was estimated by statistical counting supported by simulations. In order to activate the volume diffusion in the particles and to stabilize the formation of the L1{sub 0}-ordered state, the addition of nitrogen was used during the sputtering phase. In this phase, atomic nitrogen is incorporated interstitially into the structure of the primary particles. After annealing nitrogen effuses out of the particles and, thereby, increases the volume diffusion of the Fe and Pt atoms. The incorporation of nitrogen atoms during nucleation and their effusion at an annealing temperature of 1000 C was verified by electron energy loss spectroscopy (EELS) and X-ray absorption spectroscopy (XAS). Structural investigations on particles prepared in the presence of nitrogen shows that most of the particles are single-crystalline and about 70 % of them are L1{sub 0}-ordered. Detailed structural analysis of the nanoparticles was done by the exit wave

  20. Techniques in Gas Phase Thermolyses

    DEFF Research Database (Denmark)

    Egsgaard, Helge; Larsen, Elfinn; Carlsen, Lars

    1982-01-01

    Basic principles, capabilities and limitations of collision activation mass spectrometry are reported, with special reference to real-time analysis of flash vacuum thermolytically generated products. The analytical utility is demonstrated in terms of structure elucidation and isomerization studies...

  1. Fragmentation pathways of O-alkyl methylphosphonothionocyanidates in the gas phase: toward unambiguous structural characterization of chemicals in the Chemical Weapons Convention framework.

    Science.gov (United States)

    Saeidian, Hamid; Babri, Mehran; Ashrafi, Davood; Sarabadani, Mansour; Naseri, Mohammad Taghi

    2013-08-01

    The electron-impact (EI) mass spectra of a series of O-alkyl methylphosphonothionocyanidates were studied for Chemical Weapons Convention (CWC) purposes. General EI fragmentation pathways were constructed and discussed, and collision-induced dissociation studies of the major EI ions were performed to confirm proposed fragment structures by analyzing fragment ions of deuterated analogs and by use of density functional theory (DFT) calculations. Thiono-thiolo rearrangement, McLafferty-type rearrangement, and a previously unknown intramolecular electrophilic aromatic substitution reaction were observed and confirmed. The study also focused on differentiation of isomeric compounds. Retention indices for all compounds, and an electrophilicity index for several compounds, are reported and interpreted.

  2. Intrinsic folding of small peptide chains: spectroscopic evidence for the formation of beta-turns in the gas phase.

    Science.gov (United States)

    Chin, Wutharath; Dognon, Jean-Pierre; Piuzzi, François; Tardivel, Benjamin; Dimicoli, Iliana; Mons, Michel

    2005-01-19

    Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.

  3. Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Yaghlane, Saida Ben [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications – LSAMA, Université de Tunis, Tunis (Tunisia); Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr [Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 49707 (United States); Linguerri, Roberto; Hochlaf, Majdi, E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr [Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 bd Descartes, 77454 Marne-la-Vallée (France)

    2013-11-07

    Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.

  4. Protein Structure Prediction by Protein Threading

    Science.gov (United States)

    Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

    The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

  5. Simple setup for gas-phase h/d exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale

    DEFF Research Database (Denmark)

    Mistarz, Ulrik Hvid; Brown, Jeffery M; Haselmann, Kim F

    2014-01-01

    gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3....../D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium...

  6. Defect formation in fluoropolymer films at their condensation from a gas phase

    Science.gov (United States)

    Luchnikov, P. A.

    2018-01-01

    The questions of radiation defects, factors of influence of electronic high-frequency discharge plasma components on the molecular structure and properties of the fluoropolymer vacuum films synthesized on a substrate from a gas phase are considered. It is established that at sedimentation of fluoropolymer coverings from a gas phase in high-frequency discharge plasma in films there are radiation defects in molecular and supramolecular structure because of the influence of active plasma components which significantly influence their main properties.

  7. Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone.

    Science.gov (United States)

    Dorofeeva, Olga V; Vogt, Natalja; Vogt, Jürgen; Popik, Mikhail V; Rykov, Anatolii N; Vilkov, Lev V

    2007-07-19

    The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.

  8. Fundamental thermochemical properties of amino acids: gas-phase and aqueous acidities and gas-phase heats of formation.

    Science.gov (United States)

    Stover, Michele L; Jackson, Virgil E; Matus, Myrna H; Adams, Margaret A; Cassady, Carolyn J; Dixon, David A

    2012-03-08

    The gas-phase acidities of the 20 L-amino acids have been predicted at the composite G3(MP2) level. A broad range of structures of the neutral and anion were studied to determine the lowest energy conformer. Excellent agreement is found with the available experimental gas-phase deprotonation enthalpies, and the calculated values are within experimental error. We predict that tyrosine is deprotonated at the CO(2)H site. Cysteine is predicted to be deprotonated at the SH but the proton on the CO(2)H is shared with the S(-) site. Self-consistent reaction field (SCRF) calculations with the COSMO parametrization were used to predict the pK(a)'s of the non-zwitterion form in aqueous solution. The differences in the non-zwitterion pK(a) values were used to estimate the free energy difference between the zwitterion and nonzwitterion forms in solution. The heats of formation of the neutral compounds were calculated from atomization energies and isodesmic reactions to provide the first reliable set of these values in the gas phase. Further calculations were performed on five rare amino acids to predict their heats of formation, acidities, and pK(a) values.

  9. Molecular structures of Se(SCH3)2 and Te(SCH3)2 using gas-phase electron diffraction and ab initio and DFT geometry optimisations.

    Science.gov (United States)

    Fleischer, Holger; Wann, Derek A; Hinchley, Sarah L; Borisenko, Konstantin B; Lewis, James R; Mawhorter, Richard J; Robertson, Heather E; Rankin, David W H

    2005-10-07

    The molecular structures of Se(SCH(3))(2) and Te(SCH(3))(2) were investigated using gas-phase electron diffraction (GED) and ab initio and DFT geometry optimisations. While parameters involving H atoms were refined using flexible restraints according to the SARACEN method, parameters that depended only on heavy atoms could be refined without restraints. The GED-determined geometric parameters (r(h1)) are: rSe-S 219.1(1), rS-C 183.2(1), rC-H 109.6(4) pm; angleS-Se-S 102.9(3), angleSe-S-C 100.6(2), angleS-C-H (mean) 107.4(5), phiS-Se-S-C 87.9(20), phiSe-S-C-H 178.8(19) degrees for Se(SCH(3))(2), and rTe-S 238.1(2), rS-C 184.1(3), rC-H 110.0(6) pm; angleS-Te-S 98.9(6), angleTe-S-C 99.7(4), angleS-C-H (mean) 109.2(9), phiS-Te-S-C 73.0(48), phiTe-S-C-H 180.1(19) degrees for Te(SCH(3))(2). Ab initio and DFT calculations were performed at the HF, MP2 and B3LYP levels, employing either full-electron basis sets [3-21G(d) or 6-31G(d)] or an effective core potential with a valence basis set [LanL2DZ(d)]. The best fit to the GED structures was achieved at the MP2 level. Differences between GED and MP2 results for rS-C and angleS-Te-S were explained by the thermal population of excited vibrational states under the experimental conditions. All theoretical models agreed that each compound exists as two stable conformers, one in which the methyl groups are on the same side (g(+)g(-) conformer) and one in which they are on different sides (g(+)g(+) conformer) of the S-Y-S plane (Y = Se, Te). The conformational composition under the experimental conditions could not be resolved from the GED data. Despite GED R-factors and ab initio and DFT energies favouring the g(+)g(+) conformer, it is likely that both conformers are present, for Se(SCH(3))(2) as well as for Te(SCH(3))(2).

  10. Gas phase reactive collisions, experimental approach

    Directory of Open Access Journals (Sweden)

    Canosa A.

    2012-01-01

    Full Text Available Since 1937 when the first molecule in space has been identified, more than 150 molecules have been detected. Understanding the fate of these molecules requires having a perfect view of their photochemistry and reactivity with other partners. It is then crucial to identify the main processes that will produce and destroy them. In this chapter, a general view of experimental techniques able to deliver gas phase chemical kinetics data at low and very low temperatures will be presented. These techniques apply to the study of reactions between neutral reactants on the one hand and reactions involving charge species on the other hand.

  11. Experimental station for gas phase fluorescence spectroscopy

    International Nuclear Information System (INIS)

    Stankiewicz, M.; Garcia, E. Melero; Ruiz, J. Alvarez; Erman, P.; Hatherly, P.A.; Kivimaeki, A.; Rachlew, E.; Rius i Riu, J.

    2004-01-01

    The details of an experimental setup for gas phase atomic and molecular fluorescence measurements using synchrotron radiation are described in this article. The most significant part of the apparatus is an optical arrangement, which allows for simultaneous measurements of dispersed as well as total fluorescence intensity using an effusive gas jet and an inbuilt gas cell assembled in a convenient plug and measure configuration. The first measurements concerning fluorescence of the N 2 molecule around the N 1s edge obtained with this setup are presented

  12. Closed-cage tungsten oxide clusters in the gas phase.

    Science.gov (United States)

    Singh, D M David Jeba; Pradeep, T; Thirumoorthy, Krishnan; Balasubramanian, Krishnan

    2010-05-06

    During the course of a study on the clustering of W-Se and W-S mixtures in the gas phase using laser desorption ionization (LDI) mass spectrometry, we observed several anionic W-O clusters. Three distinct species, W(6)O(19)(-), W(13)O(29)(-), and W(14)O(32)(-), stand out as intense peaks in the regular mass spectral pattern of tungsten oxide clusters suggesting unusual stabilities for them. Moreover, these clusters do not fragment in the postsource decay analysis. While trying to understand the precursor material, which produced these clusters, we found the presence of nanoscale forms of tungsten oxide. The structure and thermodynamic parameters of tungsten clusters have been explored using relativistic quantum chemical methods. Our computed results of atomization energy are consistent with the observed LDI mass spectra. The computational results suggest that the clusters observed have closed-cage structure. These distinct W(13) and W(14) clusters were observed for the first time in the gas phase.

  13. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  14. Radical Reactions in the Gas Phase: Recent Development and Application in Biomolecules

    Directory of Open Access Journals (Sweden)

    Yang Gao

    2014-01-01

    Full Text Available This review summarizes recent literature describing the use of gas phase radical reactions for structural characterization of complex biomolecules other than peptides. Specifically, chemical derivatization, in-source chemical reaction, and gas phase ion/ion reactions have been demonstrated as effective ways to generate radical precursor ions that yield structural informative fragments complementary to those from conventional collision-induced dissociation (CID. Radical driven dissociation has been applied to a variety of biomolecules including peptides, nucleic acids, carbohydrates, and phospholipids. The majority of the molecules discussed in this review see limited fragmentation from conventional CID, and the gas phase radical reactions open up completely new dissociation channels for these molecules and therefore yield high fidelity confirmation of the structures of the target molecules. Due to the extensively studied peptide fragmentation, this review focuses only on nonpeptide biomolecules such as nucleic acids, carbohydrates, and phospholipids.

  15. Gas-phase infrared spectrum of the anionic GFP-chromophore

    NARCIS (Netherlands)

    Almasian, M.; Grzetic, J.; G. Berden,; Bakker, B.; Buma, W. J.; Oomens, J.

    2012-01-01

    The gas-phase IR spectrum of the anionic chromophore of the green fluorescent protein (p-hydroxy-benzylidene-2,3-dimethylimidazolidinone, HBDI) is recorded in the 800–1800 cm−1 frequency range using the free electron laser FELIX in combination with an electrospray ionization (ESI) Fourier

  16. Photoresponse of the protonated Schiff-base retinal chromophore in the gas phase

    DEFF Research Database (Denmark)

    Toker, Jonathan; Rahbek, Dennis Bo; Kiefer, H V

    2013-01-01

    The fragmentation, initiated by photoexcitation as well as collisionally-induced excitation, of several retinal chromophores was studied in the gas phase. The chromophore in the protonated Schiff-base form (RPSB), essential for mammalian vision, shows a remarkably selective photoresponse. The sel......The fragmentation, initiated by photoexcitation as well as collisionally-induced excitation, of several retinal chromophores was studied in the gas phase. The chromophore in the protonated Schiff-base form (RPSB), essential for mammalian vision, shows a remarkably selective photoresponse...... modifications of the chromophore. We propose that isomerizations play an important role in the photoresponse of gas-phase retinal chromophores and guide internal conversion through conical intersections. The role of protein interactions is then to control the specificity of the photoisomerization in the primary...

  17. Transferring pharmaceuticals into the gas phase

    Science.gov (United States)

    Christen, Wolfgang; Krause, Tim; Rademann, Klaus

    2008-11-01

    The dissolution of molecules of biological interest in supercritical carbon dioxide is investigated using pulsed molecular beam mass spectrometry. Due to the mild processing temperatures of most supercritical fluids, their adiabatic expansion into vacuum permits to transfer even thermally very sensitive substances into the gas phase, which is particularly attractive for pharmaceutical and biomedical applications. In addition, supercritical CO2constitutes a chemically inert solvent that is compatible with hydrocarbon-free ultrahigh vacuum conditions. Here, we report on the dissolution and pulsed supersonic jet expansion of caffeine (C8H10N4O2), the provitamin menadione (C11H8O2), and the amino acid derivative l-phenylalanine tert-butyl ester hydrochloride (C6H5CH2CH(NH2)COOC(CH3)3[dot operator]HCl), into vacuum. An on-axis residual gas analyzer is used to monitor the relative amounts of solute and solvent in the molecular beam as a function of solvent densityE The excellent selectivity and sensitivity provided by mass spectrometry permits to probe even trace amounts of solutes. The strong density variation of CO2 close to the critical point results in a pronounced pressure dependence of the relative ion currents of solute and solvent molecules, reflecting a substantial change in solubility.

  18. Resolving Gas-Phase Metallicity In Galaxies

    Science.gov (United States)

    Carton, David

    2017-06-01

    Chapter 2: As part of the Bluedisk survey we analyse the radial gas-phase metallicity profiles of 50 late-type galaxies. We compare the metallicity profiles of a sample of HI-rich galaxies against a control sample of HI-'normal' galaxies. We find the metallicity gradient of a galaxy to be strongly correlated with its HI mass fraction {M}{HI}) / {M}_{\\ast}). We note that some galaxies exhibit a steeper metallicity profile in the outer disc than in the inner disc. These galaxies are found in both the HI-rich and control samples. This contradicts a previous indication that these outer drops are exclusive to HI-rich galaxies. These effects are not driven by bars, although we do find some indication that barred galaxies have flatter metallicity profiles. By applying a simple analytical model we are able to account for the variety of metallicity profiles that the two samples present. The success of this model implies that the metallicity in these isolated galaxies may be in a local equilibrium, regulated by star formation. This insight could provide an explanation of the observed local mass-metallicity relation. Chapter 3 We present a method to recover the gas-phase metallicity gradients from integral field spectroscopic (IFS) observations of barely resolved galaxies. We take a forward modelling approach and compare our models to the observed spatial distribution of emission line fluxes, accounting for the degrading effects of seeing and spatial binning. The method is flexible and is not limited to particular emission lines or instruments. We test the model through comparison to synthetic observations and use downgraded observations of nearby galaxies to validate this work. As a proof of concept we also apply the model to real IFS observations of high-redshift galaxies. From our testing we show that the inferred metallicity gradients and central metallicities are fairly insensitive to the assumptions made in the model and that they are reliably recovered for galaxies

  19. Raman study of vibrational dynamics of aminopropylsilanetriol in gas phase

    Science.gov (United States)

    Volovšek, V.; Dananić, V.; Bistričić, L.; Movre Šapić, I.; Furić, K.

    2014-01-01

    Raman spectrum of aminopropylsilanetriol (APST) in gas phase has been recorded at room temperature in macro chamber utilizing two-mirror technique over the sample tube. Unlike predominantly trans molecular conformation in condensed phase, the spectra of vapor show that the molecules are solely in gauche conformation with intramolecular hydrogen bond N⋯Hsbnd O which reduces the molecular energy in respect to trans conformation by 0.152 eV. The assignment of the molecular spectra based on the DFT calculation is presented. The strong vibrational bands at 354 cm-1, 588 cm-1 and 3022 cm-1 are proposed for verifying the existence of the ring like, hydrogen bonded structure. Special attention was devoted to the high frequency region, where hydrogen bond vibrations are coupled to stretchings of amino and silanol groups.

  20. Comparison of catalytic ethylene polymerization in slurry and gas phase

    NARCIS (Netherlands)

    Daftaribesheli, Majid

    2009-01-01

    Polyethylene (PE) with the annual consumption of 70 million tones in 2007 is mostly produced in slurry, gas-phase or combination of both processes. This work focuses on a comparison between the slurry and gas phase processes. Why does PE produced in theses two processes can show extremely different

  1. Laser spectroscopy of a halocarbocation in the gas phase: CH2I+.

    Science.gov (United States)

    Tao, Chong; Mukarakate, Calvin; Reid, Scott A

    2006-07-26

    We report the first gas-phase observation of the electronic spectrum of a simple halocarbocation, CH2I+. The ion was generated rotationally cold (Trot approximately 20 K) using pulsed discharge methods and was detected via laser spectroscopy. The identity of the spectral carrier was confirmed by modeling the rotational contour observed in the excitation spectra and by comparison of ground state vibrational frequencies determined by single vibronic level emission spectroscopy with Density Functional Theory (DFT) predictions. The transition was assigned as 3A1 gas phase should open new avenues for study of the structure and reactivity of these important ions.

  2. Protein interfacial structure and nanotoxicology

    International Nuclear Information System (INIS)

    White, John W.; Perriman, Adam W.; McGillivray, Duncan J.; Lin, J.-M.

    2009-01-01

    Here we briefly recapitulate the use of X-ray and neutron reflectometry at the air-water interface to find protein structures and thermodynamics at interfaces and test a possibility for understanding those interactions between nanoparticles and proteins which lead to nanoparticle toxicology through entry into living cells. Stable monomolecular protein films have been made at the air-water interface and, with a specially designed vessel, the substrate changed from that which the air-water interfacial film was deposited. This procedure allows interactions, both chemical and physical, between introduced species and the monomolecular film to be studied by reflectometry. The method is briefly illustrated here with some new results on protein-protein interaction between β-casein and κ-casein at the air-water interface using X-rays. These two proteins are an essential component of the structure of milk. In the experiments reported, specific and directional interactions appear to cause different interfacial structures if first, a β-casein monolayer is attacked by a κ-casein solution compared to the reverse. The additional contrast associated with neutrons will be an advantage here. We then show the first results of experiments on the interaction of a β-casein monolayer with a nanoparticle titanium oxide sol, foreshadowing the study of the nanoparticle 'corona' thought to be important for nanoparticle-cell wall penetration.

  3. Protein interfacial structure and nanotoxicology

    Energy Technology Data Exchange (ETDEWEB)

    White, John W. [Research School of Chemistry, Australian National University, Canberra (Australia)], E-mail: jww@rsc.anu.edu.au; Perriman, Adam W.; McGillivray, Duncan J.; Lin, J.-M. [Research School of Chemistry, Australian National University, Canberra (Australia)

    2009-02-21

    Here we briefly recapitulate the use of X-ray and neutron reflectometry at the air-water interface to find protein structures and thermodynamics at interfaces and test a possibility for understanding those interactions between nanoparticles and proteins which lead to nanoparticle toxicology through entry into living cells. Stable monomolecular protein films have been made at the air-water interface and, with a specially designed vessel, the substrate changed from that which the air-water interfacial film was deposited. This procedure allows interactions, both chemical and physical, between introduced species and the monomolecular film to be studied by reflectometry. The method is briefly illustrated here with some new results on protein-protein interaction between {beta}-casein and {kappa}-casein at the air-water interface using X-rays. These two proteins are an essential component of the structure of milk. In the experiments reported, specific and directional interactions appear to cause different interfacial structures if first, a {beta}-casein monolayer is attacked by a {kappa}-casein solution compared to the reverse. The additional contrast associated with neutrons will be an advantage here. We then show the first results of experiments on the interaction of a {beta}-casein monolayer with a nanoparticle titanium oxide sol, foreshadowing the study of the nanoparticle 'corona' thought to be important for nanoparticle-cell wall penetration.

  4. Membrane proteins bind lipids selectively to modulate their structure and function.

    Science.gov (United States)

    Laganowsky, Arthur; Reading, Eamonn; Allison, Timothy M; Ulmschneider, Martin B; Degiacomi, Matteo T; Baldwin, Andrew J; Robinson, Carol V

    2014-06-05

    Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane

  5. Structural entanglements in protein complexes

    Science.gov (United States)

    Zhao, Yani; Chwastyk, Mateusz; Cieplak, Marek

    2017-06-01

    We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both termini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK, and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction.

  6. Soliton concepts and protein structure

    Science.gov (United States)

    Krokhotin, Andrei; Niemi, Antti J.; Peng, Xubiao

    2012-03-01

    Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion from a relatively small number of components. Here we propose that the modular building blocks are made of the dark soliton solution of a generalized discrete nonlinear Schrödinger equation. We find that practically all protein loops can be obtained simply by scaling the size and by joining together a number of copies of the soliton, one after another. The soliton has only two loop-specific parameters, and we compute their statistical distribution in the Protein Data Bank (PDB). We explicitly construct a collection of 200 sets of parameters, each determining a soliton profile that describes a different short loop. The ensuing profiles cover practically all those proteins in PDB that have a resolution which is better than 2.0 Å, with a precision such that the average root-mean-square distance between the loop and its soliton is less than the experimental B-factor fluctuation distance. We also present two examples that describe how the loop library can be employed both to model and to analyze folded proteins.

  7. Vibrational Spectroscopy and Gas-Phase Thermochemistry of the Model Dipeptide N-Acetyl Glycine Methyl Amide

    Science.gov (United States)

    Leavitt, Christopher; Raston, Paul; Moody, Grant; Shirley, Caitlyne; Douberly, Gary

    2014-06-01

    The structure-function relationship in proteins is widely recognized, motivating numerous investigations of isolated neutral and ionic polypeptides that generally employ conformation specific, multidimensional UV and IR spectroscopies. This data taken in conjunction with computed harmonic frequencies has provided a snapshot of the underlying molecular physics at play in many polypeptides, but few experiments have been able to probe the energetics of these systems. In this study, we use vibrational spectroscopy to measure the gas-phase enthalpy change for isomerization between two conformations of the dipeptide N-acetyl glycine methyl amide (NAGMA). A two-stage oven source is implemented producing a gas-phase equilibrium distribution of NAGMA molecules that is flash frozen upon pickup by He nanodroplets. Using polarization spectroscopy, the IR spectrum is assigned to a mixture of two conformers having intramolecular hydrogen bonds made up of either five- or seven-membered rings, C5 and C7, respectively. The interconversion enthalpy, obtained from the van't Hoff relation, is 4.52{±}0.12 kJ/mol for isomerization from the C7 to the C5-conformer. This experimental measurement is compared to computations employing a broad range of theoretical methods.

  8. Multiple Multidentate Halogen Bonding in Solution, in the Solid State, and in the (Calculated) Gas Phase.

    Science.gov (United States)

    Jungbauer, Stefan H; Schindler, Severin; Herdtweck, Eberhardt; Keller, Sandro; Huber, Stefan M

    2015-09-21

    The binding properties of neutral halogen-bond donors (XB donors) bearing two multidentate Lewis acidic motifs toward halides were investigated. Employing polyfluorinated and polyiodinated terphenyl and quaterphenyl derivatives as anion receptors, we obtained X-ray crystallographic data of the adducts of three structurally related XB donors with tetraalkylammonium chloride, bromide, and iodide. The stability of these XB complexes in solution was determined by isothermal titration calorimetry (ITC), and the results were compared to X-ray analyses as well as to calculated binding patterns in the gas phase. Density functional theory (DFT) calculations on the gas-phase complexes indicated that the experimentally observed distortion of the XB donors during multiple multidentate binding can be reproduced in 1:1 complexes with halides, whereas adducts with two halides show a symmetric binding pattern in the gas phase that is markedly different from the solid state structures. Overall, this study demonstrates the limitations in the transferability of binding data between solid state, solution, and gas phase in the study of complex multidentate XB donors. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Atomic and molecular physics in the gas phase

    International Nuclear Information System (INIS)

    Toburen, L.H.

    1990-09-01

    The spatial and temporal distributions of energy deposition by high-linear-energy-transfer radiation play an important role in the subsequent chemical and biological processes leading to radiation damage. Because the spatial structures of energy deposition events are of the same dimensions as molecular structures in the mammalian cell, direct measurements of energy deposition distributions appropriate to radiation biology are infeasible. This has led to the development of models of energy transport based on a knowledge of atomic and molecular interactions process that enable one to simulate energy transfer on an atomic scale. Such models require a detailed understanding of the interactions of ions and electrons with biologically relevant material. During the past 20 years there has been a great deal of progress in our understanding of these interactions; much of it coming from studies in the gas phase. These studies provide information on the systematics of interaction cross sections leading to a knowledge of the regions of energy deposition where molecular and phase effects are important and that guide developments in appropriate theory. In this report studies of the doubly differential cross sections, crucial to the development of stochastic energy deposition calculations and track structure simulation, will be reviewed. Areas of understanding are discussed and directions for future work addressed. Particular attention is given to experimental and theoretical findings that have changed the traditional view of secondary electron production for charged particle interactions with atomic and molecular targets

  10. Tandem differential mobility analysis-mass spectrometry reveals partial gas-phase collapse of the GroEL complex.

    Science.gov (United States)

    Hogan, Christopher J; Ruotolo, Brandon T; Robinson, Carol V; Fernandez de la Mora, Juan

    2011-04-07

    A parallel-plate differential mobility analyzer and a time-of-flight mass spectrometer (DMA-MS) are used in series to measure true mobility in dry atmospheric pressure air for mass-resolved electrosprayed GroEL tetradecamers (14-mers; ~800 kDa). Narrow mobility peaks are found (2.6-2.9% fwhm); hence, precise mobilities can be obtained for these ions without collisional activation, just following their generation by electrospray ionization. In contrast to previous studies, two conformers are found with mobilities (Z) differing by ~5% at charge state z ~ 79. By extrapolating to small z, a common mobility/charge ratio Z(0)/z = 0.0117 cm(2) V(-1) s(-1) is found for both conformers. When interpreted as if the GroEL ion surface were smooth and the gas molecule-protein collisions were perfectly elastic and specular, this mobility yields an experimental collision cross section, Ω, 11% smaller than in an earlier measurement, and close to the cross section, A(C,crystal), expected for the crystal structure (determined by a geometric approximation). However, the similarity between Ω and A(C,crystal) does not imply a coincidence between the native and gas-phase structures. The nonideal nature of protein-gas molecule collisions introduces a drag enhancement factor, ξ = 1.36, with which the true cross section A(C) is related to Ω via A(C) = Ω/ξ. Therefore, A(C) for GroEL 14-mer ions determined by DMA measurements is 0.69A(C,crystal). The factor 1.36 used here is based on the experimental Stokes-Millikan equation, as well as on prior and new numerical modeling accounting for multiple scattering events via exact hard-sphere scattering calculations. Therefore, we conclude that the gas-phase structure of the GroEL complex as electrosprayed is substantially more compact than the corresponding X-ray crystal structure.

  11. The Ultrafast Wolff Rearrangement in the Gas Phase

    Science.gov (United States)

    Steinbacher, Andreas; Roeding, Sebastian; Brixner, Tobias; Nuernberger, Patrick

    The Wolff rearrangement of gas-phase 5-diazo Meldrum's acid is disclosed with femtosecond ion spectroscopy. Distinct differences are found for 267 nm and 200 nm excitation, the latter leading to even two ultrafast rearrangement reactions.

  12. Reticulated Vitreous Carbon Electrodes for Gas Phase Pulsed Corona Reactors

    National Research Council Canada - National Science Library

    Locke, B

    1998-01-01

    A new design for gas phase pulsed corona reactors incorporating reticulated vitreous carbon electrodes is demonstrated to be effective for the removal of nitrogen oxides from synthetic air mixtures...

  13. Reticulated Vitreous Carbon Electrodes for Gas Phase Pulsed Corona Reactors

    National Research Council Canada - National Science Library

    LOCKE, B

    1999-01-01

    A new design for gas phase pulsed corona reactors incorporating reticulated vitreous carbon electrodes is demonstrated to be effective for the removal of nitrogen oxides from synthetic air mixtures...

  14. Diode Laser Raman Scattering Prototype Gas-Phase Environmental Monitoring

    National Research Council Canada - National Science Library

    Benner, Robert

    1999-01-01

    We proposed developing a diode-laser-based, full spectrum Raman scattering instrument incorporating a multipass, external cavity enhancement cell for full spectrum, gas phase analysis of environmental pollutants...

  15. Laser spectroscopy and gas-phase chemistry in CVD

    International Nuclear Information System (INIS)

    Ho, P.; Breiland, W.G.; Coltrin, M.E.

    1986-01-01

    The experimental work involves the use of laser spectroscopic techniques for in situ measurements on the gas phase in a chemical vapor deposition reactor. The theoretical part of the program consists of a computer model of the coupled fluid mechanics and gas-phase chemical kinetics of silane decomposition and subsequent reactions of intermediate species. The laser measurements provide extensive data for thoroughly testing the predictive capabilities of the model

  16. Comparison of catalytic ethylene polymerization in slurry and gas phase

    OpenAIRE

    Daftaribesheli, Majid

    2009-01-01

    Polyethylene (PE) with the annual consumption of 70 million tones in 2007 is mostly produced in slurry, gas-phase or combination of both processes. This work focuses on a comparison between the slurry and gas phase processes. Why does PE produced in theses two processes can show extremely different properties and extremely different reaction behaviour even if the same Ziegler-Natta (ZN) catalyst is used? Generally, it is known that the reason can be found in the differences of local condition...

  17. Protein Structure Refinement by Optimization

    DEFF Research Database (Denmark)

    Carlsen, Martin

    on whether the three-dimensional structure of a homologous sequence is known. Whether or not a protein model can be used for industrial purposes depends on the quality of the predicted structure. A model can be used to design a drug when the quality is high. The overall goal of this project is to assess...... that correlates maximally to a native-decoy distance. The main contribution of this thesis is methods developed for analyzing the performance of metrically trained knowledge-based potentials and for optimizing their performance while making them less dependent on the decoy set used to define them. We focus...... being at-least a local minimum of the potential. To address how far the current functional form of the potential is from an ideal potential we present two methods for finding the optimal metrically trained potential that simultaneous has a number of native structures as a local minimum. Our results...

  18. Gas-phase synthesis of semiconductor nanocrystals and its applications

    Science.gov (United States)

    Mandal, Rajib

    Luminescent nanomaterials is a newly emerging field that provides challenges not only to fundamental research but also to innovative technology in several areas such as electronics, photonics, nanotechnology, display, lighting, biomedical engineering and environmental control. These nanomaterials come in various forms, shapes and comprises of semiconductors, metals, oxides, and inorganic and organic polymers. Most importantly, these luminescent nanomaterials can have different properties owing to their size as compared to their bulk counterparts. Here we describe the use of plasmas in synthesis, modification, and deposition of semiconductor nanomaterials for luminescence applications. Nanocrystalline silicon is widely known as an efficient and tunable optical emitter and is attracting great interest for applications in several areas. To date, however, luminescent silicon nanocrystals (NCs) have been used exclusively in traditional rigid devices. For the field to advance towards new and versatile applications for nanocrystal-based devices, there is a need to investigate whether these NCs can be used in flexible and stretchable devices. We show how the optical and structural/morphological properties of plasma-synthesized silicon nanocrystals (Si NCs) change when they are deposited on stretchable substrates made of polydimethylsiloxane (PDMS). Synthesis of these NCs was performed in a nonthermal, low-pressure gas phase plasma reactor. To our knowledge, this is the first demonstration of direct deposition of NCs onto stretchable substrates. Additionally, in order to prevent oxidation and enhance the luminescence properties, a silicon nitride shell was grown around Si NCs. We have demonstrated surface nitridation of Si NCs in a single step process using non?thermal plasma in several schemes including a novel dual-plasma synthesis/shell growth process. These coated NCs exhibit SiNx shells with composition depending on process parameters. While measurements including

  19. The Genealogical Tree of Ethanol: Gas-phase Formation of Glycolaldehyde, Acetic Acid, and Formic Acid

    Science.gov (United States)

    Skouteris, Dimitrios; Balucani, Nadia; Ceccarelli, Cecilia; Vazart, Fanny; Puzzarini, Cristina; Barone, Vincenzo; Codella, Claudio; Lefloch, Bertrand

    2018-02-01

    Despite the harsh conditions of the interstellar medium, chemistry thrives in it, especially in star-forming regions where several interstellar complex organic molecules (iCOMs) have been detected. Yet, how these species are synthesized is a mystery. The majority of current models claim that this happens on interstellar grain surfaces. Nevertheless, evidence is mounting that neutral gas-phase chemistry plays an important role. In this paper, we propose a new scheme for the gas-phase synthesis of glycolaldehyde, a species with a prebiotic potential and for which no gas-phase formation route was previously known. In the proposed scheme, the ancestor is ethanol and the glycolaldehyde sister species are acetic acid (another iCOM with unknown gas-phase formation routes) and formic acid. For the reactions of the new scheme with no available data, we have performed electronic structure and kinetics calculations deriving rate coefficients and branching ratios. Furthermore, after a careful review of the chemistry literature, we revised the available chemical networks, adding and correcting several reactions related to glycolaldehyde, acetic acid, and formic acid. The new chemical network has been used in an astrochemical model to predict the abundance of glycolaldehyde, acetic acid, and formic acid. The predicted abundance of glycolaldehyde depends on the ethanol abundance in the gas phase and is in excellent agreement with the measured one in hot corinos and shock sites. Our new model overpredicts the abundance of acetic acid and formic acid by about a factor of 10, which might imply a yet incomplete reaction network.

  20. SDSL-ESR-based protein structure characterization.

    Science.gov (United States)

    Strancar, Janez; Kavalenka, Aleh; Urbancic, Iztok; Ljubetic, Ajasja; Hemminga, Marcus A

    2010-03-01

    As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structure.

  1. SVOC partitioning between the gas phase and settled dust indoors

    Science.gov (United States)

    Weschler, Charles J.; Nazaroff, William W.

    2010-09-01

    Semivolatile organic compounds (SVOCs) are a major class of indoor pollutants. Understanding SVOC partitioning between the gas phase and settled dust is important for characterizing the fate of these species indoors and the pathways by which humans are exposed to them. Such knowledge also helps in crafting measurement programs for epidemiological studies designed to probe potential associations between exposure to these compounds and adverse health effects. In this paper, we analyze published data from nineteen studies that cumulatively report measurements of dustborne and airborne SVOCs in more than a thousand buildings, mostly residences, in seven countries. In aggregate, measured median data are reported in these studies for 66 different SVOCs whose octanol-air partition coefficients ( Koa) span more than five orders of magnitude. We use these data to test a simple equilibrium model for estimating the partitioning of an SVOC between the gas phase and settled dust indoors. The results demonstrate, in central tendency, that a compound's octanol-air partition coefficient is a strong predictor of its abundance in settled dust relative to its gas phase concentration. Using median measured results for each SVOC in each study, dustborne mass fractions predicted using Koa and gas-phase concentrations correlate reasonably well with measured dustborne mass fractions ( R2 = 0.76). Combined with theoretical understanding of SVOC partitioning kinetics, the empirical evidence also suggests that for SVOCs with high Koa values, the mass fraction in settled dust may not have sufficient time to equilibrate with the gas phase concentration.

  2. Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics.

    Science.gov (United States)

    Rajabi, Khadijeh

    2015-01-01

    A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

  3. Modularity in protein structures: study on all-alpha proteins.

    Science.gov (United States)

    Khan, Taushif; Ghosh, Indira

    2015-01-01

    Modularity is known as one of the most important features of protein's robust and efficient design. The architecture and topology of proteins play a vital role by providing necessary robust scaffolds to support organism's growth and survival in constant evolutionary pressure. These complex biomolecules can be represented by several layers of modular architecture, but it is pivotal to understand and explore the smallest biologically relevant structural component. In the present study, we have developed a component-based method, using protein's secondary structures and their arrangements (i.e. patterns) in order to investigate its structural space. Our result on all-alpha protein shows that the known structural space is highly populated with limited set of structural patterns. We have also noticed that these frequently observed structural patterns are present as modules or "building blocks" in large proteins (i.e. higher secondary structure content). From structural descriptor analysis, observed patterns are found to be within similar deviation; however, frequent patterns are found to be distinctly occurring in diverse functions e.g. in enzymatic classes and reactions. In this study, we are introducing a simple approach to explore protein structural space using combinatorial- and graph-based geometry methods, which can be used to describe modularity in protein structures. Moreover, analysis indicates that protein function seems to be the driving force that shapes the known structure space.

  4. Protein enriched pasta: structure and digestibility of its protein network.

    Science.gov (United States)

    Laleg, Karima; Barron, Cécile; Santé-Lhoutellier, Véronique; Walrand, Stéphane; Micard, Valérie

    2016-02-01

    Wheat (W) pasta was enriched in 6% gluten (G), 35% faba (F) or 5% egg (E) to increase its protein content (13% to 17%). The impact of the enrichment on the multiscale structure of the pasta and on in vitro protein digestibility was studied. Increasing the protein content (W- vs. G-pasta) strengthened pasta structure at molecular and macroscopic scales but reduced its protein digestibility by 3% by forming a higher covalently linked protein network. Greater changes in the macroscopic and molecular structure of the pasta were obtained by varying the nature of protein used for enrichment. Proteins in G- and E-pasta were highly covalently linked (28-32%) resulting in a strong pasta structure. Conversely, F-protein (98% SDS-soluble) altered the pasta structure by diluting gluten and formed a weak protein network (18% covalent link). As a result, protein digestibility in F-pasta was significantly higher (46%) than in E- (44%) and G-pasta (39%). The effect of low (55 °C, LT) vs. very high temperature (90 °C, VHT) drying on the protein network structure and digestibility was shown to cause greater molecular changes than pasta formulation. Whatever the pasta, a general strengthening of its structure, a 33% to 47% increase in covalently linked proteins and a higher β-sheet structure were observed. However, these structural differences were evened out after the pasta was cooked, resulting in identical protein digestibility in LT and VHT pasta. Even after VHT drying, F-pasta had the best amino acid profile with the highest protein digestibility, proof of its nutritional interest.

  5. Mechanisms of gas phase decomposition of C-nitro compounds from quantum chemical data

    International Nuclear Information System (INIS)

    Khrapkovskii, Grigorii M; Shamov, Alexander G; Nikolaeva, E V; Chachkov, D V

    2009-01-01

    Data on the mechanisms of gas-phase monomolecular decomposition of nitroalkanes, nitroalkenes and nitroarenes obtained using modern quantum chemical methods are described systematically. The attention is focused on the discussion of multistage decomposition of nitro compounds to elementary experimentally observed products. Characteristic features of competition of different mechanisms and the effect of molecular structure on the change in the Arrhenius parameters of the primary reaction step are considered.

  6. Mechanisms of gas phase decomposition of C-nitro compounds from quantum chemical data

    Energy Technology Data Exchange (ETDEWEB)

    Khrapkovskii, Grigorii M; Shamov, Alexander G; Nikolaeva, E V; Chachkov, D V [Kazan State Technological University, Kazan (Russian Federation)

    2009-10-31

    Data on the mechanisms of gas-phase monomolecular decomposition of nitroalkanes, nitroalkenes and nitroarenes obtained using modern quantum chemical methods are described systematically. The attention is focused on the discussion of multistage decomposition of nitro compounds to elementary experimentally observed products. Characteristic features of competition of different mechanisms and the effect of molecular structure on the change in the Arrhenius parameters of the primary reaction step are considered.

  7. Neural Networks for protein Structure Prediction

    DEFF Research Database (Denmark)

    Bohr, Henrik

    1998-01-01

    This is a review about neural network applications in bioinformatics. Especially the applications to protein structure prediction, e.g. prediction of secondary structures, prediction of surface structure, fold class recognition and prediction of the 3-dimensional structure of protein backbones...

  8. Gas-phase photocatalysis in μ-reactors

    DEFF Research Database (Denmark)

    Vesborg, Peter Christian Kjærgaard; Olsen, Jakob Lind; Henriksen, Toke Riishøj

    2010-01-01

    Gas-phase photocatalysis experiments may benefit from the high sensitivity and good time response in product detection offered by μ-reactors. We demonstrate this by carrying out CO oxidation and methanol oxidation over commercial TiO2 photocatalysts in our recently developed high-sensitivity reac......Gas-phase photocatalysis experiments may benefit from the high sensitivity and good time response in product detection offered by μ-reactors. We demonstrate this by carrying out CO oxidation and methanol oxidation over commercial TiO2 photocatalysts in our recently developed high...

  9. Post-flame gas-phase sulfation of potassium chloride

    DEFF Research Database (Denmark)

    Li, Bo; Sun, Zhiwei; Li, Zhongshan

    2013-01-01

    The sulfation of KCl during biomass combustion has implications for operation and emissions: it reduces the rates of deposition and corrosion, it increases the formation of aerosols, and it leads to higher concentrations of HCl and lower concentrations of SO2 in the gas phase. Rigorously homogene......The sulfation of KCl during biomass combustion has implications for operation and emissions: it reduces the rates of deposition and corrosion, it increases the formation of aerosols, and it leads to higher concentrations of HCl and lower concentrations of SO2 in the gas phase. Rigorously...

  10. Device to remove hydrogen isotopes from a gas phase

    International Nuclear Information System (INIS)

    Morlock, G.; Wiesemes, J.; Bachner, D.

    1977-01-01

    The device described here guarantees the selective removal of hydrogen isotopes from gas phases in order to prevent the occurence of explosive H 2 gas mixtures, or to separate off radioactive tritium in nuclear plants from the gas phase. It consists of a closed container whose walls are selectively penetrable by hydrogen isotopes. It is simultaneously filled compactly and presssure-resistant with a metal bulk (e.g. powder, sponges or the like of titanium or other hydrogen isotope binding metal). Walling and bulk are maintained at suitable working temperatures by means of a system according to the Peltier effect. The whole thing is safeguarded by protective walling. (RB) [de

  11. Reactive intermediates in the gas phase generation and monitoring

    CERN Document Server

    Setser, D W

    2013-01-01

    Reactive Intermediates in the Gas Phase: Generation and Monitoring covers methods for reactive intermediates in the gas phase. The book discusses the generation and measurement of atom and radical concentrations in flow systems; the high temperature flow tubes, generation and measurement of refractory species; and the electronically excited long-lived states of atoms and diatomic molecules in flow systems. The text also describes the production and detection of reactive species with lasers in static systems; the production of small positive ions in a mass spectrometer; and the discharge-excite

  12. Structure-based barcoding of proteins.

    Science.gov (United States)

    Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin

    2014-01-01

    A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/. © 2013 The Protein Society.

  13. Improved machine learning method for analysis of gas phase chemistry of peptides

    Directory of Open Access Journals (Sweden)

    Ahn Natalie

    2008-12-01

    Full Text Available Abstract Background Accurate peptide identification is important to high-throughput proteomics analyses that use mass spectrometry. Search programs compare fragmentation spectra (MS/MS of peptides from complex digests with theoretically derived spectra from a database of protein sequences. Improved discrimination is achieved with theoretical spectra that are based on simulating gas phase chemistry of the peptides, but the limited understanding of those processes affects the accuracy of predictions from theoretical spectra. Results We employed a robust data mining strategy using new feature annotation functions of MAE software, which revealed under-prediction of the frequency of occurrence in fragmentation of the second peptide bond. We applied methods of exploratory data analysis to pre-process the information in the MS/MS spectra, including data normalization and attribute selection, to reduce the attributes to a smaller, less correlated set for machine learning studies. We then compared our rule building machine learning program, DataSqueezer, with commonly used association rules and decision tree algorithms. All used machine learning algorithms produced similar results that were consistent with expected properties for a second gas phase mechanism at the second peptide bond. Conclusion The results provide compelling evidence that we have identified underlying chemical properties in the data that suggest the existence of an additional gas phase mechanism for the second peptide bond. Thus, the methods described in this study provide a valuable approach for analyses of this kind in the future.

  14. Exploring the Photoreduction of Au(III) Complexes in the Gas-Phase

    Science.gov (United States)

    Marcum, Jesse C.; Kaufman, Sydney H.; Weber, J. Mathias

    2010-06-01

    We have used photodissociation spectroscopy to probe the electronic structure and photoreduction of Au(III) in gas-phase complexes containing Cl- and OH-. The gas-phase electronic spectrum of [AuCl_4]- closely resembles the aqueous solution spectrum, showing a lack of strong solvatochromic shifts. Substitution of Cl- ligands with OH- results in a strong blue shift, in agreement with ligand-field theory. Upon excitation, [AuCl_4]- can dissociate by loss of either one or two neutral Cl atoms, resulting in the reduction of gold from Au(III) to Au(II) and Au(I) respectively. The hydroxide substituted complex, [AuCl_2(OH)_2]-, demonstrates similar behavior but the only observable fragment channel is the loss of two neutral OH ligands, leading only to Au(I).

  15. Photoelectron spectroscopy an introduction to ultraviolet photoelectron spectroscopy in the gas phase

    CERN Document Server

    Eland, J H D

    2013-01-01

    Photoelectron Spectroscopy: An Introduction to Ultraviolet Photoelectronspectroscopy in the Gas Phase, Second Edition Photoelectron Spectroscopy: An Introduction to Ultraviolet PhotoelectronSpectroscopy in the Gas Phase, Second Edition aims to give practical approach on the subject of photoelectron spectroscopy, as well as provide knowledge on the interpretation of the photoelectron spectrum. The book covers topics such as the principles and literature of photoelectron microscopy; the main features and analysis of photoelectron spectra; ionization techniques; and energies from the photoelectron spectra. Also covered in the book are topics suc as photoelectron band structure and the applications of photoelectron spectroscopy in chemistry. The text is recommended for students and practitioners of chemistry who would like to be familiarized with the concepts of photoelectron spectroscopy and its importance in the field.

  16. SVOC partitioning between the gas phase and settled dust indoors

    DEFF Research Database (Denmark)

    Weschler, Charles J.; Nazaroff, W. W.

    2010-01-01

    Semivolatile organic compounds (SVOCs) are a major class of indoor pollutants. Understanding SVOC partitioning between the gas phase and settled dust is important for characterizing the fate of these species indoors and the pathways by which humans are exposed to them. Such knowledge also helps...

  17. Gas-Phase IR Spectroscopy of Deprotonated Amino Acids

    NARCIS (Netherlands)

    Oomens, J.; Steill, J. D.; Redlich, B.

    2009-01-01

    Gas-phase infrared multiple photon dissociation (IRMPD) spectra have been recorded for the conjugate bases of a series of amino acids (Asp, Cys, Glu, Phe, Set, Trp, Tyr). The spectra are dominated by strong symmetric and antisymmetric carboxylate stretching modes around 1300 and 1600 cm(-1),

  18. Gas phase toluene isopropylation over high silica mordenite

    Indian Academy of Sciences (India)

    Mordenite (HM) catalysts with three different Si/Al ratios were compared for their activity and selectivities in gas phase toluene isopropylation with isopropanol. Catalyst with Si/Al ratio 44.9 offered better cumene selectivity, hence, it was chosen for detailed kinetic investigations. The influence of various process parameters ...

  19. Conformational Study of DNA Sugars: from the Gas Phase to Solution

    Science.gov (United States)

    Uriarte, Iciar; Vallejo-López, Montserrat; Cocinero, Emilio J.; Corzana, Francisco; Davis, Benjamin G.

    2017-06-01

    Sugars are versatile molecules that play a variety of roles in the organism. For example, they are important in energy storage processes or as structural scaffolds. Here, we focus on the monosaccharide present in DNA by addressing the conformational and puckering properties in the gas phase of α- and β-methyl-2-deoxy-ribofuranoside and α- and β-methyl-2-deoxy-ribopiranoside. Other sugars have been previously studied in the gas phase The work presented here stems from a combination of chemical synthesis, ultrafast vaporization methods, supersonic expansions, microwave spectroscopy (both chirped-pulsed and Balle-Flygare cavity-based spectrometers) and NMR spectroscopy. Previous studies in the gas phase had been performed on 2-deoxyribose, but only piranose forms were detected. However, thanks to the combination of these techniques, we have isolated and characterized for the first time the conformational landscape of the sugar present in DNA in its biologically relevant furanose form. Our gas phase study serves as a probe of the conformational preferences of these biomolecules under isolation conditions. Thanks to the NMR experiments, we can characterize the favored conformations in solution and extract the role of the solvent in the structure and puckering of the monosaccharides. E. J. Cocinero, A. Lesarri, P. Écija, F. J. Basterretxea, J.-U. Grabow, J. A. Fernández, F. Castaño, Angew. Chem. Int. Edit. 2012, 51, 3119. P. Écija, I. Uriarte, L. Spada, B. G. Davis, W. Caminati, F. J. Basterretxea, A. Lesarri, E. J. Cocinero, Chem. Commun. 2016, 52, 6241. I. Peña, E. J. Cocinero, C. Cabezas, A. Lesarri, S. Mata, P. Écija, A. M. Daly, Á. Cimas, C. Bermúdez, F. J. Basterretxea, S. Blanco, J. A. Fernández, J. C. López, F. Castaño, J. L. Alonso, Angew. Chem. Int. Edit. 2013, 52, 11840.

  20. The interface of protein structure, protein biophysics, and molecular evolution

    Science.gov (United States)

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  1. SDSL-ESR-based protein structure characterization

    NARCIS (Netherlands)

    Strancar, J.; Kavalenka, A.A.; Urbancic, I.; Ljubetic, A.; Hemminga, M.A.

    2010-01-01

    As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be

  2. Overcoming barriers to membrane protein structure determination.

    Science.gov (United States)

    Bill, Roslyn M; Henderson, Peter J F; Iwata, So; Kunji, Edmund R S; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G; Vogel, Horst

    2011-04-01

    After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.

  3. Mapping monomeric threading to protein-protein structure prediction.

    Science.gov (United States)

    Guerler, Aysam; Govindarajoo, Brandon; Zhang, Yang

    2013-03-25

    The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions. SPRING is tested on 1838 nonhomologous protein complexes which can recognize correct quaternary template structures with a TM score >0.5 in 1115 cases after excluding homologous proteins. The average TM score of the first model is 60% and 17% higher than that by HHsearch and COTH, respectively, while the number of targets with an interface RMSD benchmark proteins. Although the relative performance of SPRING and ZDOCK depends on the level of homology filters, a combination of the two methods can result in a significantly higher model quality than ZDOCK at all homology thresholds. These data demonstrate a new efficient approach to quaternary structure recognition that is ready to use for genome-scale modeling of protein-protein interactions due to the high speed and accuracy.

  4. PSAIA – Protein Structure and Interaction Analyzer

    Directory of Open Access Journals (Sweden)

    Vlahoviček Kristian

    2008-04-01

    Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

  5. All-gas-phase synthesis of UiO-66 through modulated atomic layer deposition

    Science.gov (United States)

    Lausund, Kristian Blindheim; Nilsen, Ola

    2016-11-01

    Thin films of stable metal-organic frameworks (MOFs) such as UiO-66 have enormous application potential, for instance in microelectronics. However, all-gas-phase deposition techniques are currently not available for such MOFs. We here report on thin-film deposition of the thermally and chemically stable UiO-66 in an all-gas-phase process by the aid of atomic layer deposition (ALD). Sequential reactions of ZrCl4 and 1,4-benzenedicarboxylic acid produce amorphous organic-inorganic hybrid films that are subsequently crystallized to the UiO-66 structure by treatment in acetic acid vapour. We also introduce a new approach to control the stoichiometry between metal clusters and organic linkers by modulation of the ALD growth with additional acetic acid pulses. An all-gas-phase synthesis technique for UiO-66 could enable implementations in microelectronics that are not compatible with solvothermal synthesis. Since this technique is ALD-based, it could also give enhanced thickness control and the possibility to coat irregular substrates with high aspect ratios.

  6. Statistical parameter characteristics of gas-phase fluctuations for gas-liquid intermittent flow

    Energy Technology Data Exchange (ETDEWEB)

    Matsui, G.; Monji, H.; Takaguchi, M. [Univ. of Tsukuba (Japan)

    1995-09-01

    This study deals with theoretical analysis on the general behaviour of statistical parameters of gas-phase fluctuations and comparison of statistical parameter characteristics for the real void fraction fluctuations measured with those for the wave form modified the real fluctuations. In order to investigate the details of the relation between the behavior of the statistical parameters in real intermittent flow and analytical results obtained from information on the real flow, the distributions of statistical parameters for general fundamental wave form of gas-phase fluctuations are discussed in detail. By modifying the real gas-phase fluctuations to a trapezoidaly wave, the experimental results can be directly compared with the analytical results. The analytical results for intermittent flow show that the wave form parameter, and the total amplitude of void fraction fluctuations, affects strongly on the statistical parameter characteristics. The comparison with experiment using nitrogen gas-water intermittent flow suggests that the parameters of skewness and excess may be better as indicators of flow pattern. That is, the macroscopic nature of intermittent flow can be grasped by the skewness and the excess, and the detailed flow structure may be described by the mean and the standard deviation.

  7. Statistical parameter characteristics of gas-phase fluctuations for gas-liquid intermittent flow

    International Nuclear Information System (INIS)

    Matsui, G.; Monji, H.; Takaguchi, M.

    1995-01-01

    This study deals with theoretical analysis on the general behaviour of statistical parameters of gas-phase fluctuations and comparison of statistical parameter characteristics for the real void fraction fluctuations measured with those for the wave form modified the real fluctuations. In order to investigate the details of the relation between the behavior of the statistical parameters in real intermittent flow and analytical results obtained from information on the real flow, the distributions of statistical parameters for general fundamental wave form of gas-phase fluctuations are discussed in detail. By modifying the real gas-phase fluctuations to a trapezoidaly wave, the experimental results can be directly compared with the analytical results. The analytical results for intermittent flow show that the wave form parameter, and the total amplitude of void fraction fluctuations, affects strongly on the statistical parameter characteristics. The comparison with experiment using nitrogen gas-water intermittent flow suggests that the parameters of skewness and excess may be better as indicators of flow pattern. That is, the macroscopic nature of intermittent flow can be grasped by the skewness and the excess, and the detailed flow structure may be described by the mean and the standard deviation

  8. NAPS: Network Analysis of Protein Structures

    Science.gov (United States)

    Chakrabarty, Broto; Parekh, Nita

    2016-01-01

    Traditionally, protein structures have been analysed by the secondary structure architecture and fold arrangement. An alternative approach that has shown promise is modelling proteins as a network of non-covalent interactions between amino acid residues. The network representation of proteins provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and provide insights into structure-function relationship. We have developed a web server for network based analysis of protein structures, NAPS, that facilitates quantitative and qualitative (visual) analysis of residue–residue interactions in: single chains, protein complex, modelled protein structures and trajectories (e.g. from molecular dynamics simulations). The user can specify atom type for network construction, distance range (in Å) and minimal amino acid separation along the sequence. NAPS provides users selection of node(s) and its neighbourhood based on centrality measures, physicochemical properties of amino acids or cluster of well-connected residues (k-cliques) for further analysis. Visual analysis of interacting domains and protein chains, and shortest path lengths between pair of residues are additional features that aid in functional analysis. NAPS support various analyses and visualization views for identifying functional residues, provide insight into mechanisms of protein folding, domain-domain and protein–protein interactions for understanding communication within and between proteins. URL:http://bioinf.iiit.ac.in/NAPS/. PMID:27151201

  9. Solution NMR structure determination of proteins revisited

    International Nuclear Information System (INIS)

    Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

    2008-01-01

    This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

  10. Extracting knowledge from protein structure geometry

    DEFF Research Database (Denmark)

    Røgen, Peter; Koehl, Patrice

    2013-01-01

    potential from geometric knowledge extracted from native and misfolded conformers of protein structures. This new potential, Metric Protein Potential (MPP), has two main features that are key to its success. Firstly, it is composite in that it includes local and nonlocal geometric information on proteins...

  11. Reactions of OH radicals with 2-methyl-1-butyl, neopentyl and 1-hexyl nitrates. Structure-activity relationship for gas-phase reactions of OH with alkyl nitrates: An update

    Science.gov (United States)

    Bedjanian, Yuri; Morin, Julien; Romanias, Manolis N.

    2018-05-01

    The kinetics of the reactions 2-methyl-1-butyl (2M1BNT), neopentyl (NPTNT) and 1-hexyl nitrates (1HXNT) with OH radicals has been studied using a low pressure flow tube reactor combined with a quadrupole mass spectrometer. The rate constants of the title reactions were determined under pseudo-first order conditions from kinetics of OH consumption in excess of nitrates. The overall rate coefficients, k2M1BNT = 1.54 × 10-14 (T/298)4.85 exp (1463/T) (T = 278-538 K), kNPTNT = 1.39 × 10-14 (T/298)4.89 exp (1189/T) (T = 278-500 K) and k1HXNT = 2.23 × 10-13 (T/298)2.83 exp (853/T) cm3molecule-1s-1 (T = 306-538 K) (with conservative 15% uncertainty), were determined at a total pressure of 1 Torr of helium. The yield of trimethylacetaldehyde ((CH3)3CCHO), resulting from the abstraction by OH of an α-hydrogen atom in neopentyl nitrate, followed by α-substituted alkyl radical decomposition, was determined as 0.31 ± 0.06 at T = 298 K. The calculated tropospheric lifetimes of 2M1BNT, NPTNT and 1HXNT indicate that reaction of these nitrates with OH represents an important sink of these compounds in the atmosphere. Based on the available kinetic data, we have updated the structure-activity relationship (SAR) for reactions of alkyl nitrates with OH at T = 298 K. Good agreement (within 20%) is obtained between experimentally measured rate constants (total and that for H-atom abstraction from α carbon) and those calculated from SAR using new substituents factors for almost all the experimental data available.

  12. Zwitterionic states in gas-phase polypeptide ions revealed by 157-nm ultra-violet photodissociation

    DEFF Research Database (Denmark)

    Kjeldsen, Frank; Silivra, Oleg A; Zubarev, Roman A

    2006-01-01

    carboxylic groups relative to competing COOH losses (45 Da) from neutral carboxylic groups. Loss of CO2 is a strong indication of the presence of a zwitterionic [(+)...(-)...(+)] salt bridge in the gas-phase polypeptide cation. This method provides a tool for studying, for example, the nature of binding...... of the fragment formation should be taken into account. Cations of Trp-cage proteins exist preferentially as zwitterions, with the deprotonation position divided between the Asp9 residue and the C terminus in the ratio 3:2. The majority of dications of the same molecule are not zwitterions. Furthermore, 157-nm...

  13. Validation-driven protein-structure improvement

    NARCIS (Netherlands)

    Touw, W.G.

    2016-01-01

    High-quality protein structure models are essential for many Life Science applications, such as protein engineering, molecular dynamics, drug design, and homology modelling. The WHAT_CHECK model validation project and the PDB_REDO model optimisation project have shown that many structure models in

  14. IRMPD Action Spectroscopy of Alkali Metal Cation-Cytosine Complexes: Effects of Alkali Metal Cation Size on Gas Phase Conformation

    NARCIS (Netherlands)

    Yang, B.; Wu, R.R.; Polfer, N.C.; Berden, G.; Oomens, J.; Rodgers, M.T.

    2013-01-01

    The gas-phase structures of alkali metal cation-cytosine complexes generated by electrospray ionization are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. IRMPD action spectra of five alkali metal cation-cytosine complexes exhibit both

  15. Long-lived gas-phase radicals from combustion

    Energy Technology Data Exchange (ETDEWEB)

    Kaneko, Takashi; Furusawa, Koji; Amano, Toshiji; Okubo, Yoichi; Tsuchiya, Jun' ichi; Yoshizawa, Fujiroku; Akutsu, Yoshiaki; Tamura, Masamitsu; Yoshida, Tadao (Univ. of Tokyo (Japan))

    1989-04-20

    On indoor air pollution or fire, it is feared that the gas-phase radicals from the combustion of inflammables or fuel seriously exert an influence on the organisms as harmful matter. The gas-phase radicals were studied using the electron spin resonance (ESR) spin-trapping technique. For the spin trap solution, 0.1 mol solution of {alpha}-phenyl-N-t-butylnitron in benzene was used. As a result, apparently long-lived and highly reactive oxygen-centered radicals were detected in the smoke from polyethylene, polypropylene, polystyrene, polymethylmethacrylate, cellulose, kerosene, benzene, acetone, methanol and butylalcohol. It is suggested that the production mechanism for the radicals should be different from olefin-NOx-air system reaction, which is considered for the radicals from cigarette smoke. 11 refs., 6 figs., 2 tabs.

  16. Reactions of newly formed fission products in the gas phase

    International Nuclear Information System (INIS)

    Strickert, R.G.

    1976-01-01

    A dynamic gas-flow system was constructed which stopped fission products in the gas phase and rapidly separated (in less than 2 sec) volatile compounds from non-volatile ones. The filter assembly designed and used was shown to stop essentially all non-volatile fission products. Between 5 percent and 20 percent of tellurium fission-product isotopes reacted with several hydrocarbon gases to form volatile compounds, which passed through the filter. With carbon monoxide gas, volatile tellurium compound(s) (probably TeCO) were also formed with similar efficiencies. The upper limits for the yields of volatile compounds formed between CO and tin and antimony fission products were shown to be less than 0.3 percent, so tellurium nuclides, not their precursors, reacted with CO. It was found that CO reacted preferentially with independently produced tellurium atoms; the reaction efficiency of beta-produced atoms was only 27 +- 3 percent of that of the independently formed atoms. The selectivity, which was independent of the over-all reaction efficiency, was shown to be due to reaction of independently formed atoms in the gas phase. The gas phase reactions are believed to occur mainly at thermal energies because of the independence of the yield upon argon moderator mole-fraction (up to 80 percent). It was shown in some experiments that about one-half of the TeCO decomposed in passing through a filter and that an appreciable fraction (approximately 20 percent) of the tellurium atoms deposited on the filter reacted agin with CO. Other tellurium atoms on the filter surface (those formed by beta decay and those formed independently but not reacting in the gas phase) also reacted with CO, but probably somewhat less efficiently than atoms formed by TeCO decomposition. No evidence was found for formation of TeCO as a direct result of beta-decay

  17. Gas phase fractionation method using porous ceramic membrane

    Science.gov (United States)

    Peterson, Reid A.; Hill, Jr., Charles G.; Anderson, Marc A.

    1996-01-01

    Flaw-free porous ceramic membranes fabricated from metal sols and coated onto a porous support are advantageously used in gas phase fractionation methods. Mean pore diameters of less than 40 .ANG., preferably 5-20 .ANG. and most preferably about 15 .ANG., are permeable at lower pressures than existing membranes. Condensation of gases in small pores and non-Knudsen membrane transport mechanisms are employed to facilitate and increase membrane permeability and permselectivity.

  18. Gas Phase Hydrogenation of Levulinic Acid to gamma-Valerolactone

    NARCIS (Netherlands)

    Bonrath, Werner; Castelijns, Anna Maria Cornelia Francisca; de Vries, Johannes Gerardus; Guit, Rudolf Philippus Maria; Schuetz, Jan; Sereinig, Natascha; Vaessen, Henricus Wilhelmus Leonardus Marie

    The gas phase hydrogenation of levulinic acid to gamma-valerolactone over copper and ruthenium based catalysts in a continuous fixed-bed reactor system was investigated. Among the catalysts a copper oxide based one [50-75 % CuO, 20-25 % SiO2, 1-5 % graphite, 0.1-1 % CuCO3/Cu(OH)(2)] gave

  19. Understanding Gas-Phase Ammonia Chemistry in Protoplanetary Disks

    Science.gov (United States)

    Chambers, Lauren; Oberg, Karin I.; Cleeves, Lauren Ilsedore

    2017-01-01

    Protoplanetary disks are dynamic regions of gas and dust around young stars, the remnants of star formation, that evolve and coagulate over millions of years in order to ultimately form planets. The chemical composition of protoplanetary disks is affected by both the chemical and physical conditions in which they develop, including the initial molecular abundances in the birth cloud, the spectrum and intensity of radiation from the host star and nearby systems, and mixing and turbulence within the disk. A more complete understanding of the chemical evolution of disks enables a more complete understanding of the chemical composition of planets that may form within them, and of their capability to support life. One element known to be essential for life on Earth is nitrogen, which often is present in the form of ammonia (NH3). Recent observations by Salinas et al. (2016) reveal a theoretical discrepancy in the gas-phase and ice-phase ammonia abundances in protoplanetary disks; while observations of comets and protostars estimate the ice-phase NH3/H2O ratio in disks to be 5%, Salinas reports a gas-phase NH3/H2O ratio of ~7-84% in the disk surrounding TW Hydra, a young nearby star. Through computational chemical modeling of the TW Hydra disk using a reaction network of over 5000 chemical reactions, I am investigating the possible sources of excess gas-phase NH3 by determining the primary reaction pathways of NH3 production; the downstream chemical effects of ionization by ultraviolet photons, X-rays, and cosmic rays; and the effects of altering the initial abundances of key molecules such as N and N2. Beyond providing a theoretical explanation for the NH3 ice/gas discrepancy, this new model may lead to fuller understanding of the gas-phase formation processes of all nitrogen hydrides (NHx), and thus fuller understanding of the nitrogen-bearing molecules that are fundamental for life as we know it.

  20. Liquid-gas phase transition in asymmetric nuclear matter at finite temperature

    International Nuclear Information System (INIS)

    Maruyama, Toshiki; Tatsumi, Toshitaka; Chiba, Satoshi

    2010-01-01

    Liquid-gas phase transition is discussed in warm asymmetric nuclear matter. Some peculiar features are figured out from the viewpoint of the basic thermodynamics about the phase equilibrium. We treat the mixed phase of the binary system based on the Gibbs conditions. When the Coulomb interaction is included, the mixed phase is no more uniform and the sequence of the pasta structures appears. Comparing the results with those given by the simple bulk calculation without the Coulomb interaction, we extract specific features of the pasta structures at finite temperature.

  1. Liquid-gas phase transition in asymmetric nuclear matter at finite temperature

    Science.gov (United States)

    Maruyama, Toshiki; Tatsumi, Toshitaka; Chiba, Satoshi

    2010-03-01

    Liquid-gas phase transition is discussed in warm asymmetric nuclear matter. Some peculiar features are figured out from the viewpoint of the basic thermodynamics about the phase equilibrium. We treat the mixed phase of the binary system based on the Gibbs conditions. When the Coulomb interaction is included, the mixed phase is no more uniform and the sequence of the pasta structures appears. Comparing the results with those given by the simple bulk calculation without the Coulomb interaction, we extract specific features of the pasta structures at finite temperature.

  2. Gas phase decontamination of gaseous diffusion process equipment

    International Nuclear Information System (INIS)

    Bundy, R.D.; Munday, E.B.; Simmons, D.W.; Neiswander, D.W.

    1994-01-01

    D ampersand D of the process facilities at the gaseous diffusion plants (GDPs) will be an enormous task. The EBASCO estimate places the cost of D ampersand D of the GDP at the K-25 Site at approximately $7.5 billion. Of this sum, nearly $4 billion is associated with the construction and operation of decontamination facilities and the dismantlement and transport of contaminated process equipment to these facilities. In situ long-term low-temperature (LTLT) gas phase decontamination is being developed and demonstrated at the K-25 site as a technology that has the potential to substantially lower these costs while reducing criticality and safeguards concerns and worker exposure to hazardous and radioactive materials. The objective of gas phase decontamination is to employ a gaseous reagent to fluorinate nonvolatile uranium deposits to form volatile LJF6, which can be recovered by chemical trapping or freezing. The LTLT process permits the decontamination of the inside of gas-tight GDP process equipment at room temperature by substituting a long exposure to subatmospheric C1F for higher reaction rates at higher temperatures. This paper outlines the concept for applying LTLT gas phase decontamination, reports encouraging laboratory experiments, and presents the status of the design of a prototype mobile system. Plans for demonstrating the LTLT process on full-size gaseous diffusion equipment are also outlined briefly

  3. Heterochiral Knottin Protein: Folding and Solution Structure.

    Science.gov (United States)

    Mong, Surin K; Cochran, Frank V; Yu, Hongtao; Graziano, Zachary; Lin, Yu-Shan; Cochran, Jennifer R; Pentelute, Bradley L

    2017-10-31

    Homochirality is a general feature of biological macromolecules, and Nature includes few examples of heterochiral proteins. Herein, we report on the design, chemical synthesis, and structural characterization of heterochiral proteins possessing loops of amino acids of chirality opposite to that of the rest of a protein scaffold. Using the protein Ecballium elaterium trypsin inhibitor II, we discover that selective β-alanine substitution favors the efficient folding of our heterochiral constructs. Solution nuclear magnetic resonance spectroscopy of one such heterochiral protein reveals a homogeneous global fold. Additionally, steered molecular dynamics simulation indicate β-alanine reduces the free energy required to fold the protein. We also find these heterochiral proteins to be more resistant to proteolysis than homochiral l-proteins. This work informs the design of heterochiral protein architectures containing stretches of both d- and l-amino acids.

  4. Amino acid code of protein secondary structure.

    Science.gov (United States)

    Shestopalov, B V

    2003-01-01

    The calculation of protein three-dimensional structure from the amino acid sequence is a fundamental problem to be solved. This paper presents principles of the code theory of protein secondary structure, and their consequence--the amino acid code of protein secondary structure. The doublet code model of protein secondary structure, developed earlier by the author (Shestopalov, 1990), is part of this theory. The theory basis are: 1) the name secondary structure is assigned to the conformation, stabilized only by the nearest (intraresidual) and middle-range (at a distance no more than that between residues i and i + 5) interactions; 2) the secondary structure consists of regular (alpha-helical and beta-structural) and irregular (coil) segments; 3) the alpha-helices, beta-strands and coil segments are encoded, respectively, by residue pairs (i, i + 4), (i, i + 2), (i, i = 1), according to the numbers of residues per period, 3.6, 2, 1; 4) all such pairs in the amino acid sequence are codons for elementary structural elements, or structurons; 5) the codons are divided into 21 types depending on their strength, i.e. their encoding capability; 6) overlappings of structurons of one and the same structure generate the longer segments of this structure; 7) overlapping of structurons of different structures is forbidden, and therefore selection of codons is required, the codon selection is hierarchic; 8) the code theory of protein secondary structure generates six variants of the amino acid code of protein secondary structure. There are two possible kinds of model construction based on the theory: the physical one using physical properties of amino acid residues, and the statistical one using results of statistical analysis of a great body of structural data. Some evident consequences of the theory are: a) the theory can be used for calculating the secondary structure from the amino acid sequence as a partial solution of the problem of calculation of protein three

  5. K-nearest uphill clustering in the protein structure space

    KAUST Repository

    Cui, Xuefeng; Gao, Xin

    2016-01-01

    The protein structure classification problem, which is to assign a protein structure to a cluster of similar proteins, is one of the most fundamental problems in the construction and application of the protein structure space. Early manually curated

  6. Automated protein structure calculation from NMR data

    International Nuclear Information System (INIS)

    Williamson, Mike P.; Craven, C. Jeremy

    2009-01-01

    Current software is almost at the stage to permit completely automatic structure determination of small proteins of <15 kDa, from NMR spectra to structure validation with minimal user interaction. This goal is welcome, as it makes structure calculation more objective and therefore more easily validated, without any loss in the quality of the structures generated. Moreover, it releases expert spectroscopists to carry out research that cannot be automated. It should not take much further effort to extend automation to ca 20 kDa. However, there are technological barriers to further automation, of which the biggest are identified as: routines for peak picking; adoption and sharing of a common framework for structure calculation, including the assembly of an automated and trusted package for structure validation; and sample preparation, particularly for larger proteins. These barriers should be the main target for development of methodology for protein structure determination, particularly by structural genomics consortia

  7. Structural anatomy of telomere OB proteins.

    Science.gov (United States)

    Horvath, Martin P

    2011-10-01

    Telomere DNA-binding proteins protect the ends of chromosomes in eukaryotes. A subset of these proteins are constructed with one or more OB folds and bind with G+T-rich single-stranded DNA found at the extreme termini. The resulting DNA-OB protein complex interacts with other telomere components to coordinate critical telomere functions of DNA protection and DNA synthesis. While the first crystal and NMR structures readily explained protection of telomere ends, the picture of how single-stranded DNA becomes available to serve as primer and template for synthesis of new telomere DNA is only recently coming into focus. New structures of telomere OB fold proteins alongside insights from genetic and biochemical experiments have made significant contributions towards understanding how protein-binding OB proteins collaborate with DNA-binding OB proteins to recruit telomerase and DNA polymerase for telomere homeostasis. This review surveys telomere OB protein structures alongside highly comparable structures derived from replication protein A (RPA) components, with the goal of providing a molecular context for understanding telomere OB protein evolution and mechanism of action in protection and synthesis of telomere DNA.

  8. Understanding Protein-Protein Interactions Using Local Structural Features

    DEFF Research Database (Denmark)

    Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier

    2013-01-01

    Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... interacting and non-interacting protein pairs to classify the structural features that sustain the binding (or non-binding) behavior. Our study indicates that not only the interacting region but also the rest of the protein surface are important for the interaction fate. The interpretation...... to score the likelihood of the interaction between two proteins and to develop a method for the prediction of PPIs. We have tested our method on several sets with unbalanced ratios of interactions and non-interactions to simulate real conditions, obtaining accuracies higher than 25% in the most unfavorable...

  9. GAS PHASE SELECTIVE PHOTOXIDATION OF ALCOHOLS USING LIGHT-ACTIVATED TITANIUM DIOXIDE AND MOLECULAR OXYGEN

    Science.gov (United States)

    Gas Phase Selective Oxidation of Alcohols Using Light-Activated Titanium Dioxide and Molecular Oxygen Gas phase selective oxidations of various primary and secondary alcohols are studied in an indigenously built stainless steel up-flow photochemical reactor using ultravi...

  10. Algorithms for Protein Structure Prediction

    DEFF Research Database (Denmark)

    Paluszewski, Martin

    -trace. Here we present three different approaches for reconstruction of C-traces from predictable measures. In our first approach [63, 62], the C-trace is positioned on a lattice and a tabu-search algorithm is applied to find minimum energy structures. The energy function is based on half-sphere-exposure (HSE......) is more robust than standard Monte Carlo search. In the second approach for reconstruction of C-traces, an exact branch and bound algorithm has been developed [67, 65]. The model is discrete and makes use of secondary structure predictions, HSE, CN and radius of gyration. We show how to compute good lower...... bounds for partial structures very fast. Using these lower bounds, we are able to find global minimum structures in a huge conformational space in reasonable time. We show that many of these global minimum structures are of good quality compared to the native structure. Our branch and bound algorithm...

  11. Structural symmetry and protein function.

    Science.gov (United States)

    Goodsell, D S; Olson, A J

    2000-01-01

    The majority of soluble and membrane-bound proteins in modern cells are symmetrical oligomeric complexes with two or more subunits. The evolutionary selection of symmetrical oligomeric complexes is driven by functional, genetic, and physicochemical needs. Large proteins are selected for specific morphological functions, such as formation of rings, containers, and filaments, and for cooperative functions, such as allosteric regulation and multivalent binding. Large proteins are also more stable against denaturation and have a reduced surface area exposed to solvent when compared with many individual, smaller proteins. Large proteins are constructed as oligomers for reasons of error control in synthesis, coding efficiency, and regulation of assembly. Symmetrical oligomers are favored because of stability and finite control of assembly. Several functions limit symmetry, such as interaction with DNA or membranes, and directional motion. Symmetry is broken or modified in many forms: quasisymmetry, in which identical subunits adopt similar but different conformations; pleomorphism, in which identical subunits form different complexes; pseudosymmetry, in which different molecules form approximately symmetrical complexes; and symmetry mismatch, in which oligomers of different symmetries interact along their respective symmetry axes. Asymmetry is also observed at several levels. Nearly all complexes show local asymmetry at the level of side chain conformation. Several complexes have reciprocating mechanisms in which the complex is asymmetric, but, over time, all subunits cycle through the same set of conformations. Global asymmetry is only rarely observed. Evolution of oligomeric complexes may favor the formation of dimers over complexes with higher cyclic symmetry, through a mechanism of prepositioned pairs of interacting residues. However, examples have been found for all of the crystallographic point groups, demonstrating that functional need can drive the evolution of

  12. Efficient protein structure search using indexing methods.

    Science.gov (United States)

    Kim, Sungchul; Sael, Lee; Yu, Hwanjo

    2013-01-01

    Understanding functions of proteins is one of the most important challenges in many studies of biological processes. The function of a protein can be predicted by analyzing the functions of structurally similar proteins, thus finding structurally similar proteins accurately and efficiently from a large set of proteins is crucial. A protein structure can be represented as a vector by 3D-Zernike Descriptor (3DZD) which compactly represents the surface shape of the protein tertiary structure. This simplified representation accelerates the searching process. However, computing the similarity of two protein structures is still computationally expensive, thus it is hard to efficiently process many simultaneous requests of structurally similar protein search. This paper proposes indexing techniques which substantially reduce the search time to find structurally similar proteins. In particular, we first exploit two indexing techniques, i.e., iDistance and iKernel, on the 3DZDs. After that, we extend the techniques to further improve the search speed for protein structures. The extended indexing techniques build and utilize an reduced index constructed from the first few attributes of 3DZDs of protein structures. To retrieve top-k similar structures, top-10 × k similar structures are first found using the reduced index, and top-k structures are selected among them. We also modify the indexing techniques to support θ-based nearest neighbor search, which returns data points less than θ to the query point. The results show that both iDistance and iKernel significantly enhance the searching speed. In top-k nearest neighbor search, the searching time is reduced 69.6%, 77%, 77.4% and 87.9%, respectively using iDistance, iKernel, the extended iDistance, and the extended iKernel. In θ-based nearest neighbor serach, the searching time is reduced 80%, 81%, 95.6% and 95.6% using iDistance, iKernel, the extended iDistance, and the extended iKernel, respectively.

  13. Protein structure: geometry, topology and classification

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, William R.; May, Alex C.W.; Brown, Nigel P.; Aszodi, Andras [Division of Mathematical Biology, National Institute for Medical Research, London (United Kingdom)

    2001-04-01

    The structural principals of proteins are reviewed and analysed from a geometric perspective with a view to revealing the underlying regularities in their construction. Computer methods for the automatic comparison and classification of these structures are then reviewed with an analysis of the statistical significance of comparing different shapes. Following an analysis of the current state of the classification of proteins, more abstract geometric and topological representations are explored, including the occurrence of knotted topologies. The review concludes with a consideration of the origin of higher-level symmetries in protein structure. (author)

  14. Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

    Science.gov (United States)

    Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

    2008-11-15

    Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

  15. MOLECULAR SPECTROSCPY AND REACTIONS OF ACTINIDES IN THE GAS PHASE AND CRYOGENIC MATRICES

    Energy Technology Data Exchange (ETDEWEB)

    Heaven, Michael C.; Gibson, John K.; Marcalo, Joaquim

    2009-02-01

    temperature or below. For many spectroscopic measurements, low temperatures have been achieved by co-condensing the actinide vapor in rare gas or inert molecule host matrices. Spectra recorded in matrices are usually considered to be minimally perturbed. Trapping the products from gas-phase reactions that occur when trace quantities of reactants are added to the inert host gas has resulted in the discovery of many new actinide species. Selected aspects of the matrix isolation data were discussed in chapter 17. In the present chapter we review the spectroscopic matrix data in terms of its relationship to gas-phase measurements, and update the description of the new reaction products found in matrices to reflect the developments that have occurred during the past two years. Spectra recorded in matrix environments are usually considered to be minimally perturbed, and this expectation is borne out for many closed shell actinide molecules. However, there is growing evidence that significant perturbations can occur for open shell molecules, resulting in geometric distortions and/or electronic state reordering. Studies of actinide reactions in the gas phase provide an opportunity to probe the relationship between electronic structure and reactivity. Much of this work has focused on the reactions of ionic species, as these may be selected and controlled using various forms of mass spectrometry. As an example of the type of insight derived from reaction studies, it has been established that the reaction barriers for An+ ions are determined by the promotion energies required to achieve the 5fn6d7s configuration. Gas-phase reaction studies also provide fundamental thermodynamic properties such as bond dissociation and ionization energies. In recent years, an increased number of gas-phase ion chemistry studies of bare (atomic) and ligated (molecular) actinide ions have appeared, in which relevant contributions to fundamental actinide chemistry have been made. These studies were initiated

  16. Fast loop modeling for protein structures

    Science.gov (United States)

    Zhang, Jiong; Nguyen, Son; Shang, Yi; Xu, Dong; Kosztin, Ioan

    2015-03-01

    X-ray crystallography is the main method for determining 3D protein structures. In many cases, however, flexible loop regions of proteins cannot be resolved by this approach. This leads to incomplete structures in the protein data bank, preventing further computational study and analysis of these proteins. For instance, all-atom molecular dynamics (MD) simulation studies of structure-function relationship require complete protein structures. To address this shortcoming, we have developed and implemented an efficient computational method for building missing protein loops. The method is database driven and uses deep learning and multi-dimensional scaling algorithms. We have implemented the method as a simple stand-alone program, which can also be used as a plugin in existing molecular modeling software, e.g., VMD. The quality and stability of the generated structures are assessed and tested via energy scoring functions and by equilibrium MD simulations. The proposed method can also be used in template-based protein structure prediction. Work supported by the National Institutes of Health [R01 GM100701]. Computer time was provided by the University of Missouri Bioinformatics Consortium.

  17. Simultaneous determination of protein structure and dynamics

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, M. A.

    2005-01-01

    at the atomic level about the structural and dynamical features of proteins-with the ability of molecular dynamics simulations to explore a wide range of protein conformations. We illustrate the method for human ubiquitin in solution and find that there is considerable conformational heterogeneity throughout......We present a protocol for the experimental determination of ensembles of protein conformations that represent simultaneously the native structure and its associated dynamics. The procedure combines the strengths of nuclear magnetic resonance spectroscopy-for obtaining experimental information...... the protein structure. The interior atoms of the protein are tightly packed in each individual conformation that contributes to the ensemble but their overall behaviour can be described as having a significant degree of liquid-like character. The protocol is completely general and should lead to significant...

  18. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  19. CASCADER: An m-chain gas-phase radionuclide transport and fate model

    International Nuclear Information System (INIS)

    Cawlfield, D.E.; Been, K.B.; Emer, D.F.; Lindstrom, F.T.; Shott, G.J.

    1993-06-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and/or diffusion. Furthermore, parent and daughter radionuclides may decay as they are transported in the soil. This is volume two to the CASCADER series, titled CASCADR8. It embodies the concepts presented in volume one of this series. To properly understand how the CASCADR8 model works, the reader should read volume one first. This volume presents the input and output file structure for CASCADR8, and a set of realistic scenarios for buried sources of radon gas

  20. CASCADER: An M-chain gas-phase radionuclide transport and fate model

    International Nuclear Information System (INIS)

    Cawlfield, D.E.; Emer, D.F.; Lindstrom, F.T.; Shott, G.J.

    1993-09-01

    Chemicals and radionuclides move either in the gas-phase, liquid-phase, or both phases in soils. They may be acted upon by either biological or abiotic processes through advection and/or dispersion. Additionally during the transport of parent and daughter radionuclides in soil, radionuclide decay may occur. This version of CASCADER called CASCADR9 starts with the concepts presented in volumes one and three of this series. For a proper understanding of how the model works, the reader should read volume one first. Also presented in this volume is a set of realistic scenarios for buried sources of radon gas, and the input and output file structure for CASCADER9

  1. Human cancer protein-protein interaction network: a structural perspective.

    Directory of Open Access Journals (Sweden)

    Gozde Kar

    2009-12-01

    Full Text Available Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network. The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%. We illustrate the interface related affinity properties of two cancer-related hub

  2. Protein Structure and the Sequential Structure of mRNA

    DEFF Research Database (Denmark)

    Brunak, Søren; Engelbrecht, Jacob

    1996-01-01

    entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment, By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets, These signals do not originate from......A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed, We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting...... protein, The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain, A complete search for GenBank nucleotide sequences coding for structural...

  3. Protein structure database search and evolutionary classification.

    Science.gov (United States)

    Yang, Jinn-Moon; Tung, Chi-Hua

    2006-01-01

    As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

  4. Modeling protein structures: construction and their applications.

    Science.gov (United States)

    Ring, C S; Cohen, F E

    1993-06-01

    Although no general solution to the protein folding problem exists, the three-dimensional structures of proteins are being successfully predicted when experimentally derived constraints are used in conjunction with heuristic methods. In the case of interleukin-4, mutagenesis data and CD spectroscopy were instrumental in the accurate assignment of secondary structure. In addition, the tertiary structure was highly constrained by six cysteines separated by many residues that formed three disulfide bridges. Although the correct structure was a member of a short list of plausible structures, the "best" structure was the topological enantiomer of the experimentally determined conformation. For many proteases, other experimentally derived structures can be used as templates to identify the secondary structure elements. In a procedure called modeling by homology, the structure of a known protein is used as a scaffold to predict the structure of another related protein. This method has been used to model a serine and a cysteine protease that are important in the schistosome and malarial life cycles, respectively. The model structures were then used to identify putative small molecule enzyme inhibitors computationally. Experiments confirm that some of these nonpeptidic compounds are active at concentrations of less than 10 microM.

  5. Proteins with Novel Structure, Function and Dynamics

    Science.gov (United States)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  6. Overcoming barriers to membrane protein structure determination

    NARCIS (Netherlands)

    Bill, Roslyn M.; Henderson, Peter J. F.; Iwata, So; Kunji, Edmund R. S.; Michel, Hartmut; Neutze, Richard; Newstead, Simon; Poolman, Bert; Tate, Christopher G.; Vogel, Horst

    After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new

  7. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  8. Delivering Transmembrane Peptide Complexes to the Gas Phase Using Nanodiscs and Electrospray Ionization

    Science.gov (United States)

    Li, Jun; Richards, Michele R.; Kitova, Elena N.; Klassen, John S.

    2017-10-01

    The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)2+ ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å2 (conformation 1, C1), 708 Å2 (C2), and 737 Å2 (C3). The addition of NH4CH3CO2 produced (2GA + 2Na)2+ and (2GA + H + Na)2+ ions, with Ω similar to those of C1, C2, and C3, as well as (2GA + 2H)2+, (2GA + 2NH4)2+, and (2GA + H + NH4)2+ ions, which adopt a single conformation with a Ω similar to that of C2. These results suggest that the nature of the charging agents, imparted by the ESI process, can influence dimer conformation in the gas phase. Notably, the POPC NDs produced exclusively (2GA + 2NH4)2+ dimer ions; the DMPC NDs produced both (2GA + 2H)2+ and (2GA + 2NH4)2+ dimer ions. While the Ω of (2GA + 2H)2+ is similar to that of C2, the (2GA + 2NH4)2+ ions from NDs adopt a more compact structure, with a Ω of 656 Å2. It is proposed that this compact structure corresponds to the ion conducting single stranded head-to-head helical GA dimer. These findings highlight the potential of NDs, combined with ESI, for transferring transmembrane peptide complexes directly from lipid bilayers to the gas phase. [Figure not available: see fulltext.

  9. A 'periodic table' for protein structures.

    Science.gov (United States)

    Taylor, William R

    2002-04-11

    Current structural genomics programs aim systematically to determine the structures of all proteins coded in both human and other genomes, providing a complete picture of the number and variety of protein structures that exist. In the past, estimates have been made on the basis of the incomplete sample of structures currently known. These estimates have varied greatly (between 1,000 and 10,000; see for example refs 1 and 2), partly because of limited sample size but also owing to the difficulties of distinguishing one structure from another. This distinction is usually topological, based on the fold of the protein; however, in strict topological terms (neglecting to consider intra-chain cross-links), protein chains are open strings and hence are all identical. To avoid this trivial result, topologies are determined by considering secondary links in the form of intra-chain hydrogen bonds (secondary structure) and tertiary links formed by the packing of secondary structures. However, small additions to or loss of structure can make large changes to these perceived topologies and such subjective solutions are neither robust nor amenable to automation. Here I formalize both secondary and tertiary links to allow the rigorous and automatic definition of protein topology.

  10. Gas phase spectroscopic study of unstable molecules using FTIR technique

    International Nuclear Information System (INIS)

    Allaf, A.W.; Alibrahim, M.; Kassem, M.

    1998-01-01

    A new route has been developed, leading to the production of phosphorus (III) oxycyanide, OPCN and phosphorus (III) oxycyanate, OPOCN by an on-line process using phosphoryl chloride, POCL 3 as a starting material passed over heated silver at 870 Centigrade and then reacted with AgCN and KOCN heated at 270 Centigrade and 590 Centigrade to produce OPCN and OPOCN respectively. The gas phase fourier transform infrared spectra reported for the first time show the two characterized bonds of OPCN and OPOCN at 2165 cm -1 and 2130 cm -1 , assigned to the C≡N stretching fundamentals of OPCN and OPOCN respectively. (Author)

  11. The nuclear liquid gas phase transition and phase coexistence

    International Nuclear Information System (INIS)

    Chomaz, Ph.

    2001-01-01

    In this talk we will review the different signals of liquid gas phase transition in nuclei. From the theoretical side we will first discuss the foundations of the concept of equilibrium, phase transition and critical behaviors in infinite and finite systems. From the experimental point of view we will first recall the evidences for some strong modification of the behavior of hot nuclei. Then we will review quantitative detailed analysis aiming to evidence phase transition, to define its order and phase diagram. Finally, we will present a critical discussion of the present status of phase transitions in nuclei and we will draw some lines for future development of this field. (author)

  12. The nuclear liquid gas phase transition and phase coexistence

    Energy Technology Data Exchange (ETDEWEB)

    Chomaz, Ph

    2001-07-01

    In this talk we will review the different signals of liquid gas phase transition in nuclei. From the theoretical side we will first discuss the foundations of the concept of equilibrium, phase transition and critical behaviors in infinite and finite systems. From the experimental point of view we will first recall the evidences for some strong modification of the behavior of hot nuclei. Then we will review quantitative detailed analysis aiming to evidence phase transition, to define its order and phase diagram. Finally, we will present a critical discussion of the present status of phase transitions in nuclei and we will draw some lines for future development of this field. (author)

  13. Angular intensity of a gas-phase field ionization source

    International Nuclear Information System (INIS)

    Orloff, J.; Swanson, L.W.

    1979-01-01

    Angular intensities of 1 μA sr -1 have been measured for a gas-phase field ionization source in an optical column under practical operating conditions. The source, which was differentially pumped and cooled to 77 K, utilized a -oriented iridium emitter and precooled hydrogen gas at 10 -2 Torr. The ion beam was collimated with an electrostatic lens and detected below an aperture subtending 0.164 msr. A transmitted current of approx.10 -10 A was measured at voltages corresponding to a field of approx. =2.2 V/A at the emitter

  14. Gas-Phase Enrichment of Multiply Charged Peptide Ions by Differential Ion Mobility Extend the Comprehensiveness of SUMO Proteome Analyses

    Science.gov (United States)

    Pfammatter, Sibylle; Bonneil, Eric; McManus, Francis P.; Thibault, Pierre

    2018-04-01

    The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines. Here, we exploited the unusual structure of SUMO peptides to facilitate their separation by high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the coverage of SUMO proteome analysis. Upon trypsin digestion, branched peptides contain a SUMO remnant side chain and predominantly form triply protonated ions that facilitate their gas-phase separation using FAIMS. We evaluated the mobility characteristics of synthetic SUMO peptides and further demonstrated the application of FAIMS to profile the changes in protein SUMOylation of HEK293 cells following heat shock, a condition known to affect this modification. FAIMS typically provided a 10-fold improvement of detection limit of SUMO peptides, and enabled a 36% increase in SUMO proteome coverage compared to the same LC-MS/MS analyses performed without FAIMS. [Figure not available: see fulltext.

  15. An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides.

    Science.gov (United States)

    Plummer, Chelsea E; Stover, Michele L; Bokatzian, Samantha S; Davis, John T M; Dixon, David A; Cassady, Carolyn J

    2015-07-30

    Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

  16. Gas-phase fragmentation of peptides to increase the spatial resolution of the Hydrogen Exchange Mass Spectrometry experiment

    DEFF Research Database (Denmark)

    Jensen, Pernille Foged; Rand, Kasper Dyrberg

    2016-01-01

    are produced after precursor ion selection and thus do not add complexity to the LC-MS analysis. The key to obtaining optimal spatial resolution in a hydrogen exchange mass spectrometry (HX-MS) experiment is the fragmentation efficiency. This chapter discusses common fragmentation techniques like collision....../D scrambling, thus making them suitable for HX applications. By combining the classic bottom-up HX-MS workflow with gas-phase fragmentation by ETD, detailed information on protein HX can be obtained....

  17. Structural analysis of recombinant human protein QM

    International Nuclear Information System (INIS)

    Gualberto, D.C.H.; Fernandes, J.L.; Silva, F.S.; Saraiva, K.W.; Affonso, R.; Pereira, L.M.; Silva, I.D.C.G.

    2012-01-01

    Full text: The ribosomal protein QM belongs to a family of ribosomal proteins, which is highly conserved from yeast to humans. The presence of the QM protein is necessary for joining the 60S and 40S subunits in a late step of the initiation of mRNA translation. Although the exact extra-ribosomal functions of QM are not yet fully understood, it has been identified as a putative tumor suppressor. This protein was reported to interact with the transcription factor c-Jun and thereby prevent c-Jun actives genes of the cellular growth. In this study, the human QM protein was expressed in bacterial system, in the soluble form and this structure was analyzed by Circular Dichroism and Fluorescence. The results of Circular Dichroism showed that this protein has less alpha helix than beta sheet, as described in the literature. QM protein does not contain a leucine zipper region; however the ion zinc is necessary for binding of QM to c-Jun. Then we analyzed the relationship between the removal of zinc ions and folding of protein. Preliminary results obtained by the technique Fluorescence showed a gradual increase in fluorescence with the addition of increasing concentration of EDTA. This suggests that the zinc is important in the tertiary structure of the protein. More studies are being made for better understand these results. (author)

  18. Gas Phase Chromatography of some Group 4, 5, and 6 Halides

    Energy Technology Data Exchange (ETDEWEB)

    Sylwester, Eric Robert [Univ. of California, Berkeley, CA (United States)

    1998-10-01

    Gas phase chromatography using The Heavy Element Volatility Instrument (HEVI) and the On Line Gas Apparatus (OLGA III) was used to determine volatilities of ZrBr4, HfBr4, RfBr4, NbBr5, TaOBr3, HaCl5, WBr6, FrBr, and BiBr3. Short-lived isotopes of Zr, Hf, Rf, Nb, Ta, Ha, W, and Bi were produced via compound nucleus reactions at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory and transported to the experimental apparatus using a He gas transport system. The isotopes were halogenated, separated from the other reaction products, and their volatilities determined by isothermal gas phase chromatography. Adsorption Enthalpy (ΔHa) values for these compounds were calculated using a Monte Carlo simulation program modeling the gas phase chromatography column. All bromides showed lower volatility than molecules of similar molecular structures formed as chlorides, but followed similar trends by central element. Tantalum was observed to form the oxybromide, analogous to the formation of the oxychloride under the same conditions. For the group 4 elements, the following order in volatility and ΔHa was observed: RfBr4 > ZrBr4 > HfBr4. The ΔHa values determined for the group 4, 5, and 6 halides are in general agreement with other experimental data and theoretical predictions. Preliminary experiments were performed on Me-bromides. A new measurement of the half-life of 261Rf was performed. 261Rf was produced via the 248Cm(18O, 5n) reaction and observed with a half-life of 74-6+7 seconds, in excellent agreement with the previous measurement of 78-6+11 seconds. We recommend a new half-life of 75±7 seconds for 261Rf based on these two measurements. Preliminary studies in transforming HEVI from an isothermal (constant

  19. Preconceptual design of the gas-phase decontamination demonstration cart

    International Nuclear Information System (INIS)

    Munday, E.B.

    1993-12-01

    Removal of uranium deposits from the interior surfaces of gaseous diffusion equipment will be a major portion of the overall multibillion dollar effort to decontaminate and decommission the gaseous diffusion plants. Long-term low-temperature (LTLT) gas-phase decontamination is being developed at the K-25 Site as an in situ decontamination process that is expected to significantly lower the decontamination costs, reduce worker exposure to radioactive materials, and reduce safeguard concerns. This report documents the preconceptual design of the process equipment that is necessary to conduct a full-scale demonstration of the LTLT method in accordance with the process steps listed above. The process equipment and method proposed in this report are not intended to represent a full-scale production campaign design and operation, since the gas evacuation, gas charging, and off-gas handling systems that would be cost effective in a production campaign are not cost effective for a first-time demonstration. However, the design presented here is expected to be applicable to special decontamination projects beyond the demonstration, which could include the Deposit Recovery Program. The equipment will therefore be sized to a 200 ft size 1 converter (plus a substantial conservative design margin), which is the largest item of interest for gas phase decontamination in the Deposit Recovery Program. The decontamination equipment will allow recovery of the UF 6 , which is generated from the reaction of ClF 3 with the uranium deposits, by use of NaF traps

  20. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  1. On characterization of anisotropic plant protein structures

    NARCIS (Netherlands)

    Krintiras, G.A.; Göbel, J.; Bouwman, W.G.; Goot, van der A.J.; Stefanidis, G.D.

    2014-01-01

    In this paper, a set of complementary techniques was used to characterize surface and bulk structures of an anisotropic Soy Protein Isolate (SPI)–vital wheat gluten blend after it was subjected to heat and simple shear flow in a Couette Cell. The structured biopolymer blend can form a basis for a

  2. Hidden Structural Codes in Protein Intrinsic Disorder.

    Science.gov (United States)

    Borkosky, Silvia S; Camporeale, Gabriela; Chemes, Lucía B; Risso, Marikena; Noval, María Gabriela; Sánchez, Ignacio E; Alonso, Leonardo G; de Prat Gay, Gonzalo

    2017-10-17

    Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.

  3. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Haibo [Iowa State Univ., Ames, IA (United States)

    2003-01-01

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  4. Protein structure recognition: From eigenvector analysis to structural threading method

    Science.gov (United States)

    Cao, Haibo

    In this work, we try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. We found a strong correlation between amino acid sequence and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, we give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part include discussions of interactions among amino acids residues, lattice HP model, and the designablity principle. In the second part, we try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in our eigenvector study of protein contact matrix. We believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, we discuss a threading method based on the correlation between amino acid sequence and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, we list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches.

  5. Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

    International Nuclear Information System (INIS)

    Haibo Cao

    2003-01-01

    In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This part includes discussions of interactions among amino acids residues, lattice HP model, and the design ability principle. In the second part, they try to establish the correlation between amino acid sequence and the corresponding native structure of the protein. This correlation was observed in the eigenvector study of protein contact matrix. They believe the correlation is universal, thus it can be used in automatic partition of protein structures into folding domains. In the third part, they discuss a threading method based on the correlation between amino acid sequences and ominant eigenvector of the structure contact-matrix. A mathematically straightforward iteration scheme provides a self-consistent optimum global sequence-structure alignment. The computational efficiency of this method makes it possible to search whole protein structure databases for structural homology without relying on sequence similarity. The sensitivity and specificity of this method is discussed, along with a case of blind test prediction. In the appendix, they list the overall performance of this threading method in CASP5 blind test in comparison with other existing approaches

  6. Structure and non-structure of centrosomal proteins.

    Science.gov (United States)

    Dos Santos, Helena G; Abia, David; Janowski, Robert; Mortuza, Gulnahar; Bertero, Michela G; Boutin, Maïlys; Guarín, Nayibe; Méndez-Giraldez, Raúl; Nuñez, Alfonso; Pedrero, Juan G; Redondo, Pilar; Sanz, María; Speroni, Silvia; Teichert, Florian; Bruix, Marta; Carazo, José M; Gonzalez, Cayetano; Reina, José; Valpuesta, José M; Vernos, Isabelle; Zabala, Juan C; Montoya, Guillermo; Coll, Miquel; Bastolla, Ugo; Serrano, Luis

    2013-01-01

    Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php.

  7. Structural deformation upon protein-protein interaction: a structural alphabet approach.

    Science.gov (United States)

    Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

    2008-02-28

    In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

  8. Structural deformation upon protein-protein interaction: A structural alphabet approach

    Directory of Open Access Journals (Sweden)

    Lecornet Hélène

    2008-02-01

    Full Text Available Abstract Background In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. Results In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%. This proportion is even greater in the interface regions (41%. Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Conclusion Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

  9. Beta-structures in fibrous proteins.

    Science.gov (United States)

    Kajava, Andrey V; Squire, John M; Parry, David A D

    2006-01-01

    The beta-form of protein folding, one of the earliest protein structures to be defined, was originally observed in studies of silks. It was then seen in early studies of synthetic polypeptides and, of course, is now known to be present in a variety of guises as an essential component of globular protein structures. However, in the last decade or so it has become clear that the beta-conformation of chains is present not only in many of the amyloid structures associated with, for example, Alzheimer's Disease, but also in the prion structures associated with the spongiform encephalopathies. Furthermore, X-ray crystallography studies have revealed the high incidence of the beta-fibrous proteins among virulence factors of pathogenic bacteria and viruses. Here we describe the basic forms of the beta-fold, summarize the many different new forms of beta-structural fibrous arrangements that have been discovered, and review advances in structural studies of amyloid and prion fibrils. These and other issues are described in detail in later chapters.

  10. Fibrous Protein Structures: Hierarchy, History and Heroes.

    Science.gov (United States)

    Squire, John M; Parry, David A D

    2017-01-01

    During the 1930s and 1940s the technique of X-ray diffraction was applied widely by William Astbury and his colleagues to a number of naturally-occurring fibrous materials. On the basis of the diffraction patterns obtained, he observed that the structure of each of the fibres was dominated by one of a small number of different types of molecular conformation. One group of fibres, known as the k-m-e-f group of proteins (keratin - myosin - epidermin - fibrinogen), gave rise to diffraction characteristics that became known as the α-pattern. Others, such as those from a number of silks, gave rise to a different pattern - the β-pattern, while connective tissues yielded a third unique set of diffraction characteristics. At the time of Astbury's work, the structures of these materials were unknown, though the spacings of the main X-ray reflections gave an idea of the axial repeats and the lateral packing distances. In a breakthrough in the early 1950s, the basic structures of all of these fibrous proteins were determined. It was found that the long protein chains, composed of strings of amino acids, could be folded up in a systematic manner to generate a limited number of structures that were consistent with the X-ray data. The most important of these were known as the α-helix, the β-sheet, and the collagen triple helix. These studies provided information about the basic building blocks of all proteins, both fibrous and globular. They did not, however, provide detailed information about how these molecules packed together in three-dimensions to generate the fibres found in vivo. A number of possible packing arrangements were subsequently deduced from the X-ray diffraction and other data, but it is only in the last few years, through the continued improvements of electron microscopy, that the packing details within some fibrous proteins can now be seen directly. Here we outline briefly some of the milestones in fibrous protein structure determination, the role of the

  11. Regenerable Air Purification System for Gas-Phase Contaminant Control

    Science.gov (United States)

    Constantinescu, Ileana C.; Finn, John E.; LeVan, M. Douglas; Lung, Bernadette (Technical Monitor)

    2000-01-01

    Tests of a pre-prototype regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an adsorbent column have been performed at NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. During the normal operation mode, contaminants are removed from the air on the column. Regeneration of the column is performed on-line. During regeneration, contaminants are displaced and destroyed inside the closed oxidation loop. In this presentation we discuss initial experimental results for the performance of RAPS in the removal and treatment of several important spacecraft contaminant species from air.

  12. SILP catalysis in gas-phase hydroformylation and carbonylation

    Energy Technology Data Exchange (ETDEWEB)

    Riisager, A.; Fehrmann, R. [Technical Univ. of Denmark, Lyngby (Denmark). Dept. of Chemistry; Haumann, M.; Wasserscheid, P. [Univ. Erlangen-Nuernberg (Germany). Lehrstuhl fuer Chemische Reaktionstechnik

    2006-07-01

    Supported ionic liquid phase (SILP) catalysts are new materials consisting of an ionic liquid-metal catalyst solution highly dispersed on a porous support. The use of a non-volatile, ionic liquid catalyst phase in SILP catalysts results in a stable heterogeneous-type material with selectivity and efficiency like homogeneous catalysts. The silica-supported SILP Rh-bisphosphine hydroformylation catalyst exhibited good activities and excellent selectivities in gas phase hydroformylation with stability exceeding 700 hours time-on-stream. Spectroscopic and kinetic data confirmed the homogeneous nature of the catalyst. In the Rh- SILP catalysed carbonylation of methanol the formation of undesired by-products could be suppressed by variation of residence time and gas pressure. (orig.)

  13. Synthesis and Gas Phase Thermochemistry of Germanium-Containing Compounds

    Energy Technology Data Exchange (ETDEWEB)

    Classen, Nathan Robert [Iowa State Univ., Ames, IA (United States)

    2002-01-01

    The driving force behind much of the work in this dissertation was to gain further understanding of the unique olefin to carbene isomerization observed in the thermolysis of 1,1-dimethyl-2-methylenesilacyclobutane by finding new examples of it in other silicon and germanium compounds. This lead to the examination of a novel phenylmethylenesilacyclobut-2-ene, which did not undergo olefin to carbene rearrangement. A synthetic route to methylenegermacyclobutanes was developed, but the methylenegermacyclobutane system exhibited kinetic instability, making the study of the system difficult. In any case the germanium system decomposed through a complex mechanism which may not include olefin to carbene isomerization. However, this work lead to the study of the gas phase thermochemistry of a series of dialkylgermylene precursors in order to better understand the mechanism of the thermal decomposition of dialkylgermylenes. The resulting dialkylgermylenes were found to undergo a reversible intramolecular β C-H insertion mechanism.

  14. Zpif's law in the liquid gas phase transition of nuclei

    International Nuclear Information System (INIS)

    Ma, Y.G.

    1999-01-01

    Zpif's law in the field of linguistics is tested in the nuclear disassembly within the framework of isospin dependent lattice gas model. It is found that the average cluster charge (or mass) of rank n in the charge (or mass) list shows exactly inversely to its rank, i.e., there exists Zpif's law, at the phase transition temperature. This novel criterion shall be helpful to search the nuclear liquid gas phase transition experimentally and theoretically. In addition, the finite size scaling of the effective phase transition temperature at which the Zpif's law appears is studied for several systems with different mass and the critical exponents of ν and β are tentatively extracted. (orig.)

  15. FLUIDDYNAMIC ASPECTS OF GAS-PHASE ETHYLENE POLYMERIZATION REACTOR DESIGN

    Directory of Open Access Journals (Sweden)

    Guardani R.

    1998-01-01

    Full Text Available The relative importance of design variables affecting the fluiddynamic behavior of a fluidized bed reactor for the gas-phase ethylene polymerization is discussed, based on mathematical modeling. The three-phase bubbling fluidized bed model is based on axially distributed properties for the bubble, cloud and emulsion phases, combined with correlations for population balance and entrainment. Under the operating conditions adopted in most industrial processes, the reactor performance is affected mainly by the reaction rate and solids entrainment. Simulation results indicate that an adequate design of the freeboard and particle collecting equipment is of primary importance in order to produce polymeric particles with the desired size distribution, as well as to keep entrainment and catalyst feed rates at adequate levels.

  16. Conformational Study of Taurine in the Gas Phase

    Science.gov (United States)

    Cortijo, Vanessa; Sanz, M. Eugenia; López, Juan C.; Alonso, José L.

    2009-08-01

    The conformational preferences of the amino sulfonic acid taurine (NH2-CH2-CH2-SO3H) have been investigated in the gas phase by laser ablation molecular beam Fourier transform microwave spectroscopy (LA-MB-FTMW) in the 6-14 GHz frequency range. One conformer has been observed, and its rotational, centrifugal distortion, and hyperfine quadrupole coupling constants have been determined from the analysis of its rotational spectrum. Comparison of the experimental constants with those calculated theoretically identifies the detected conformer unambiguously. The observed conformer of taurine is stabilized by an intramolecular hydrogen bond O-H···N between the hydrogen of the sulfonic acid group and the nitrogen atom of the amino group.

  17. Gas phase chromatography of halides of elements 104 and 105

    International Nuclear Information System (INIS)

    Tuerler, A.; Gregorich, K.E.; Czerwinski, K.R.; Hannink, N.J.; Henderson, R.A.; Hoffman, D.C.; Kacher, C.D.; Kadkhodayan, B.; Kreek, S.A.; Lee, D.M.; Leyba, J.D.; Nurmia, M.J.; Gaeggeler, H.W.; Jost, D.T.; Kovacs, J.; Scherer, U.W.; Vermeulen, D.; Weber, A.; Barth, H.; Gober, M.K.; Kratz, J.V.; Bruechle, W.; Schaedel, M.; Schimpf, E.; Gober, M.K.; Kratz, J.V.; Zimmermann, H.P.

    1991-04-01

    On-line isothermal gas phase chromatography was used to study halides of 261 104 (T 1/2 = 65 s) and 262,263 105 (T 1/2 = 34 s and 27 s) produced an atom-at-a time via the reactions 248 Cm( 18 O, 5n) and 249 Bk( 18 O, 5n, 4n), respectively. Using HBr and HCl gas as halogenating agents, we were able to produce volatile bromides and chlorides of the above mentioned elements and study their behavior compared to their lighter homologs in Groups 4 or 5 of the periodic table. Element 104 formed more volatile bromides than its homolog Hf. In contrast, element 105 bromides were found to be less volatile than the bromides of the group 5 elements Nb and Ta. Both 104 and Hf chlorides were observed to be more volatile than their respective bromides. 31 refs., 8 figs

  18. Technical Procedures Management in Gas-Phase Detoxification Laboratory

    International Nuclear Information System (INIS)

    Cardona Garcia, A. I.; Sanchez Cabrero, B.

    2000-01-01

    The natural cycle of Volatile Organic Compounds (VOCs) has been disturbed by the industrial and socioeconomic activities of human beings. This imbalance in the environment has affected the ecosystems and the human health. Initiatives have been planned to mitigate these adverse effects. In order to minimize the hazardous effects, initiatives have been proposed for the treatment of gaseous emissions. The solar photo catalysis appears as a clear and renewable technology in front of the conventional ones.In CIEMAT this line is being investigated as the base of a future implementation at a pre industrial scale.Technical procedures are written in this document for testing Gas-Phase detoxification at lab scale in the Renewable Energy Department (DER) CIEMAT- Madrid to eliminate the VOCs by using the solar photo catalysis technology. (Author) 34 refs

  19. Gas-phase synthesis of magnetic metal/polymer nanocomposites

    Science.gov (United States)

    Starsich, Fabian H. L.; Hirt, Ann M.; Stark, Wendelin J.; Grass, Robert N.

    2014-12-01

    Highly magnetic metal Co nanoparticles were produced via reducing flame spray pyrolysis, and directly coated with an epoxy polymer in flight. The polymer content in the samples varied between 14 and 56 wt% of nominal content. A homogenous dispersion of Co nanoparticles in the resulting nanocomposites was visualized by electron microscopy. The size and crystallinity of the metallic fillers was not affected by the polymer, as shown by XRD and magnetic hysteresis measurements. The good control of the polymer content in the product nanocomposite was shown by elemental analysis. Further, the successful polymerization in the gas phase was demonstrated by electron microscopy and size measurements. The presented effective, dry and scalable one-step synthesis method for highly magnetic metal nanoparticle/polymer composites presented here may drastically decrease production costs and increase industrial yields.

  20. Gas-Phase Thermolysis of a Thioketen-S-Oxide

    DEFF Research Database (Denmark)

    Carlsen, Lars; Egsgaard, Helge; Schaumann, Ernst

    1980-01-01

    The unimolecular gas-phase thermolytic decomposition of 1,1,3,3-tetramethyl-2-thiocarbonylcyclohexane S-oxide (3) has been studied as a function of temperature by a flash vacuum thermolysis (f.v.t.) technique. The products detected are the carbenes (4) and (5), the ketone (6), the keten (7......), the thioketone (8), and the thioketen (9). The product ratio is highly dependent on the thermolysis temperature. The thermolysis of (3) is mechanistically rationalized by assuming the existence of only two concurrent primary processes, which are (a) extrusion of atomic oxygen, leading to the thioketen (9...... and CSO leading to the carbenes (5) and (4), respectively, are observed. Owing to an apparently very short half-life of the oxathiiran (10), only the decomposition products of the three-membered ring compound have been detected. These are the thioketone (8), formed by rearrangement of (10) into the α...

  1. Statistical Physics of Nanoparticles in the Gas Phase

    CERN Document Server

    Hansen, Klavs

    2013-01-01

    Thermal processes are ubiquitous and an understanding of thermal phenomena is essential for a complete description of the physics of nanoparticles, both for the purpose of modeling the dynamics of the particles and for the correct interpretation of experimental data. This book has the twofold aim to present coherently the relevant results coming from the recent scientific literature and to guide the readers through the process of deriving results, enabling them to explore the limits of the mathematical approximations and test the power of the method. The book is focused on the fundamental properties of nanosystems in the gas phase. For this reason there is a strong emphasis on microcanonical physics. Each chapter is enriched with exercises and 3 Appendices provide additional useful materials.

  2. Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution.

    Science.gov (United States)

    Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M Eugenia; Molteni, Carla

    2017-04-14

    The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

  3. Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

    Science.gov (United States)

    Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M. Eugenia; Molteni, Carla

    2017-04-01

    The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

  4. Surfactants from the gas phase may promote cloud droplet formation.

    Science.gov (United States)

    Sareen, Neha; Schwier, Allison N; Lathem, Terry L; Nenes, Athanasios; McNeill, V Faye

    2013-02-19

    Clouds, a key component of the climate system, form when water vapor condenses upon atmospheric particulates termed cloud condensation nuclei (CCN). Variations in CCN concentrations can profoundly impact cloud properties, with important effects on local and global climate. Organic matter constitutes a significant fraction of tropospheric aerosol mass, and can influence CCN activity by depressing surface tension, contributing solute, and influencing droplet activation kinetics by forming a barrier to water uptake. We present direct evidence that two ubiquitous atmospheric trace gases, methylglyoxal (MG) and acetaldehyde, known to be surface-active, can enhance aerosol CCN activity upon uptake. This effect is demonstrated by exposing acidified ammonium sulfate particles to 250 parts per billion (ppb) or 8 ppb gas-phase MG and/or acetaldehyde in an aerosol reaction chamber for up to 5 h. For the more atmospherically relevant experiments, i.e., the 8-ppb organic precursor concentrations, significant enhancements in CCN activity, up to 7.5% reduction in critical dry diameter for activation, are observed over a timescale of hours, without any detectable limitation in activation kinetics. This reduction in critical diameter enhances the apparent particle hygroscopicity up to 26%, which for ambient aerosol would lead to cloud droplet number concentration increases of 8-10% on average. The observed enhancements exceed what would be expected based on Köhler theory and bulk properties. Therefore, the effect may be attributed to the adsorption of MG and acetaldehyde to the gas-aerosol interface, leading to surface tension depression of the aerosol. We conclude that gas-phase surfactants may enhance CCN activity in the atmosphere.

  5. Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation.

    Science.gov (United States)

    Straus, Rita N; Jockusch, Rebecca A

    2017-02-01

    An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes. Graphical Abstract ᅟ.

  6. A Kernel for Protein Secondary Structure Prediction

    OpenAIRE

    Guermeur , Yann; Lifchitz , Alain; Vert , Régis

    2004-01-01

    http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=10338&mode=toc; International audience; Multi-class support vector machines have already proved efficient in protein secondary structure prediction as ensemble methods, to combine the outputs of sets of classifiers based on different principles. In this chapter, their implementation as basic prediction methods, processing the primary structure or the profile of multiple alignments, is investigated. A kernel devoted to the task is in...

  7. 3D bioprinting of structural proteins.

    Science.gov (United States)

    Włodarczyk-Biegun, Małgorzata K; Del Campo, Aránzazu

    2017-07-01

    3D bioprinting is a booming method to obtain scaffolds of different materials with predesigned and customized morphologies and geometries. In this review we focus on the experimental strategies and recent achievements in the bioprinting of major structural proteins (collagen, silk, fibrin), as a particularly interesting technology to reconstruct the biochemical and biophysical composition and hierarchical morphology of natural scaffolds. The flexibility in molecular design offered by structural proteins, combined with the flexibility in mixing, deposition, and mechanical processing inherent to bioprinting technologies, enables the fabrication of highly functional scaffolds and tissue mimics with a degree of complexity and organization which has only just started to be explored. Here we describe the printing parameters and physical (mechanical) properties of bioinks based on structural proteins, including the biological function of the printed scaffolds. We describe applied printing techniques and cross-linking methods, highlighting the modifications implemented to improve scaffold properties. The used cell types, cell viability, and possible construct applications are also reported. We envision that the application of printing technologies to structural proteins will enable unprecedented control over their supramolecular organization, conferring printed scaffolds biological properties and functions close to natural systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Functions and structures of eukaryotic recombination proteins

    International Nuclear Information System (INIS)

    Ogawa, Tomoko

    1994-01-01

    We have found that Rad51 and RecA Proteins form strikingly similar structures together with dsDNA and ATP. Their right handed helical nucleoprotein filaments extend the B-form DNA double helixes to 1.5 times in length and wind the helix. The similarity and uniqueness of their structures must reflect functional homologies between these proteins. Therefore, it is highly probable that similar recombination proteins are present in various organisms of different evolutional states. We have succeeded to clone RAD51 genes from human, mouse, chicken and fission yeast genes, and found that the homologues are widely distributed in eukaryotes. The HsRad51 and MmRad51 or ChRad51 proteins consist of 339 amino acids differing only by 4 or 12 amino acids, respectively, and highly homologous to both yeast proteins, but less so to Dmcl. All of these proteins are homologous to the region from residues 33 to 240 of RecA which was named ''homologous core. The homologous core is likely to be responsible for functions common for all of them, such as the formation of helical nucleoprotein filament that is considered to be involved in homologous pairing in the recombination reaction. The mouse gene is transcribed at a high level in thymus, spleen, testis, and ovary, at lower level in brain and at a further lower level in some other tissues. It is transcribed efficiently in recombination active tissues. A clear functional difference of Rad51 homologues from RecA was suggested by the failure of heterologous genes to complement the deficiency of Scrad51 mutants. This failure seems to reflect the absence of a compatible partner, such as ScRad52 protein in the case of ScRad51 protein, between different species. Thus, these discoveries play a role of the starting point to understand the fundamental gene targeting in mammalian cells and in gene therapy. (J.P.N.)

  9. Gas-Phase Reactions of Dimethyl Disulfide with Aliphatic Carbanions - A Mass Spectrometry and Computational Study

    Science.gov (United States)

    Franczuk, Barbara; Danikiewicz, Witold

    2018-03-01

    Ion-molecule reactions of Me2S2 with a wide range of aliphatic carbanions differing by structure and proton affinity values have been studied in the gas phase using mass spectrometry techniques and DFT calculations. The analysis of the spectra shows a variety of product ions formed via different reaction mechanisms, depending on the structure and proton affinity of the carbanion. Product ions of thiophilic reaction ( m/z 47), SN2 ( m/z 79), and E2 elimination - addition sequence of reactions ( m/z 93) can be observed. Primary products of thiophilic reaction can undergo subsequent SN2 and proton transfer reactions. Gibbs free energy profiles calculated for experimentally observed reactions using PBE0/6-311+G(2d,p) method show good agreement with experimental results. [Figure not available: see fulltext.

  10. On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins.

    Science.gov (United States)

    Habka, S; Sohn, W Y; Vaquero-Vara, V; Géléoc, M; Tardivel, B; Brenner, V; Gloaguen, E; Mons, M

    2018-01-31

    Asparagine (Asn) is a powerful turn-inducer residue, with a large propensity to occupy the second position in the central region of β-turns of proteins. The present work aims at investigating the role of a local anchoring between the Asn side chain and the main chain in this remarkable property. For this purpose, the H-bonding patterns of an asparagine residue in an isolated protein chain fragment forming a γ- or a β-turn have been determined using IR/UV double resonance gas phase spectroscopy on laser-desorbed, jet-cooled short models in conjunction with relevant quantum chemistry calculations. These gas phase data provide evidence for an original double anchoring linking the Asn primary amide side chain (SC), which adopts a gauche+ rotameric form, to its main chain (MC) local environment. From both IR spectroscopic evidence (H-bond induced red shifts) and quantum chemistry, Asn SC is found to behave as a stronger H-bond acceptor than donor, resulting in stronger MC→SC H-bonds than SC→MC ones. These gas phase structural data, relevant to a hydrophobic environment, have been used as a reference to assess the anchoring taking place in high resolution crystallized proteins of the Protein Data Bank. This approach reveals that, when the SC adopts a gauche+ orientation, the stronger MC→SC bonds are preserved in many cases whereas the SC→MC bonds are always disrupted, in qualitative agreement with the gas phase ranking of these interactions. Most interestingly, when Asn occupies the second position of central part of a β-turn (i.e., the very turn-inducer position), the MC→SC H-bonds are also disrupted and replaced by a water-mediated SC to MC anchoring. Owing to the specific features of the hydrated Asn side chain, we propose that it could be a turn precursor structure, able to facilitate turn formation in the early events of the folding process.

  11. Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry.

    Science.gov (United States)

    Xiao, Yiming; Konermann, Lars

    2015-08-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N(2) bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N(2) bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N(2) sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, "semi-unfolded" ↔ "native" ↔ "globally unfolded" → "aggregated". This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS. © 2015 The Protein Society.

  12. Protein structure based prediction of catalytic residues.

    Science.gov (United States)

    Fajardo, J Eduardo; Fiser, Andras

    2013-02-22

    Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific reference databases.

  13. Discrete Haar transform and protein structure.

    Science.gov (United States)

    Morosetti, S

    1997-12-01

    The discrete Haar transform of the sequence of the backbone dihedral angles (phi and psi) was performed over a set of X-ray protein structures of high resolution from the Brookhaven Protein Data Bank. Afterwards, the new dihedral angles were calculated by the inverse transform, using a growing number of Haar functions, from the lower to the higher degree. New structures were obtained using these dihedral angles, with standard values for bond lengths and angles, and with omega = 0 degree. The reconstructed structures were compared with the experimental ones, and analyzed by visual inspection and statistical analysis. When half of the Haar coefficients were used, all the reconstructed structures were not yet collapsed to a tertiary folding, but they showed yet realized most of the secondary motifs. These results indicate a substantial separation of structural information in the space of Haar transform, with the secondary structural information mainly present in the Haar coefficients of lower degrees, and the tertiary one present in the higher degree coefficients. Because of this separation, the representation of the folded structures in the space of Haar transform seems a promising candidate to encompass the problem of premature convergence in genetic algorithms.

  14. Recognition of functional sites in protein structures.

    Science.gov (United States)

    Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

    2004-06-04

    Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

  15. Infrared multiple photon dissociation action spectroscopy of alkali metal cation-cyclen complexes: Effects of alkali metal cation size on gas-phase conformation

    NARCIS (Netherlands)

    Austin, C.A.; Chen, Y.; Kaczan, C.M.; Berden, G.; Oomens, J.; Rodgers, M.T.

    2013-01-01

    The gas-phase structures of alkali metal cationized complexes of cyclen (1,4,7,10-tetraazacyclododecane) are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and electronic structure theory calculations. The measured IRMPD action spectra of four M+(cyclen) complexes are

  16. Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal

    OpenAIRE

    Bordoli, Lorenza; Schwede, Torsten

    2012-01-01

    Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of appl...

  17. GAS-PHASE CHEMISTRY OF THE CYANATE ION, OCN−

    International Nuclear Information System (INIS)

    Cole, Callie A.; Wang, Zhe-Chen; Bierbaum, Veronica M.; Snow, Theodore P.

    2015-01-01

    Cyanate (OCN − ) is the only ion to date whose presence has been confirmed in the icy mantles that coat interstellar dust grains. Understanding the chemical behavior of cyanate at a fundamental level is therefore integral to the advancement of astrochemistry. We seek to unravel the chemistry of this intriguing anion through a combination of gas-phase experiments and theoretical explorations. Our approach is twofold: first, employing a flowing afterglow-selected ion flow tube apparatus, the reactions between OCN − and three of the most abundant atomic species in the interstellar medium, hydrogen, nitrogen, and oxygen, are examined. Hydrogen atoms readily react by associative detachment, but the remarkable stability of OCN − does not give rise to an observable reaction with either nitrogen or oxygen atoms. To explain these results, the potential energy surfaces of several reactions are investigated at the B3LYP/6-311++G(d,p) level of theory. Second, collision induced dissociation experiments involving deprotonated uracil, thymine, and cytosine in an ion trap mass spectrometer reveal an interesting connection between these pyrimidine nucleobase anions and OCN − . Theoretical calculations at the B3LYP/6-311++G(d,p) level of theory are performed to delineate the mechanisms of dissociation and explore the possible role of OCN − as a biomolecule precursor

  18. The Influence of Mixing in High Temperature Gas Phase Reactions

    DEFF Research Database (Denmark)

    Østberg, Martin

    1996-01-01

    by injection of NH3 with carrier gas into the flue gas. NH3 can react with NO and form N2, but a competing reaction path is the oxidation of NH3 to NO.The SNR process is briefly described and it is shown by chemical kinetic modelling that OH radicals under the present conditions will initiate the reaction......The objective of this thesis is to describe the mixing in high temperature gas phase reactions.The Selective Non-Catalytic Reduction of NOx (referred as the SNR process) using NH3 as reductant was chosen as reaction system. This in-furnace denitrification process is made at around 1200 - 1300 K...... diffusion. The SNR process is simulated using the mixing model and an empirical kinetic model based on laboratory experiments.A bench scale reactor set-up has been built using a natural gas burner to provide the main reaction gas. The set-up has been used to perform an experimental investigation...

  19. Gas phase reactions of nitrogen oxides with olefins

    Energy Technology Data Exchange (ETDEWEB)

    Altshuller, A P; Cohen, I

    1961-01-01

    The nature of the condensation products formed in the gas phase reactions of nitrogen dioxide and nitric oxide with pentene-1, 2-methylbutene-2, and 2-methylbutadiene-1,3 was investigated. The reactants were combined at partial pressures in the range of 0.1 to 2.5 mm with the total pressure at one atmosphere. The products were determined by infrared and ultraviolet spectroscopy and colorimetry. The condensates included primary and secondary nitro compounds and alkyl nitrates. Strong hydroxyl and single bond carbon to oxygen stretching vibrations indicate the presence of either nitroalcohols or simple aliphatic alcohols formed through oxidation reactions. Carbonyl stretching frequencies observable in some of the reactions support the conclusion that a portion of the reactants disappear by oxidation rather than by nitration processes. The available results do not indicate the presence of appreciable amounts of tert.-nitro compounds, conjugated nitro-olefins, or gem-dinitro-alkanes. The reactivities of the olefins with the nitrogen oxides are in the decreasing order: 2-methyl-butadiene-1,3, 2-methylbutene-2, pentene-1. 20 references.

  20. Frequency metrology of a photomixing source for gas phase spectroscopy

    Science.gov (United States)

    Hindle, Francis; Mouret, Gael; Yang, Chun; Cuisset, Arnaud; Bocquet, Robin; Lours, Michel; Rovera, Daniele

    2010-08-01

    The availability of frequency combs has opened new possibilities for the measurement of optical frequencies. Photomixing is an attractive solution for high resolution THz spectroscopy of gases due to the narrow spectral resolution and ability to access the 100 GHz to 3.5 THz range. One limitation of present photomixing spectrometers is the accuracy with which the THz frequency is established. Measurement of the centre frequency gas phase molecular transitions requires an accuracy better than 100 kHz in order to allow spectroscopic constants to be determined. Standard optical techniques like those employed in wavelength meters can only provide accuracies in the order of 50 MHz. We have used a turnkey fibre based frequency comb and a standard photomixing configuration to realize a THz synthesizer with an accuracy of around 50kHz. Two ECDLs used to pump the photomixer are phase locked onto the frequency comb and provide a tuning range of 10 MHz. In order to extend the tuning range an additional phase locked ECLD has been added to obtain a range in excess of 100 MHz. The absorption profiles of many Doppler limited transitions of carbonyl sulphide and formaldehyde have been measured to validate this instrument.

  1. Precursor-Less Coating of Nanoparticles in the Gas Phase

    Directory of Open Access Journals (Sweden)

    Tobias V. Pfeiffer

    2015-03-01

    Full Text Available This article introduces a continuous, gas-phase method for depositing thin metallic coatings onto (nanoparticles using a type of physical vapor deposition (PVD at ambient pressure and temperature. An aerosol of core particles is mixed with a metal vapor cloud formed by spark ablation by passing the aerosol through the spark zone using a hollow electrode configuration. The mixing process rapidly quenches the vapor, which condenses onto the core particles at a timescale of several tens of milliseconds in a manner that can be modeled as bimodal coagulation. Gold was deposited onto core nanoparticles consisting of silver or polystyrene latex, and silver was deposited onto gold nanoparticles. The coating morphology depends on the relative surface energies of the core and coating materials, similar to the growth mechanisms known for thin films: a coating made of a substance having a high surface energy typically results in a patchy coverage, while a coating material with a low surface energy will normally “wet” the surface of a core particle. The coated particles remain gas-borne, allowing further processing.

  2. Nucleation and dissociation of nano-particles in gas phase

    International Nuclear Information System (INIS)

    Feiden, P.

    2007-09-01

    This work deals with the study of nano-particles formation in gas phase and their dissociation pathways after an optical excitation. The clusters formation decomposes in two steps: a seed is formed (nucleation phase) and sticks atoms during its propagation in a sodium atomic vapor (growth phase). Those two steps have been observed separately for homogeneous Na n and heterogeneous Na n X particles (X = (NaOH) 2 or (Na 2 O) 2 ). The growth mechanism is well interpreted by a Monte Carlo simulation taking into account an accretion mechanism with hard-sphere cross section. The homogeneous nucleation mechanism has been highlighted by a direct comparison with the Classical Nucleation Theory predictions. The clusters fragmentation of ionic Na + (NaOH) p et Na + (NaF) p particles is studied in the second part. The way clusters fragment with size when they are excited optically is compared with theoretical previsions: this highlights the existence of an energetic barrier for special size of clusters. Finally, the fragmentation of doubly charged Na + Na + (NaOH) p clusters shows a competition between the fission into two single charged fragments and the unimolecular evaporation of a neutral fragment. (author)

  3. Conformational reduction of DOPA in the gas phase studied by laser desorption supersonic jet laser spectroscopy.

    Science.gov (United States)

    Ishiuchi, Shun-ichi; Mitsuda, Haruhiko; Asakawa, Toshiro; Miyazaki, Mitsuhiko; Fujii, Masaaki

    2011-05-07

    The conformational reduction in catecholamine neurotransmitters was studied by resonance enhanced multi photon ionization (REMPI), ultraviolet-ultraviolet (UV-UV) hole burning and infrared (IR) dip spectroscopy with applying a laser desorption supersonic jet technique to DOPA, which is one of the catecholamine neurotransmitters and has one more phenolic OH group than tyrosine. It is concluded that DOPA has a single observable conformer in the gas phase at low temperature. Quantum chemical calculations at several levels with or without the dispersion correction were also carried out to study stable conformations. From the comparison between the computational IR spectra and the experimental ones, the most stable structure was determined. It is strongly suggested that the conformational reduction is caused by electrostatic interactions, such as a dipole-dipole interaction, between the chain and OH groups. This journal is © the Owner Societies 2011

  4. Nanocrystalline AL2 O2 powders produced by laser induced gas phase reactions

    International Nuclear Information System (INIS)

    Borsella, E.; Botti, S.; Martelli, S.; Zappa, G.; Giorgi, R.; Turt, S.

    1993-01-01

    Nanocrystalline Al 2 O 3 powders were successfully synthesized by a CO 2 laser-driven gas-phase reaction involving trimethylaluminium (Al(CH 3 ) 3 ) and nitrous-oxide (N 2 O). Ethylene (C 2 H 4 ) was added as gas sensitizer. The as-synthesized powder particles showed a considerable carbon contamination and an amorphous-like structure. After thermal treatment at 1200-1400 degrees C, the powder was transformed to hexagonal a-Al 2 O 3 with very low carbon contamination as confirmed by X-ray diffraction, X-ray photo-electron spectroscopy and chemical analysis. The calcinated powders resulted to be spherical single crystal nanoparticles with a mean size of 15-20 nm, as determined by X-ray diffraction, electron microscopy and B.E.T. specific surface measurements. The laser synthesized Al 2 O 3 particles are well suited dispersoids for intermetallic alloy technology

  5. PCNA Structure and Interactions with Partner Proteins

    KAUST Repository

    Oke, Muse; Zaher, Manal S.; Hamdan, Samir

    2018-01-01

    Proliferating cell nuclear antigen (PCNA) consists of three identical monomers that topologically encircle double-stranded DNA. PCNA stimulates the processivity of DNA polymerase δ and, to a less extent, the intrinsically highly processive DNA polymerase ε. It also functions as a platform that recruits and coordinates the activities of a large number of DNA processing proteins. Emerging structural and biochemical studies suggest that the nature of PCNA-partner proteins interactions is complex. A hydrophobic groove at the front side of PCNA serves as a primary docking site for the consensus PIP box motifs present in many PCNA-binding partners. Sequences that immediately flank the PIP box motif or regions that are distant from it could also interact with the hydrophobic groove and other regions of PCNA. Posttranslational modifications on the backside of PCNA could add another dimension to its interaction with partner proteins. An encounter of PCNA with different DNA structures might also be involved in coordinating its interactions. Finally, the ability of PCNA to bind up to three proteins while topologically linked to DNA suggests that it would be a versatile toolbox in many different DNA processing reactions.

  6. PCNA Structure and Interactions with Partner Proteins

    KAUST Repository

    Oke, Muse

    2018-01-29

    Proliferating cell nuclear antigen (PCNA) consists of three identical monomers that topologically encircle double-stranded DNA. PCNA stimulates the processivity of DNA polymerase δ and, to a less extent, the intrinsically highly processive DNA polymerase ε. It also functions as a platform that recruits and coordinates the activities of a large number of DNA processing proteins. Emerging structural and biochemical studies suggest that the nature of PCNA-partner proteins interactions is complex. A hydrophobic groove at the front side of PCNA serves as a primary docking site for the consensus PIP box motifs present in many PCNA-binding partners. Sequences that immediately flank the PIP box motif or regions that are distant from it could also interact with the hydrophobic groove and other regions of PCNA. Posttranslational modifications on the backside of PCNA could add another dimension to its interaction with partner proteins. An encounter of PCNA with different DNA structures might also be involved in coordinating its interactions. Finally, the ability of PCNA to bind up to three proteins while topologically linked to DNA suggests that it would be a versatile toolbox in many different DNA processing reactions.

  7. Protein secondary structure: category assignment and predictability

    DEFF Research Database (Denmark)

    Andersen, Claus A.; Bohr, Henrik; Brunak, Søren

    2001-01-01

    In the last decade, the prediction of protein secondary structure has been optimized using essentially one and the same assignment scheme known as DSSP. We present here a different scheme, which is more predictable. This scheme predicts directly the hydrogen bonds, which stabilize the secondary......-forward neural network with one hidden layer on a data set identical to the one used in earlier work....

  8. Protein-mediated surface structuring in biomembranes

    Directory of Open Access Journals (Sweden)

    Maggio B.

    2005-01-01

    Full Text Available The lipids and proteins of biomembranes exhibit highly dissimilar conformations, geometrical shapes, amphipathicity, and thermodynamic properties which constrain their two-dimensional molecular packing, electrostatics, and interaction preferences. This causes inevitable development of large local tensions that frequently relax into phase or compositional immiscibility along lateral and transverse planes of the membrane. On the other hand, these effects constitute the very codes that mediate molecular and structural changes determining and controlling the possibilities for enzymatic activity, apposition and recombination in biomembranes. The presence of proteins constitutes a major perturbing factor for the membrane sculpturing both in terms of its surface topography and dynamics. We will focus on some results from our group within this context and summarize some recent evidence for the active involvement of extrinsic (myelin basic protein, integral (Folch-Lees proteolipid protein and amphitropic (c-Fos and c-Jun proteins, as well as a membrane-active amphitropic phosphohydrolytic enzyme (neutral sphingomyelinase, in the process of lateral segregation and dynamics of phase domains, sculpturing of the surface topography, and the bi-directional modulation of the membrane biochemical reactivity.

  9. Gas-phase thermolysis reaction of formaldehyde diperoxide. Kinetic study and theoretical mechanisms

    Energy Technology Data Exchange (ETDEWEB)

    Jorge, Nelly Lidia [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain); Area de Quimica Fisica Facultad de Ciencias Exactas y Naturales y Agrimensura, UNNE, Avda. Libertad 5460, 3400 Corrientes (Argentina); Romero, Jorge Marcelo [Area de Quimica Fisica Facultad de Ciencias Exactas y Naturales y Agrimensura, UNNE, Avda. Libertad 5460, 3400 Corrientes (Argentina); Grand, Andre [INAC, SCIB, Laboratoire ' Lesions des Acides Nucleiques' , UMR CEA-UJF E3, CEA-Grenoble, 17 Rue des Martyrs, 38054 Grenoble cedex 9 (France); Hernandez-Laguna, Alfonso, E-mail: ahlaguna@ugr.es [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Av. Las Palmeras 4, 18100 Armilla, Granada (Spain)

    2012-01-17

    Highlights: Black-Right-Pointing-Pointer Kinetic and mechanism of the gas-phase thermolysis of tetroxane were determined. Black-Right-Pointing-Pointer Gas chromatography and computational potential energy surfaces were performed. Black-Right-Pointing-Pointer A mechanism in steps looked like the most probable mechanism. Black-Right-Pointing-Pointer A spin-orbit coupling appeared at the singlet and triple diradical open structures. Black-Right-Pointing-Pointer A non-adiabatic crossing from the singlet to the triplet state occurred. - Abstract: Gas-phase thermolysis reaction of formaldehyde diperoxide (1,2,4,5-tetroxane) was performed in an injection chamber of a gas chromatograph at a range of 463-503 K. The average Arrhenius activation energy and pre-exponential factor were 29.3 {+-} 0.8 kcal/mol and 5.2 Multiplication-Sign 10{sup 13} s{sup -1}, respectively. Critical points and reaction paths of the ground singlet and first triplet potential energy surfaces (PES) were calculated, using DFT method at BHANDHLYP/6-311+G{sup Asterisk-Operator Asterisk-Operator} level of the theory. Also, G3 calculations were performed on the reactant and products. Reaction by the ground-singlet and first-triplet states turned out to be endothermic and exothermic, respectively. The mechanism in three steps seemed to be the most probable one. An electronically non-adiabatic process appeared, in which a crossing, at an open diradical structure, from the singlet to the triplet state PES occurred, due to a spin-orbit coupling, yielding an exothermic reaction. Theoretical kinetic constant coming from the non- adiabatic transition from the singlet to the triplet state agrees with the experimental values.

  10. Gas-phase thermolysis reaction of formaldehyde diperoxide. Kinetic study and theoretical mechanisms

    International Nuclear Information System (INIS)

    Jorge, Nelly Lidia; Romero, Jorge Marcelo; Grand, André; Hernández-Laguna, Alfonso

    2012-01-01

    Highlights: ► Kinetic and mechanism of the gas-phase thermolysis of tetroxane were determined. ► Gas chromatography and computational potential energy surfaces were performed. ► A mechanism in steps looked like the most probable mechanism. ► A spin–orbit coupling appeared at the singlet and triple diradical open structures. ► A non-adiabatic crossing from the singlet to the triplet state occurred. - Abstract: Gas-phase thermolysis reaction of formaldehyde diperoxide (1,2,4,5-tetroxane) was performed in an injection chamber of a gas chromatograph at a range of 463–503 K. The average Arrhenius activation energy and pre-exponential factor were 29.3 ± 0.8 kcal/mol and 5.2 × 10 13 s −1 , respectively. Critical points and reaction paths of the ground singlet and first triplet potential energy surfaces (PES) were calculated, using DFT method at BHANDHLYP/6-311+G ∗∗ level of the theory. Also, G3 calculations were performed on the reactant and products. Reaction by the ground-singlet and first-triplet states turned out to be endothermic and exothermic, respectively. The mechanism in three steps seemed to be the most probable one. An electronically non-adiabatic process appeared, in which a crossing, at an open diradical structure, from the singlet to the triplet state PES occurred, due to a spin–orbit coupling, yielding an exothermic reaction. Theoretical kinetic constant coming from the non- adiabatic transition from the singlet to the triplet state agrees with the experimental values.

  11. Homolytic iodination and nitration of some benzene derivatives in the gas phase

    International Nuclear Information System (INIS)

    Vonk, W.F.M.

    1980-01-01

    Two gas phase reactions, involving the iodination and nitration of benzene derivatives, are described. The experimental techniques of the apparatus and the methods used are outlined. The kinetic H/D isotope effect in the gas phase nitration of benzene with NO 2 is determined. (C.F.)

  12. CHAOS. III. GAS-PHASE ABUNDANCES IN NGC 5457

    Energy Technology Data Exchange (ETDEWEB)

    Croxall, Kevin V.; Pogge, Richard W. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Berg, Danielle A. [Center for Gravitation, Cosmology and Astrophysics, Department of Physics, University of Wisconsin Milwaukee, 1900 East Kenwood Boulevard, Milwaukee, WI 53211 (United States); Skillman, Evan D. [Minnesota Institute for Astrophysics, University of Minnesota, 116 Church Street SE, Minneapolis, MN 55455 (United States); Moustakas, John [Department of Physics and Astronomy, Siena College, 515 Loudon Road, Loudonville, NY 12211 (United States)

    2016-10-10

    We present Large Binocular Telescope observations of 109 H ii regions in NGC 5457 (M101) obtained with the Multi-Object Double Spectrograph. We have robust measurements of one or more temperature-sensitive auroral emission lines for 74 H ii regions, permitting the measurement of “direct” gas-phase abundances. Comparing the temperatures derived from the different ionic species, we find: (1) strong correlations of T [N ii] with T [S iii] and T [O iii], consistent with little or no intrinsic scatter; (2) a correlation of T [S iii] with T [O iii], but with significant intrinsic dispersion; (3) overall agreement between T [N ii], T [S ii], and T [O ii], as expected, but with significant outliers; (4) the correlations of T [N ii] with T [S iii] and T [O iii] match the predictions of photoionization modeling while the correlation of T [S iii] with T [O iii] is offset from the prediction of photoionization modeling. Based on these observations, which include significantly more observations of lower excitation H ii regions, missing in many analyses, we inspect the commonly used ionization correction factors (ICFs) for unobserved ionic species and propose new empirical ICFs for S and Ar. We have discovered an unexpected population of H ii regions with a significant offset to low values in Ne/O, which defies explanation. We derive radial gradients in O/H and N/O which agree with previous studies. Our large observational database allows us to examine the dispersion in abundances, and we find intrinsic dispersions of 0.074 ± 0.009 in O/H and 0.095 ± 0.009 in N/O (at a given radius). We stress that this measurement of the intrinsic dispersion comes exclusively from direct abundance measurements of H ii regions in NGC 5457.

  13. The properties of gas-phase multiply charged ions

    International Nuclear Information System (INIS)

    Newson, K.A.

    1999-01-01

    This thesis presents the results of a series of experiments investigating the reactivity of gas-phase molecular dications with various neutral collision partners, at collision energies between 3 and 13 eV in the laboratory frame, using a crossed-beam apparatus. The experiment involves the measurement of product ion intensities, which are determined by means of time-of-flight mass spectrometry. The experimental apparatus and methodology, together with the areas of theory important to ion chemistry, are described in the thesis. The product ions of greatest interest are those ions formed by bond-forming (chemical) reactivity. The relative intensities of such product ions, and those ions formed as a result of electron-transfer reactions, are, when recorded as a function of the collision energy, a powerful probe of the reaction mechanism. Additionally, where appropriate, the reactions are examined for isotope effects by using the isotopic analogue of the neutral collision partner. The results of the experiments indicate that no intermolecular isotope effects are present in the reactions of CF 2 2+ and CF 3 2+ with H 2 and D 2 neutral targets. In addition, the observed collision energy dependence is symptomatic of the absence of a barrier to reaction. These observations suggest that the reactions proceed via an impulsive direct reaction mechanism. Such a conclusion casts doubt on the applicability of the Landau-Zener model of H - /D - transfer reactivity. Other results presented in this thesis include the first reported observation of a bond-forming reaction between a molecular dication (CF2 2+ ) and a polyatomic neutral species (NH 3 ). Finally, the branching ratio of the products of bond-forming reactions between CF 2 2+ with HD indicates the operation of a strong intramolecular isotope effect, favouring the formation of the deuterated product. This observation points to a reaction mechanism in which the bond-formation is preceded by electron-transfer. (author)

  14. Dissociative electron attachment to the gas-phase nucleobase hypoxanthine

    Energy Technology Data Exchange (ETDEWEB)

    Dawley, M. Michele [Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Tanzer, Katrin; Denifl, Stephan, E-mail: Stephan.Denifl@uibk.ac.at, E-mail: Sylwia.Ptasinska.1@nd.edu [Institut für Ionenphysik und Angewandte Physik, and Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Technikerstr. 25, A-6020 Innsbruck (Austria); Carmichael, Ian [Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Ptasińska, Sylwia, E-mail: Stephan.Denifl@uibk.ac.at, E-mail: Sylwia.Ptasinska.1@nd.edu [Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556 (United States)

    2015-06-07

    We present high-resolution measurements of the dissociative electron attachment (DEA) to isolated gas-phase hypoxanthine (C{sub 5}H{sub 4}N{sub 4}O, Hyp), a tRNA purine base. The anion mass spectra and individual ion efficiency curves from Hyp were measured as a function of electron energy below 9 eV. The mass spectra at 1 and 6 eV exhibit the highest anion yields, indicating possible common precursor ions that decay into the detectable anionic fragments. The (Hyp − H) anion (C{sub 5}H{sub 3}N{sub 4}O{sup −}) exhibits a sharp resonant peak at 1 eV, which we tentatively assign to a dipole-bound state of the keto-N1H,N9H tautomer in which dehydrogenation occurs at either the N1 or N9 position based upon our quantum chemical computations (B3LYP/6-311+G(d,p) and U(MP2-aug-cc-pVDZ+)) and prior studies with adenine. This closed-shell dehydrogenated anion is the dominant fragment formed upon electron attachment, as with other nucleobases. Seven other anions were also observed including (Hyp − NH){sup −}, C{sub 4}H{sub 3}N{sub 4}{sup −}/C{sub 4}HN{sub 3}O{sup −}, C{sub 4}H{sub 2}N{sub 3}{sup −}, C{sub 3}NO{sup −}/HC(HCN)CN{sup −}, OCN{sup −}, CN{sup −}, and O{sup −}. Most of these anions exhibit broad but weak resonances between 4 and 8 eV similar to many analogous anions from adenine. The DEA to Hyp involves significant fragmentation, which is relevant to understanding radiation damage of biomolecules.

  15. Uptake of Organic Gas Phase Species by 1-Methylnaphthalene

    Science.gov (United States)

    Zhang, H.; Xia, J.; Davidovits, P.; Jayne, J. T.; Kolb, C. E.; Worsnop, D. R.

    2002-12-01

    Using a droplet train apparatus, the mass accommodation coefficients (α) on 1-methylnapthalene of gas phase m-xylene, ethylbenzene, butylbenzene, α-pinene, γ-terpinene, and 2-methyl-2-hexanol were measured as a function of temperature (265 K to 296 K). 1-methylnapthalene was selected as a surrogate for hydrophobic and aromatic hydrocarbons found in tropospheric aerosols. The mass accommodation coefficients (α) of all the molecules obtained from these measurements exhibit negative temperature dependence. The upper and lower values of α at 265 K and 296 K respectively are: for m-xylene 0.44 and 0.26; for ethylbenzene 0.37 and 0.22; for butylbenzene 0.47 and 0.31; for α-pinene 0.47 and 0.096; for γ-terpinene 0.39 and 0.12; for 2-methyl-2-hexanol 0.44 and 0.26. The uptake measurements also yielded values for the product HDl1/2 for most of the molecules studied (H = Henry's law constant, Dl = liquid phase diffusion coefficient). Using calculated values of Dl the Henry's law constant is obtained, and expressed in the form ln H (M/atm) = -A + B/T. The A and B values for the molecules studied are listed in Table 1. Table 1: A and B values for the Henry's law constant H expressed as ln H (M/atm) = -A + B/T \\ m-xylene: A=7.20, B=4060\\ethylbenzene: A=5.81, B=3660\\butylbenzene: A=16.95, B=7330α-pinene: A=15.69, B=6360\\2-methyl-2-hexanol: A=9.95, B=4760

  16. Kinetics of the gas-phase tritium oxidation reaction

    International Nuclear Information System (INIS)

    Failor, R.A.

    1989-01-01

    Homogeneous gas-phase kinetics of tritium oxidation (2T 2 + O 2 →2T 2 O) have been studied with a model that accounts explicitly for radiolysis of the major species and the kinetics of the subsequent reactions of ionic, excited-state, and neutral species. Results from model calculations are given for 10 -4 -1.0 mol% T 2 in O 2 (298 K, 1 atm). As the reaction evolves three different mechanisms control T 2 O production, each with a different overall rate expression and a different order with respect to the T 2 concentration. The effects of self-radiolysis of pure T 2 on the tritium oxidation reaction were calculated. Tritium atoms, the primary product of T 2 self-radiolysis, altered the oxidation mechanism only during the first few seconds following the initiation of the T 2 -O 2 reaction. Ozone, an important intermediate in T 2 oxidation, was monitored in-situ by U.V. absorption spectroscopy for 0.01-1.0 mol% T 2 an 1 atm O 2 . The shape of the experimental ozone time profile agreed with the model predictions. As predicted, the measured initial rate of ozone production varied linearly with initial T 2 concentration ([T 2 ] 0.6 o ), but at an initial rate one-third the predicted value. The steady-state ozone concentration ([O 3 ]ss) was predicted to be dependent on [T 2 ] 0.3 o , but the measured value was [T 2 ] 0.6 o , resulting in four times higher [O 3 ]ss than predicted for a 1.0% T 2 -O 2 mixture. Adding H 2 to the T 2 -O 2 mixture, to provide insight into the differences between the radiolytic and chemical behavior of the tritium, produced a greater decrease in [O 3 ]ss than predicted. Adjusting the reaction cell surface-to-volume ratio showed implications of minor surface removal of ozone

  17. Dissociative attachment reactions of electrons with gas phase superacids

    International Nuclear Information System (INIS)

    Liu, X.

    1992-01-01

    Using the flowing afterglow Langmuir probe (FALP) technique, dissociative attachment coefficients β for reactions of electrons with gas phase superacids HCo(PF 3 ) 4 , HRh(PF 3 ) 4 and carbonyl hydride complexes HMn(CO) 5 , HRe(CO) 5 have been determined under thermal conditions over the approximate temperature range 300∼550 K. The superacids react relatively slowly ( max ) with free electrons in a thermal plasma, and the values of β obtained this far do not show a correlation between acidity and β. The pioneer researchers in this field had speculated that any superacid would be a rapid attacher of electrons; it was found that this speculation is not true in general. The product distribution of electron attachment reaction to HCo(PF 3 ) 4 was found to be independent of temperature even though the β[HCo(PF 3 ) 4 ] increases with temperature. This proposes that the electron attachment process occurs well before the excited complex dissociates. In addition, the activation energy of HCo(PF 3 ) 4 for electron attachment has been derived from the Arrhenius plots. The carbonyl hydride complexes, HMn(CO) 5 and HRe(CO) 5 , react relatively rapidly (>1/4 of β max ) with free electrons in thermal plasma. This indicates that these reactions cannot be significantly endothermic. Observation of rapid attachment for these non-superacids shows that the Mn-CO and Re-CO bonds are weaker than the Mn-H and Re-H bonds, respectively. Comparisons between the carbonyl and trifluorophosphine cases implies that fast electron capture is related more to the CO ligand than to the transition-metal species

  18. Gas-Phase Combustion Synthesis of Aluminum Nitride Powder

    Science.gov (United States)

    Axelbaum, R. L.; Lottes, C. R.; Huertas, J. I.; Rosen, L. J.

    1996-01-01

    Due to its combined properties of high electrical resistivity and high thermal conductivity aluminum nitride (AlN) is a highly desirable material for electronics applications. Methods are being sought for synthesis of unagglomerated, nanometer-sized powders of this material, prepared in such a way that they can be consolidated into solid compacts having minimal oxygen content. A procedure for synthesizing these powders through gas-phase combustion is described. This novel approach involves reacting AlCl3, NH3, and Na vapors. Equilibrium thermodynamic calculations show that 100% yields can be obtained for these reactants with the products being AlN, NaCl, and H2. The NaCl by-product is used to coat the AlN particles in situ. The coating allows for control of AlN agglomeration and protects the powders from hydrolysis during post-flame handling. On the basis of thermodynamic and kinetic considerations, two different approaches were employed to produce the powder, in co-flow diffusion flame configurations. In the first approach, the three reactants were supplied in separate streams. In the second, the AlCl3 and NH3 were premixed with HCl and then reacted with Na vapor. X-ray diffraction (XRD) spectra of as-produced powders show only NaCl for the first case and NaCl and AlN for the second. After annealing at 775 C tinder dynamic vacuum, the salt was removed and XRD spectra of powders from both approaches show only AlN. Aluminum metal was also produced in the co-flow flame by reacting AlCl3 with Na. XRD spectra of as-produced powders show the products to be only NaCl and elemental aluminum.

  19. Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

    Science.gov (United States)

    Li, Tao; Li, Qian-Zhong

    2012-11-07

    RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

  20. Gas Phase Thz Spectroscopy of Organosulfide and Organophosphorous Compounds Using a Synchrotron Source

    Science.gov (United States)

    Cuisset, Arnaud; Smirnova, Irina; Bocquet, Robin; Hindle, Francis; Mouret, Gael; Sadovskii, Dmitrii A.; Pirali, Olivier; Roy, Pascale

    2011-06-01

    This study concerns the gas phase rovibrational spectroscopy of organosulfide and organophosphorous which are considered as non toxic model compounds in the analysis of chemical weapon materials, high pathogenic and mutagenic agents, and other environmentally interesting air-borne species. The coupling of the synchrotron radiation with multipass cells and the FTIR spectrometer allowed to obtain very conclusive results in term of sensitivity and resolution and improved the previous results obtained with classical sources. For DMSO, using an optical path of 150 m the spectra have been recorded at the ultimate resolution of 0.001 Cm-1 allowing to fully resolve the rotational structure of the lowest vibrational modes observed in the THz region. In the 290 - 420 Cm-1 region, the rovibrational spectrum of the "perpendicular" and "parallel" vibrational bands associated with, respectively, the asymmetric ν23 and symmetric ν11 bending modes of DMSO have been recorded with a resolution of 1.5× 10-3 Cm-1. The gas phase vibrational spectra of organophosphorous compounds were measured by FTIR spectroscopy using the vapor pressure of the compounds. Except for TBP, the room temperature vapor pressure was sufficient to detect all active vibrational modes from THz to NIR domain. Contrary to DMSO, the rotational patterns of alkyl phosphates and alkyl phosphonates could not be resolved; only a vibrational analysis may be performed. Nevertheless, the spectral fingerprints observed in the THz region allowed a clear discrimination between the molecules and between the different molecular conformations. A. Cuisset, G. Mouret, O. Pirali, P. Roy, F. Cazier, H. Nouali, J. Demaison, J. Phys. Chem. B, 2008, 112:, 12516-12525 A. Cuisset, L. Nanobashvili, I. Smirnova, R. Bocquet, F. Hindle, G. Mouret, O. Pirali, P. Roy and D. A. Sadovskií, Chem. Phys. Lett., 2010, 492: 30-34 I. Smirnova, A. Cuisset, R. Bocquet, F. Hindle, G. Mouret, O. Pirali, P. Roy, J. Phys. Chem. B, 2010, 114: 16936-16947.

  1. Molecular simulation of excess isotherm and excess enthalpy change in gas-phase adsorption.

    Science.gov (United States)

    Do, D D; Do, H D; Nicholson, D

    2009-01-29

    We present a new approach to calculating excess isotherm and differential enthalpy of adsorption on surfaces or in confined spaces by the Monte Carlo molecular simulation method. The approach is very general and, most importantly, is unambiguous in its application to any configuration of solid structure (crystalline, graphite layer or disordered porous glass), to any type of fluid (simple or complex molecule), and to any operating conditions (subcritical or supercritical). The behavior of the adsorbed phase is studied using the partial molar energy of the simulation box. However, to characterize adsorption for comparison with experimental data, the isotherm is best described by the excess amount, and the enthalpy of adsorption is defined as the change in the total enthalpy of the simulation box with the change in the excess amount, keeping the total number (gas + adsorbed phases) constant. The excess quantities (capacity and energy) require a choice of a reference gaseous phase, which is defined as the adsorptive gas phase occupying the accessible volume and having a density equal to the bulk gas density. The accessible volume is defined as the mean volume space accessible to the center of mass of the adsorbate under consideration. With this choice, the excess isotherm passes through a maximum but always remains positive. This is in stark contrast to the literature where helium void volume is used (which is always greater than the accessible volume) and the resulting excess can be negative. Our definition of enthalpy change is equivalent to the difference between the partial molar enthalpy of the gas phase and the partial molar enthalpy of the adsorbed phase. There is no need to assume ideal gas or negligible molar volume of the adsorbed phase as is traditionally done in the literature. We illustrate this new approach with adsorption of argon, nitrogen, and carbon dioxide under subcritical and supercritical conditions.

  2. Gas phase enthalpies of formation of nitrobenzamides using combustion calorimetry and thermal analysis

    International Nuclear Information System (INIS)

    Ximello, Arturo; Flores, Henoc; Rojas, Aarón; Adriana Camarillo, E.; Patricia Amador, M.

    2014-01-01

    Graphical abstract: - Highlights: • Formation enthalpies of the nitrobenzamides were derived from combustion calorimetry. • Enthalpies of vaporisation and sublimation were calculated by thermogravimetry. • From gas phase enthalpies of formation the stability of the isomers is studied. • Stability of isomers is not driven by a steric hindrance between functional groups. - Abstract: The standard molar energies of combustion of 2-nitrobenzamide, 3-nitrobenzamide and 4-nitrobenzamide were determined with an isoperibolic, static-bomb, combustion calorimeter. From the combustion results, the standard molar enthalpies of combustion and formation for these compounds in the condensed phase at T = 298.15 K were derived. Subsequently, to determine the enthalpies of sublimation, the vapour pressure data as a function of the temperature for the compounds under investigation were estimated using thermogravimetry by applying Langmuir’s equation, and the enthalpies of vaporisation were derived. Standard enthalpies of fusion were measured by differential scanning calorimetry then added to those of vaporisation to obtain reliable results for the enthalpy of sublimation. From the combustion and sublimation data, the gas phase enthalpies of formation were determined to be (−138.9 ± 3.5) kJ · mol −1 , (−122.9 ± 2.9) kJ · mol −1 and (−108.5 ± 3.7) kJ · mol −1 for the ortho, meta and para isomers of nitrobenzamide, respectively. The meaning of these results with regard to the enthalpic stability of these molecular structures is discussed herein

  3. Classification of proteins: available structural space for molecular modeling.

    Science.gov (United States)

    Andreeva, Antonina

    2012-01-01

    The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim to group proteins based on their structural relationships. Some of these classification schemes explore the concept of structural neighbourhood (structural continuum), whereas other utilize the notion of protein evolution and thus provide a discrete rather than continuum view of protein structure space. This chapter presents a strategy for classification of proteins with known three-dimensional structure. Steps in the classification process along with basic definitions are introduced. Examples illustrating some fundamental concepts of protein folding and evolution with a special focus on the exceptions to them are presented.

  4. Protein crystal structure analysis using synchrotron radiation at atomic resolution

    International Nuclear Information System (INIS)

    Nonaka, Takamasa

    1999-01-01

    We can now obtain a detailed picture of protein, allowing the identification of individual atoms, by interpreting the diffraction of X-rays from a protein crystal at atomic resolution, 1.2 A or better. As of this writing, about 45 unique protein structures beyond 1.2 A resolution have been deposited in the Protein Data Bank. This review provides a simplified overview of how protein crystallographers use such diffraction data to solve, refine, and validate protein structures. (author)

  5. Predicting Protein Secondary Structure with Markov Models

    DEFF Research Database (Denmark)

    Fischer, Paul; Larsen, Simon; Thomsen, Claus

    2004-01-01

    we are considering here, is to predict the secondary structure from the primary one. To this end we train a Markov model on training data and then use it to classify parts of unknown protein sequences as sheets, helices or coils. We show how to exploit the directional information contained...... in the Markov model for this task. Classifications that are purely based on statistical models might not always be biologically meaningful. We present combinatorial methods to incorporate biological background knowledge to enhance the prediction performance....

  6. GIS: a comprehensive source for protein structure similarities.

    Science.gov (United States)

    Guerler, Aysam; Knapp, Ernst-Walter

    2010-07-01

    A web service for analysis of protein structures that are sequentially or non-sequentially similar was generated. Recently, the non-sequential structure alignment algorithm GANGSTA+ was introduced. GANGSTA+ can detect non-sequential structural analogs for proteins stated to possess novel folds. Since GANGSTA+ ignores the polypeptide chain connectivity of secondary structure elements (i.e. alpha-helices and beta-strands), it is able to detect structural similarities also between proteins whose sequences were reshuffled during evolution. GANGSTA+ was applied in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), which consists of >10,000 protein domains yielding about 55 x 10(6) possible protein structure alignments. Here, we provide the resulting protein structure alignments as a public web-based service, named GANGSTA+ Internet Services (GIS). We also allow to browse the ASTRAL40 database of protein structures with GANGSTA+ relative to an externally given protein structure using different constraints to select specific results. GIS allows us to analyze protein structure families according to the SCOP classification scheme. Additionally, users can upload their own protein structures for pairwise protein structure comparison, alignment against all protein structures of the ASTRAL40 database (SCOP version 1.75) or symmetry analysis. GIS is publicly available at http://agknapp.chemie.fu-berlin.de/gplus.

  7. Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

    Science.gov (United States)

    Bordoli, Lorenza; Schwede, Torsten

    2012-01-01

    Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of applications. Since the usefulness of a model for specific application is determined by its accuracy, model quality estimation is an essential component of protein structure prediction. Comparative protein modeling has become a routine approach in many areas of life science research since fully automated modeling systems allow also nonexperts to build reliable models. In this chapter, we describe practical approaches for automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

  8. Structure based alignment and clustering of proteins (STRALCP)

    Science.gov (United States)

    Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

    2013-06-18

    Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

  9. Alpha complexes in protein structure prediction

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2015-01-01

    Reducing the computational effort and increasing the accuracy of potential energy functions is of utmost importance in modeling biological systems, for instance in protein structure prediction, docking or design. Evaluating interactions between nonbonded atoms is the bottleneck of such computations......-complexes from scratch for every configuration encountered during the search for the native structure would make this approach hopelessly slow. However, it is argued that kinetic a-complexes can be used to reduce the computational effort of determining the potential energy when "moving" from one configuration...... to a neighboring one. As a consequence, relatively expensive (initial) construction of an a-complex is expected to be compensated by subsequent fast kinetic updates during the search process. Computational results presented in this paper are limited. However, they suggest that the applicability of a...

  10. Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

    Science.gov (United States)

    Finkelstein, A. V.

    1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

  11. Detection methods for atoms and radicals in the gas phase

    Science.gov (United States)

    Hack, W.

    This report lists atoms and free radicals in the gas phase which are of interest for environmental and flame chemistry and have been detected directly. The detection methods which have been used are discussed with respect to their range of application, specificity and sensitivity. In table 1, detection methods for the five atoms of group IV (C, Si, Ge, Sn, Pb) and about 60 radicals containing at least one atom of group IV are summarized (CH, Cd, Cf, CC1, CBr, Cn, Cs, CSe, CH2, CD2, Chf, Cdf, CHC1, CHBr, CF2, CC12, CBr2, CFC1, CFBr, CH3, CD3, CF3, CH2F, CH2C1, CH2Br, CHF2, CHC12, CHBr2, Hco, Fco, CH30, CD30, CH2OH, CH3S, Nco, CH4N, CH302, CF302; C2, C2N, C2H, C20, C2HO, C2H3, C2F3, C2H5, C2HsO, C2H4OH, CH3CO, CD3CO, C2H3O, C2H502, CH3COO2, C2H4N, C2H6N, C3; Si, SiF, SiF2, SiO, SiC, Si2; Ge, GeC, GeO, GeF, GeF2, GeCl2, Sn, SnF, SnO, SnF2, Pb, PbF, PbF2, PbO, PbS). In table 2 detection methods for about 25 other atoms and 60 radicals are listed: (H, D, O, O2, Oh, Od, HO2, DO2, F, Ci, Br, I, Fo, Cio, BrO, Io, FO2, C1O2, Li, Na, K, Rb, Cs, N, N3, Nh, Nd, Nf, Nci, NBr, NH2, ND2, Nhd, Nhf, NF2, NC12, N2H3, No, NO2, NO3, Hno, Dno, P, Ph, Pd, Pf, Pci, PH2, PD2, PF2, Po, As, AsO, AsS, Sb, Bi, S, S2, Sh, Sd, Sf, SF2, So, Hso, Dso, Sn, Se, Te, Se2, SeH, SeD, SeF, SeO, SeS, SeN, TeH, TeO, Bh, BH2, Bo, Bn, B02, Cd, Hg, UF5). The tables also cite some recent kinetic applications of the various methods.

  12. Electron-beam synthesis of fuel in the gas phase

    International Nuclear Information System (INIS)

    Ponomarev, A.V.; Holodkova, E.M.; Ershov, B.G.

    2011-01-01

    Complete text of publication follows. Tendencies of world development focus attention on a vegetative biomass as on the major raw resource for future chemistry and a fuel industry. The significant potential for perfection of biomass conversion processes is concentrated in the field of radiation-chemical methods. Both the mode of post-radiation distillation and mode of electron-beam distillation of biomass have been investigated as well as the mode of gas-phase synthesis of liquid engine fuel from of biomass distillation products. Synergistic action of radiation and temperature has been analyzed at use of the accelerated electron beams allowing to combine radiolysis with effective radiation heating of a material without use of additional heaters. At dose rate above 1 kGy/s the electron-beam irradiation results in intensive decomposition of a biomass and evaporation of formed fragments with obtaining of a liquid condensate (∼ 60 wt%), CO 2 and Co gases (13-18 wt%) and charcoal in the residue. Biomass distillation at radiation heating allows to increase almost three times an organic liquid yield in comparison with pyrolysis. The majority of liquid products from cellulose is represented by the furan derivatives considered among the very perspective components for alternative engine fuels. Distilled-off gases and vapors are diluted with gaseous C 1 -C 5 alkanes and again are exposed to an irradiation to produce liquid fuel from a biomass. This transformation is based on a method of electron-beam circulation conversion of gaseous C 1 -C 5 alkanes (Ponomarev, A.V., Radiat. Phys. Chem., 78, 48, 2009) which consists in formation and removal of liquid products with high degree of carbon skeleton branching. The isomers ratio in a liquid may be controlled by means of change of an irradiation condition and initial gas composition. The irradiation of gaseous alkanes together with vaporous products of biomass destruction allows to synthesize the fuel enriched by conventional

  13. Importance of the gas phase role to the prediction of energetic material behavior: An experimental study

    International Nuclear Information System (INIS)

    Ali, A.N.; Son, S.F.; Asay, B.W.; Sander, R.K.

    2005-01-01

    Various thermal (radiative, conductive, and convective) initiation experiments are performed to demonstrate the importance of the gas phase role in combustion modeling of energetic materials (EM). A previously published condensed phase model that includes a predicted critical irradiance above which ignition is not possible is compared to experimental laser ignition results for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 2,4,6-trinitrotoluene (TNT). Experimental results conflict with the predicted critical irradiance concept. The failure of the model is believed to result from a misconception about the role of the gas phase in the ignition process of energetic materials. The model assumes that ignition occurs at the surface and that evolution of gases inhibits ignition. High speed video of laser ignition, oven cook-off and hot wire ignition experiments captures the ignition of HMX and TNT in the gas phase. A laser ignition gap test is performed to further evaluate the effect of gas phase laser absorption and gas phase disruption on the ignition process. Results indicate that gas phase absorption of the laser energy is probably not the primary factor governing the gas phase ignition observations. It is discovered that a critical gap between an HMX pellet and a salt window of 6 mm±0.4 mm exists below which ignition by CO 2 laser is not possible at the tested irradiances of 29 W/cm 2 and 38 W/cm 2 for HMX ignition. These observations demonstrate that a significant disruption of the gas phase, in certain scenarios, will inhibit ignition, independent of any condensed phase processes. These results underscore the importance of gas phase processes and illustrate that conditions can exist where simple condensed phase models are inadequate to accurately predict the behavior of energetic materials

  14. Importance of the gas phase role to the prediction of energetic material behavior: An experimental study

    Science.gov (United States)

    Ali, A. N.; Son, S. F.; Asay, B. W.; Sander, R. K.

    2005-03-01

    Various thermal (radiative, conductive, and convective) initiation experiments are performed to demonstrate the importance of the gas phase role in combustion modeling of energetic materials (EM). A previously published condensed phase model that includes a predicted critical irradiance above which ignition is not possible is compared to experimental laser ignition results for octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 2,4,6-trinitrotoluene (TNT). Experimental results conflict with the predicted critical irradiance concept. The failure of the model is believed to result from a misconception about the role of the gas phase in the ignition process of energetic materials. The model assumes that ignition occurs at the surface and that evolution of gases inhibits ignition. High speed video of laser ignition, oven cook-off and hot wire ignition experiments captures the ignition of HMX and TNT in the gas phase. A laser ignition gap test is performed to further evaluate the effect of gas phase laser absorption and gas phase disruption on the ignition process. Results indicate that gas phase absorption of the laser energy is probably not the primary factor governing the gas phase ignition observations. It is discovered that a critical gap between an HMX pellet and a salt window of 6mm±0.4mm exists below which ignition by CO2 laser is not possible at the tested irradiances of 29W /cm2 and 38W/cm2 for HMX ignition. These observations demonstrate that a significant disruption of the gas phase, in certain scenarios, will inhibit ignition, independent of any condensed phase processes. These results underscore the importance of gas phase processes and illustrate that conditions can exist where simple condensed phase models are inadequate to accurately predict the behavior of energetic materials.

  15. Exceptionally High Proton and Lithium Cation Gas-Phase Basicity of the Anti-Diabetic Drug Metformin.

    Science.gov (United States)

    Raczyńska, Ewa D; Gal, Jean-François; Maria, Pierre-Charles; Michalec, Piotr; Zalewski, Marcin

    2017-11-16

    Substituted biguanides are known for their biological effect, and a few of them are used as drugs, the most prominent example being metformin (1,1-dimethylbiguanide, IUPAC name: N,N-dimethylimidodicarbonimidic diamide). Because of the presence of hydrogen atoms at the amino groups, biguanides exhibit a multiple tautomerism. This aspect of their structures was examined in detail for unsubstituted biguanide and metformin in the gas phase. At the density functional theory (DFT) level {essentially B3LYP/6-311+G(d,p)}, the most stable structures correspond to the conjugated, push-pull, system (NR 2 )(NH 2 )C═N-C(═NH)NH 2 (R = H, CH 3 ), further stabilized by an internal hydrogen bond. The structural and energetic aspects of protonation and lithium cation adduct formation of biguanide and metformin was examined at the same level of theory. The gas-phase protonation energetics reveal that the more stable tautomer is protonated at the terminal imino C═NH site, still with an internal hydrogen bond maintaining the structure of the neutral system. The calculated proton affinity and gas-phase basicity of the two molecules reach the domain of superbasicity. By contrast, the lithium cation prefers to bind the less stable, not fully conjugated, tautomer (NR 2 )C(═NH)-NH-C(═NH)NH 2 of biguanides, in which the two C═NH groups are separated by NH. This less stable form of biguanides binds Li + as a bidentate ligand, in agreement with what was reported in the literature for other metal cations in the solid phase. The quantitative assessment of resonance in biguanide, in metformin and in their protonated forms, using the HOMED and HOMA indices, reveals an increase in electron delocalization upon protonation. On the contrary, the most stable lithium cation adducts are less conjugated than the stable neutral biguanides, because the metal cation is better coordinated by the not-fully conjugated bidentate tautomer.

  16. Structural determination of intact proteins using mass spectrometry

    Science.gov (United States)

    Kruppa, Gary [San Francisco, CA; Schoeniger, Joseph S [Oakland, CA; Young, Malin M [Livermore, CA

    2008-05-06

    The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.

  17. Gas-phase nitrosation of ethylene and related events in the C2H4NO+ landscape.

    Science.gov (United States)

    Gerbaux, Pascal; Dechamps, Noemie; Flammang, Robert; Nam, Pham Cam; Nguyen, Minh Tho; Djazi, Fayçal; Berruyer, Florence; Bouchoux, Guy

    2008-06-19

    The C2H4NO(+) system has been examined by means of quantum chemical calculations using the G2 and G3B3 approaches and tandem mass spectrometry experiments. Theoretical investigation of the C2H4NO(+) potential-energy surface includes 19 stable C2H4NO(+) structures and a large set of their possible interconnections. These computations provide insights for the understanding of the (i) addition of the nitrosonium cation NO(+) to the ethylene molecule, (ii) skeletal rearrangements evidenced in previous experimental studies on comparable systems, and (iii) experimental identification of new C2H4NO(+) structures. It is predicted from computation that gas-phase nitrosation of ethylene may produce C2H4(*)NO(+) adducts, the most stable structure of which is a pi-complex, 1, stabilized by ca. 65 kJ/mol with respect to its separated components. This complex was produced in the gas phase by a transnitrosation process involving as reactant a complex between water and NO(+) (H2O.NO(+)) and the ethylene molecule and fully characterized by collisional experiments. Among the other C 2H 4NO (+) structures predicted by theory to be protected against dissociation or isomerization by significant energy barriers, five were also experimentally identified. These finding include structures CH3CHNO(+) (5), CH 3CNOH (+) ( 8), CH3NHCO(+) (18), CH3NCOH(+) (19), and an ion/neutral complex CH2O...HCNH(+) (12).

  18. Infrared spectroscopy of gas-phase clusters using a free-electron laser

    International Nuclear Information System (INIS)

    Heijnsbergen, D. van; Helden, G. von; Meijer, G.

    2002-01-01

    Most clusters produced in the gas phase, especially those containing metals, remain largely uncharaterized, among these are transition metal - carbide, -oxide and -nitride clusters. A method for recording IR spectra of strongly bound gas-phase clusters is presented. It is based on a free-electron laser called Felix, characterized by wide wavelength tuning range, covering almost the full 'molecular finger print' region, high power and fluence which make it suited to excite gas-phase species i.e. gas -phase clusters. Neutral clusters were generated by laser vaporization technique, ions that were created after the interaction with the free-electron laser were analyzed in a flight mass spectrometer. Experiments were run with titanium carbide clusters and their IR spectra given. It was shown that this method is suited to strongly bound clusters with low ionization energies, a condition met for many pure metal clusters and metal compound clusters. (nevyjel)

  19. Gas-phase water-mediated equilibrium between methylglyoxal and its geminal diol

    Science.gov (United States)

    Axson, Jessica L.; Takahashi, Kaito; De Haan, David O.; Vaida, Veronica

    2010-01-01

    In aqueous solution, aldehydes, and to a lesser extent ketones, hydrate to form geminal diols. We investigate the hydration of methylglyoxal (MG) in the gas phase, a process not previously considered to occur in water-restricted environments. In this study, we spectroscopically identified methylglyoxal diol (MGD) and obtained the gas-phase partial pressures of MG and MGD. These results, in conjunction with the relative humidity, were used to obtain the equilibrium constant, KP, for the water-mediated hydration of MG in the gas phase. The Gibbs free energy for this process, ΔG°, obtained as a result, suggests a larger than expected gas-phase diol concentration. This may have significant implications for understanding the role of organics in atmospheric chemistry. PMID:20142510

  20. Protein structure similarity from principle component correlation analysis

    Directory of Open Access Journals (Sweden)

    Chou James

    2006-01-01

    Full Text Available Abstract Background Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. Results We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. Conclusion The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum

  1. Gas phase ion/molecule reactions as studied by Fourier Transform Ion Cyclotron Resonance mass spectrometry

    International Nuclear Information System (INIS)

    Joergensen, S.I.

    1985-01-01

    The subject of this thesis is gas phase ion/molecule reactions as studied by Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry (chapter 2 contains a short description of this method). Three chapters are mainly concerned with mechanistic aspects of gas phase ion/molecule reactions. An equally important aspect of the thesis is the stability and reactivity of α-thio carbanions, dipole stabilized carbanions and homoenolate anions, dealt with in the other four chapters. (Auth.)

  2. An atmospheric pressure flow reactor: Gas phase kinetics and mechanism in tropospheric conditions without wall effects

    Science.gov (United States)

    Koontz, Steven L.; Davis, Dennis D.; Hansen, Merrill

    1988-01-01

    A new type of gas phase flow reactor, designed to permit the study of gas phase reactions near 1 atm of pressure, is described. A general solution to the flow/diffusion/reaction equations describing reactor performance under pseudo-first-order kinetic conditions is presented along with a discussion of critical reactor parameters and reactor limitations. The results of numerical simulations of the reactions of ozone with monomethylhydrazine and hydrazine are discussed, and performance data from a prototype flow reactor are presented.

  3. Ultrafast electronic relaxation of excited state vitamin B12 in the gas phase

    International Nuclear Information System (INIS)

    Shafizadeh, Niloufar; Poisson, Lionel; Soep, Benoit

    2008-01-01

    The time evolution of electronically excited vitamin B 12 (cyanocobalamin) has been observed for the first time in the gas phase. It reveals an ultrafast decay to a state corresponding to metal excitation. This decay is interpreted as resulting from a ring to metal electron transfer. This opens the observation of the excited state of other complex biomimetic systems in the gas phase, the key to the characterisation of their complex evolution through excited electronic states

  4. Wigner Distribution Functions as a Tool for Studying Gas Phase Alkali Metal Plus Noble Gas Collisions

    Science.gov (United States)

    2014-03-27

    WIGNER DISTRIBUTION FUNCTIONS AS A TOOL FOR STUDYING GAS PHASE ALKALI METAL PLUS NOBLE GAS COLLISIONS THESIS Keith A. Wyman, Second Lieutenant, USAF...the U.S. Government and is not subject to copyright protection in the United States. AFIT-ENP-14-M-39 WIGNER DISTRIBUTION FUNCTIONS AS A TOOL FOR...APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED AFIT-ENP-14-M-39 WIGNER DISTRIBUTION FUNCTIONS AS A TOOL FOR STUDYING GAS PHASE ALKALI METAL PLUS

  5. A new method for determining gas phase heat of formation of aromatic energetic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Keshavarz, Mohammad H. [Department of Chemistry, Malek-ashtar University of Technology, Shahin-shahr P. O. Box 83145/115 (Iran); Tehrani, Masoud K. [Department of Physics, Malek-ashtar University of Technology, Shahin-shahr P. O. Box 83145/115 (Iran)

    2007-04-15

    A new correlation is introduced for desk calculation of gas phase heat of formation of aromatic energetic compounds that contain the elements of carbon, hydrogen, nitrogen and oxygen. Predicted gas phase heats of formation for 26 energetic compounds have a root mean square of deviation from experiment of 20.67 kJ/mol, which is in good agreement with respect to measured values of oxygen-lean and oxygen-rich aromatic energetic compounds. (Abstract Copyright [2007], Wiley Periodicals, Inc.)

  6. Nonlinear deterministic structures and the randomness of protein sequences

    CERN Document Server

    Huang Yan Zhao

    2003-01-01

    To clarify the randomness of protein sequences, we make a detailed analysis of a set of typical protein sequences representing each structural classes by using nonlinear prediction method. No deterministic structures are found in these protein sequences and this implies that they behave as random sequences. We also give an explanation to the controversial results obtained in previous investigations.

  7. The structure of a cholesterol-trapping protein

    Science.gov (United States)

    cholesterol-trapping protein Contact: Dan Krotz, dakrotz@lbl.gov Berkeley Lab Science Beat Lab website index Institute researchers determined the three-dimensional structure of a protein that controls cholesterol level in the bloodstream. Knowing the structure of the protein, a cellular receptor that ensnares

  8. STRUCTURAL FEATURES OF PLANT CHITINASES AND CHITIN-BINDING PROTEINS

    NARCIS (Netherlands)

    BEINTEMA, JJ

    1994-01-01

    Structural features of plant chitinases and chitin-binding proteins are discussed. Many of these proteins consist of multiple domains,of which the chitin-binding hevein domain is a predominant one. X-ray and NMR structures of representatives of the major classes of these proteins are available now,

  9. Monoterpene oxidation in an oxidative flow reactor: SOA yields and the relationship between bulk gas-phase properties and organic aerosol growth

    Science.gov (United States)

    Friedman, B.; Link, M.; Farmer, D.

    2016-12-01

    We use an oxidative flow reactor (OFR) to determine the secondary organic aerosol (SOA) yields of five monoterpenes (alpha-pinene, beta-pinene, limonene, sabinene, and terpinolene) at a range of OH exposures. These OH exposures correspond to aging timescales of a few hours to seven days. We further determine how SOA yields of beta-pinene and alpha-pinene vary as a function of seed particle type (organic vs. inorganic) and seed particle mass concentration. We hypothesize that the monoterpene structure largely accounts for the observed variance in SOA yields for the different monoterpenes. We also use high-resolution time-of-flight chemical ionization mass spectrometry to calculate the bulk gas-phase properties (O:C and H:C) of the monoterpene oxidation systems as a function of oxidant concentrations. Bulk gas-phase properties can be compared to the SOA yields to assess the capability of the precursor gas-phase species to inform the SOA yields of each monoterpene oxidation system. We find that the extent of oxygenated precursor gas-phase species corresponds to SOA yield.

  10. Isomers and conformational barriers of gas phase nicotine, nornicotine and their protonated forms

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Tomoki; Farone, William A.; Xantheas, Sotiris S.

    2014-07-17

    We report extensive conformational searches of the neutral nicotine, nornicotine and their protonated analogs that are based on ab-initio second order Møller-Plesset perturbation (MP2) electronic structure calculations. Initial searches were performed with the 6-31G(d,p) and the energetics of the most important structures were further refined from geometry optimizations with the aug-cc-pVTZ basis set. Based on the calculated free energies at T=298 K for the gas phase molecules, neutral nicotine has two dominant trans conformers, whereas neutral nornicotine is a mixture of several conformers. For nicotine, the protonation on both the pyridine and the pyrrolidine sites is energetically competitive, whereas nornicotine prefers protonation on the pyridine nitrogen. The protonated form of nicotine is mainly a mixture of two pyridine-protonated trans conformers and two pyrrolidine-protonated trans conformers, whereas the protonated form of nornicotine is a mixture of four pyridine-protonated trans conformers. Nornicotine is conformationally more flexible than nicotine, however it is less protonated at the biologically important pyrrolidine nitrogen site. The lowest energy isomers for each case were found to interconvert via low (< 6 kcal/mol) rotational barriers around the pyridine-pyrrolidine bond.

  11. Nanoparticles from the Gas Phase as Building Blocks for Electrical Devices

    International Nuclear Information System (INIS)

    Fissan, H.; Kennedy, M.K.; Krinke, T.J.; Kruis, F.E.

    2003-01-01

    Electrical device development is driven by miniaturization and possibilities to use new chemical and physical effects. Nanotechnology offers both aspects. The structural dimensions of materials and devices are small and because of that large exchange surfaces are provided but also effects like quantum effects may occur and be used to get new or at least improved properties of nanostructured materials and devices.Nanoparticles are of special interest because of their nanodimensions in all three directions, so that nanoeffects become most prominent. They can be synthesized in solid materials, in liquids and in gases. Gas synthesis has several advantages compared to the other phases, especially the high cleanliness which can be achieved. In case of electrical devices the particles have to be deposited onto substrates in a structured way.The substrate may consist out of microelectronic devices in which the deposited nanoparticles are introduced for the basic function. In case of a transistor this would be the gate function, in case of a sensor this would be the sensing layer, where the contact with the measurement object takes place. For two kinds of particles SnO 2 and PbS, synthesized in the gas phase, we demonstrate the way how to create devices with improved sensor properties

  12. Resonant x-ray emission from gas-phase TiCl{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Hague, C.F.; Tronc, M. [Universite Pierre et Marie Curie, Paris (France); De Groot, F. [Univ. of Groningen (Netherlands)] [and others

    1997-04-01

    Resonant x-ray emission spectroscopy (RXES) has proved to be a powerful tool for studying the electronic structure of condensed matter. Over the past few years it has been used mainly for studying the valence bands of solids and condensed molecules. Very recently the advent of high brightness photon beams provided by third generation synchrotron radiation source undulators, associated with efficient x-ray emission spectrometers has made it possible to perform experiments on free diatomic molecular systems. RXE spectra of free molecules are of prime importance to gain insight into their electronic structure and bonding as they reflect the symmetry of orbitals engaged in the two-electron, two-step process with the l = 0, {+-}2 parity-conserving selection rule, and are free from solid state effects which can introduce difficulties in the interpretation. They provide information (more so than XAS) on the core excited states, and, when performed at fixed incident photon energy as a function of the emitted photon energy, on the electronic excitation (charge transfer, multiplet states). Moreover the anisotropy of the angular distribution of resonant x-ray emission affects the relative intensity of the emission peaks and provides information concerning the symmetries of final states. This is a preliminary report on what are the first RXE spectra of a 3d transition metal complex in the gas phase. The experiment concerns the Ti 3d {yields}2p emission spectrum of TiCl{sub 4} over the 450 to 470 eV region.

  13. Resonant x-ray emission from gas-phase TiCl4

    International Nuclear Information System (INIS)

    Hague, C.F.; Tronc, M.; De Groot, F.

    1997-01-01

    Resonant x-ray emission spectroscopy (RXES) has proved to be a powerful tool for studying the electronic structure of condensed matter. Over the past few years it has been used mainly for studying the valence bands of solids and condensed molecules. Very recently the advent of high brightness photon beams provided by third generation synchrotron radiation source undulators, associated with efficient x-ray emission spectrometers has made it possible to perform experiments on free diatomic molecular systems. RXE spectra of free molecules are of prime importance to gain insight into their electronic structure and bonding as they reflect the symmetry of orbitals engaged in the two-electron, two-step process with the l = 0, ±2 parity-conserving selection rule, and are free from solid state effects which can introduce difficulties in the interpretation. They provide information (more so than XAS) on the core excited states, and, when performed at fixed incident photon energy as a function of the emitted photon energy, on the electronic excitation (charge transfer, multiplet states). Moreover the anisotropy of the angular distribution of resonant x-ray emission affects the relative intensity of the emission peaks and provides information concerning the symmetries of final states. This is a preliminary report on what are the first RXE spectra of a 3d transition metal complex in the gas phase. The experiment concerns the Ti 3d →2p emission spectrum of TiCl 4 over the 450 to 470 eV region

  14. Soft X-ray photoemission spectroscopy of selected neurotransmitters in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Maris, Assimo; Melandri, Sonia; Evangelisti, Luca; Caminati, Walther [Dipartimento di Chimica ' G. Ciamician' dell' Universita, Via Selmi 2, I-40126 Bologna (Italy); Giuliano, Barbara M. [Departamento de Quimica da Universidade de Coimbra, 3004-535 Coimbra (Portugal); Plekan, Oksana [Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste (Italy); Feyer, Vitaliy [Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste (Italy); Electronic Properties (PGI-6), Peter Gruenberg Institute, Forschungszentrum Juelich GmbH, Leo-Brandt-Strasse, 52428 Juelich (Germany); Richter, Robert [Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste (Italy); Coreno, Marcello [CNR-IMIP, Montelibretti, I-00016 Rome (Italy); Prince, Kevin C., E-mail: kevin.prince@elettra.trieste.it [Sincrotrone Trieste, in Area Science Park, I-34149 Basovizza, Trieste (Italy); CNR-IOM, Laboratorio TASC, I-34149 Basovizza, Trieste (Italy)

    2012-09-15

    Highlights: Black-Right-Pointing-Pointer Neurotransmitter molecules. Black-Right-Pointing-Pointer Photoelectron spectroscopy. Black-Right-Pointing-Pointer Electronic structure. Black-Right-Pointing-Pointer Weak hydrogen bonding. -- Abstract: The valence molecular orbitals and core levels of tyramine, tryptamine and tryptophol in the gas phase have been studied using X-ray photoelectron spectroscopy (XPS) and theoretical methods. The energies of the outer valence region spectrum are found to be in agreement with previously reported He I spectra, while new data on the inner valence molecular orbitals are reported. The structures in the carbon, nitrogen and oxygen core level spectra of these molecules have been identified and assigned. These compounds are characterised by conformers with hydrogen bonding in which the {pi} systems of the phenol and indole groups act as hydrogen acceptors, but a spectroscopic signature of this hydrogen bond was not observed. This is in contrast with our previous spectra of amino acids, where conformers with specific hydrogen bonding showed strong effects in core level spectra. We attribute the difference to the weaker strength of the {pi}-hydrogen bonding.

  15. Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

    Science.gov (United States)

    Kinjo, Akira R; Nakamura, Haruki

    2013-01-01

    Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

  16. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

    KAUST Repository

    Cui, Xuefeng; Lu, Zhiwu; Wang, Sheng; Jing-Yan Wang, Jim; Gao, Xin

    2016-01-01

    Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment

  17. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-01-01

    operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching

  18. K-nearest uphill clustering in the protein structure space

    KAUST Repository

    Cui, Xuefeng

    2016-08-26

    The protein structure classification problem, which is to assign a protein structure to a cluster of similar proteins, is one of the most fundamental problems in the construction and application of the protein structure space. Early manually curated protein structure classifications (e.g., SCOP and CATH) are very successful, but recently suffer the slow updating problem because of the increased throughput of newly solved protein structures. Thus, fully automatic methods to cluster proteins in the protein structure space have been designed and developed. In this study, we observed that the SCOP superfamilies are highly consistent with clustering trees representing hierarchical clustering procedures, but the tree cutting is very challenging and becomes the bottleneck of clustering accuracy. To overcome this challenge, we proposed a novel density-based K-nearest uphill clustering method that effectively eliminates noisy pairwise protein structure similarities and identifies density peaks as cluster centers. Specifically, the density peaks are identified based on K-nearest uphills (i.e., proteins with higher densities) and K-nearest neighbors. To our knowledge, this is the first attempt to apply and develop density-based clustering methods in the protein structure space. Our results show that our density-based clustering method outperforms the state-of-the-art clustering methods previously applied to the problem. Moreover, we observed that computational methods and human experts could produce highly similar clusters at high precision values, while computational methods also suggest to split some large superfamilies into smaller clusters. © 2016 Elsevier B.V.

  19. Use of designed sequences in protein structure recognition.

    Science.gov (United States)

    Kumar, Gayatri; Mudgal, Richa; Srinivasan, Narayanaswamy; Sandhya, Sankaran

    2018-05-09

    Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure. We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation. The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as 'linkers', where natural linkers between distant proteins are unavailable. This article was reviewed by Oliviero Carugo, Christine Orengo and Srikrishna Subramanian.

  20. Moisture effects on greenhouse gases generation in nitrifying gas-phase compost biofilters.

    Science.gov (United States)

    Maia, Guilherme D N; Day, George B; Gates, Richard S; Taraba, Joseph L; Coyne, Mark S

    2012-06-01

    Gas-phase compost biofilters are extensively used in concentrated animal feeding operations to remove odors and, in some cases, ammonia from air sources. The expected biochemical pathway for these predominantly aerobic systems is nitrification. However, non-uniform media with low oxygen levels can shift biofilter microbial pathways to denitrification, a source of greenhouse gases. Several factors contribute to the formation of anoxic/anaerobic zones: media aging, media and particle structure, air velocity distribution, compaction, biofilm thickness, and moisture content (MC) distribution. The present work studies the effects of media moisture conditions on ammonia (NH(3)) removal and greenhouse gas generation (nitrous oxide, N(2)O and methane, CH(4)) for gas-phase compost biofilters subject to a 100-day controlled drying process. Continuous recordings were made for the three gases and water vapor (2.21-h sampling cycle, each cycle consisted of three gas species, and water vapor, for a total of 10,050 data points). Media moisture conditions were classified into three corresponding media drying rate (DR) stages: Constant DR (wetter media), falling DR, and stable-dry system. The first-half of the constant DR period (0-750 h; MC=65-52%, w.b.) facilitated high NH(3) removal rates, but higher N(2)O generation and no CH(4) generation. At the drier stages of the constant DR (750-950 h; MC=52-48%, w.b.) NH(3) removal remained high but N(2)O net generation decreased to near zero. In the falling DR stage (1200-1480 h; MC=44-13%) N(2)O generation decreased, CH(4) increased, and NH(3) was no longer removed. No ammonia removal or greenhouse gas generation was observed in the stable-dry system (1500-2500 h; MC=13%). These results indicate that media should remain toward the drier region of the constant DR (in close proximity to the falling DR stage; MC=50%, approx.), to maintain high levels of NH(3) removal, reduced levels of N(2)O generation, and nullify levels of CH(4

  1. Using an alignment of fragment strings for comparing protein structures

    DEFF Research Database (Denmark)

    Friedberg, Iddo; Harder, Tim; Kolodny, Rachel

    2007-01-01

    . RESULTS: Here we describe the use of a particular structure fragment library, denoted here as KL-strings, for the 1D representation of protein structure. Using KL-strings, we develop an infrastructure for comparing protein structures with a 1D representation. This study focuses on the added value gained...

  2. Rheology and structure of milk protein gels

    NARCIS (Netherlands)

    Vliet, van T.; Lakemond, C.M.M.; Visschers, R.W.

    2004-01-01

    Recent studies on gel formation and rheology of milk gels are reviewed. A distinction is made between gels formed by aggregated casein, gels of `pure` whey proteins and gels in which both casein and whey proteins contribute to their properties. For casein' whey protein mixtures, it has been shown

  3. A hidden markov model derived structural alphabet for proteins.

    Science.gov (United States)

    Camproux, A C; Gautier, R; Tufféry, P

    2004-06-04

    Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1A root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction.

  4. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

  5. Ion Mobility Spectrometry-Mass Spectrometry Coupled with Gas-Phase Hydrogen/Deuterium Exchange for Metabolomics Analyses

    Science.gov (United States)

    Maleki, Hossein; Karanji, Ahmad K.; Majuta, Sandra; Maurer, Megan M.; Valentine, Stephen J.

    2018-02-01

    Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas. The relative HDX reactivity of a wide variety of molecules is discussed in light of the various molecular structures. Additionally, hydrogen accessibility scoring (HAS) and HDX kinetics modeling of candidate ( in silico) ion structures is utilized to estimate the relative ion conformer populations giving rise to specific HDX behavior. These data interpretation methods are discussed with a focus on developing predictive tools for HDX behavior. Finally, an example is provided in which ion mobility information is supplemented with HDX reactivity data to aid identification efforts of compounds in a metabolite extract.

  6. Synthesis of refractory organic matter in the ionized gas phase of the solar nebula.

    Science.gov (United States)

    Kuga, Maïa; Marty, Bernard; Marrocchi, Yves; Tissandier, Laurent

    2015-06-09

    In the nascent solar system, primitive organic matter was a major contributor of volatile elements to planetary bodies, and could have played a key role in the development of the biosphere. However, the origin of primitive organics is poorly understood. Most scenarios advocate cold synthesis in the interstellar medium or in the outer solar system. Here, we report the synthesis of solid organics under ionizing conditions in a plasma setup from gas mixtures (H2(O)-CO-N2-noble gases) reminiscent of the protosolar nebula composition. Ionization of the gas phase was achieved at temperatures up to 1,000 K. Synthesized solid compounds share chemical and structural features with chondritic organics, and noble gases trapped during the experiments reproduce the elemental and isotopic fractionations observed in primitive organics. These results strongly suggest that both the formation of chondritic refractory organics and the trapping of noble gases took place simultaneously in the ionized areas of the protoplanetary disk, via photon- and/or electron-driven reactions and processing. Thus, synthesis of primitive organics might not have required a cold environment and could have occurred anywhere the disk is ionized, including in its warm regions. This scenario also supports N2 photodissociation as the cause of the large nitrogen isotopic range in the solar system.

  7. Gas-phase spectroscopic studies of heavy elements compounds (group V) using FTIR technique

    International Nuclear Information System (INIS)

    Allaf, A. W.; Ajji, Z.

    1998-12-01

    Antimony oxide trihalide, OSbX3 where X=F, CI and Br, and antimony (III) oxychloride, OSbC1 molecules were produced by an on-line process for the first time using antimony chloride SbC13 passed over heated silver oxide then followed by passing the obtained products over heated NaF and heated KBr for SbOF3 and OSbBr3, respectively. The obtained OSbC13 reacts with heated silver to produce OSbC1. The products have been characterized by the infrared spectra of their vapors. The low resolution gas-phase Fourier transform infrared spectrum, reported for the first time, shows the most characteristic band of OSbX3 at 1272, 1217 and 1200 cm -1 and the bands are assigned to the O=Sb stretching fundamental of OSbX3 were X=F, Cl and Br, respectively. The band at 1200 cm -1 needs more experimental investigation. The band at 924 cm -1 is assigned to the O=Sb stretching fundamental of OSbCl molecule. This result is in consistent with expectation and shifted to lower frequency in comparison with arsenic analogous molecule which is investigated by matrix-isolation technique. The work will be continued in order to cover the bismuth and arsenic compounds of similar structures. (author)

  8. An optical spectrum of a large isolated gas-phase PAH cation: C78H26+

    Science.gov (United States)

    Zhen, Junfeng; Mulas, Giacomo; Bonnamy, Anthony; Joblin, Christine

    2016-01-01

    A gas-phase optical spectrum of a large polycyclic aromatic hydrocarbon (PAH) cation - C78H26+- in the 410-610 nm range is presented. This large all-benzenoid PAH should be large enough to be stable with respect to photodissociation in the harsh conditions prevailing in the interstellar medium (ISM). The spectrum is obtained via multi-photon dissociation (MPD) spectroscopy of cationic C78H26 stored in the Fourier Transform Ion Cyclotron Resonance (FT-ICR) cell using the radiation from a mid-band optical parametric oscillator (OPO) laser. The experimental spectrum shows two main absorption peaks at 431 nm and 516 nm, in good agreement with a theoretical spectrum computed via time-dependent density functional theory (TD-DFT). DFT calculations indicate that the equilibrium geometry, with the absolute minimum energy, is of lowered, nonplanar C2 symmetry instead of the more symmetric planar D2h symmetry that is usually the minimum for similar PAHs of smaller size. This kind of slightly broken symmetry could produce some of the fine structure observed in some diffuse interstellar bands (DIBs). It can also favor the folding of C78H26+ fragments and ultimately the formation of fullerenes. This study opens up the possibility to identify the most promising candidates for DIBs amongst large cationic PAHs. PMID:26942230

  9. Gas-phase spectroscopy of synephrine by laser desorption supersonic jet technique.

    Science.gov (United States)

    Ishiuchi, Shun-ichi; Asakawa, Toshiro; Mitsuda, Haruhiko; Miyazaki, Mitsuhiko; Chakraborty, Shamik; Fujii, Masaaki

    2011-09-22

    In our previous work, we found that synephrine has six conformers in the gas phase, while adrenaline, which is a catecholamine and has the same side chain as synephrine, has been reported to have only two conformers. To determine the conformational geometries of synephrine, we measured resonance enhanced multiphoton ionization, ultraviolet-ultraviolet hole burning, and infrared dip spectra by utilizing the laser desorption supersonic jet technique. By comparing the observed infrared spectra with theoretical ones, we assigned geometries except for the orientations of the phenolic OH group. Comparison between the determined structures of synephrine and those of 2-methylaminno-1-phenylethanol, which has the same side chain as synephrine but no phenol OH group, leads to the conclusion that the phenolic OH group in synephrine does not affect the conformational flexibility of the side chain. In the case of adrenaline, which is expected to have 12 conformers if there are no interactions between the catecholic OH groups and the side chain, some interactions possibly exist between them because only two conformations are observed. By estimation of the dipole-dipole interaction energy between partial dipole moments of the catecholic OH groups and the side chain, it was concluded that the dipole-dipole interaction stabilizes specific conformers which are actually observed. © 2011 American Chemical Society

  10. Conformal and highly luminescent monolayers of Alq3 prepared by gas-phase molecular layer deposition.

    Science.gov (United States)

    Räupke, André; Albrecht, Fabian; Maibach, Julia; Behrendt, Andreas; Polywka, Andreas; Heiderhoff, Ralf; Helzel, Jonatan; Rabe, Torsten; Johannes, Hans-Hermann; Kowalsky, Wolfgang; Mankel, Eric; Mayer, Thomas; Görrn, Patrick; Riedl, Thomas

    2014-01-22

    The gas-phase molecular layer deposition (MLD) of conformal and highly luminescent monolayers of tris(8-hydroxyquinolinato)aluminum (Alq3) is reported. The controlled formation of Alq3 monolayers is achieved for the first time by functionalization of the substrate with amino groups, which serve as initial docking sites for trimethyl aluminum (TMA) molecules binding datively to the amine. Thereby, upon exposure to 8-hydroxyquinoline (8-HQ), the self-limiting formation of highly luminescent Alq3 monolayers is afforded. The growth process and monolayer formation were studied and verified by in situ quartz crystal monitoring, optical emission and absorption spectroscopy, and X-ray photoelectron spectroscopy. The nature of the MLD process provides an avenue to coat arbitrarily shaped 3D surfaces and porous structures with high surface areas, as demonstrated in this work for silica aerogels. The concept presented here paves the way to highly sensitive luminescent sensors and dye-sensitized metal oxides for future applications (e.g., in photocatalysis and solar cells).

  11. Single-step gas phase synthesis of stable iron aluminide nanoparticles with soft magnetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Vernieres, Jerome, E-mail: Jerome.vernieres@oist.jp; Benelmekki, Maria; Kim, Jeong-Hwan; Grammatikopoulos, Panagiotis; Diaz, Rosa E. [Nanoparticles by Design Unit, Okinawa Institute of Science and Technology (OIST) Graduate University, 1919-1 Tancha, Onna Son, Okinawa 904-0495 (Japan); Bobo, Jean-François [Centre d’Elaboration de Materiaux et d’Etudes Structurales (CEMES), 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4 (France); Sowwan, Mukhles, E-mail: Mukhles@oist.jp [Nanoparticles by Design Unit, Okinawa Institute of Science and Technology (OIST) Graduate University, 1919-1 Tancha, Onna Son, Okinawa 904-0495 (Japan); Nanotechnology Research Laboratory, Al-Quds University, P.O. Box 51000, East Jerusalem, Palestine (Country Unknown)

    2014-11-01

    Soft magnetic alloys at the nanoscale level have long generated a vivid interest as candidate materials for technological and biomedical purposes. Consequently, controlling the structure of bimetallic nanoparticles in order to optimize their magnetic properties, such as high magnetization and low coercivity, can significantly boost their potential for related applications. However, traditional synthesis methods stumble upon the long standing challenge of developing true nanoalloys with effective control over morphology and stability against oxidation. Herein, we report on a single-step approach to the gas phase synthesis of soft magnetic bimetallic iron aluminide nanoparticles, using a versatile co-sputter inert gas condensation technique. This method allowed for precise morphological control of the particles; they consisted of an alloy iron aluminide crystalline core (DO{sub 3} phase) and an alumina shell, which reduced inter-particle interactions and also prevented further oxidation and segregation of the bimetallic core. Remarkably, the as-deposited alloy nanoparticles show interesting soft magnetic properties, in that they combine a high saturation magnetization (170 emu/g) and low coercivity (less than 20 Oe) at room temperature. Additional functionality is tenable by modifying the surface of the particles with a polymer, to ensure their good colloidal dispersion in aqueous environments.

  12. A computational and spectroscopic study of the gas-phase conformers of adrenaline

    Science.gov (United States)

    Çarçabal, P.; Snoek, L. C.; van Mourik, T.

    The conformational landscapes of the neurotransmitter l-adrenaline (l-epinephrine) and its diastereoisomer pseudo-adrenaline, isolated in the gas phase and un-protonated, have been investigated by using a combination of mass-selected ultraviolet and infrared holeburn spectroscopy, following laser desorption of the sample into a pulsed supersonic argon jet, and DFT and ab initio computation (at the B3LYP/6-31+G*, MP2/6-31+G* and MP2/aug-cc-pVDZ levels of theory). Both for adrenaline and its diastereoisomer, pseudo-adrenaline, one dominant molecular conformation, very similar to the one seen in noradrenaline, has been observed. It could be assigned to an extended side-chain structure (AG1a) stabilized by an OH → N intramolecular hydrogen bond. An intramolecular hydrogen bond is also formed between the neighbouring hydroxyl groups on the catechol ring. The presence of further conformers for both diastereoisomers could not be excluded, but overlapping electronic spectra and low ion signals prevented further assignments.

  13. Ultrafast excited-state relaxation of a binuclear Ag(i) phosphine complex in gas phase and solution.

    Science.gov (United States)

    Kruppa, S V; Bäppler, F; Klopper, W; Walg, S P; Thiel, W R; Diller, R; Riehn, C

    2017-08-30

    The binuclear complex [Ag 2 (dcpm) 2 ](PF 6 ) 2 (dcpm = bis(dicyclohexylphosphino)methane) exhibits a structure with a close silver-silver contact mediated by the bridging ligand and thus a weak argentophilic interaction. Upon electronic excitation this cooperative effect is strongly increased and determines the optical and luminescence properties of the compound. We have studied here the ultrafast electronic dynamics in parallel in gas phase by transient photodissociation and in solution by transient absorption. In particular, we report the diverse photofragmentation pathways of isolated [Ag 2 (dcpm) 2 ] 2+ in an ion trap and its gas phase UV photodissociation spectrum. By pump-probe fragmentation action spectroscopy (λ ex = 260 nm) in the gas phase, we have obtained fragment-specific transients which exhibit a common ultrafast multiexponential decay. This is fitted to four time constants (0.6/5.8/100/>1000 ps), highlighting complex intrinsic photophysical processes. Remarkably, multiexponential dynamics (0.9/8.5/73/604 ps) are as well found for the relaxation dynamics in acetonitrile solution. Ab initio calculations at the level of approximate coupled-cluster singles-doubles (CC2) theory of ground and electronically excited states of the reduced model system [Ag 2 (dmpm) 2 ] 2+ (dmpm = bis(dimethylphosphino)methane) indicate a shortening of the Ag-Ag distance upon excitation by 0.3-0.4 Å. In C 2 geometry two close-lying singlet states S 1 ( 1 MC(dσ*-pπ), 1 B, 4.13 eV) and S 2 ( 1 MC(dσ*-pσ), 1 A, 4.45 eV) are found. The nearly dark S 1 state has not been reported so far. The excitation of the S 2 state carries a large oscillator strength for the calculated vertical transition (266 nm). Two related triplets are calculated at T 1 (3.87 eV) and T 2 (3.90 eV). From these findings we suggest possible relaxation pathways with the two short time constants ascribed to ISC/IVR and propose from the obtained similar values in gas phase that the fast solution dynamics

  14. Compare local pocket and global protein structure models by small structure patterns

    KAUST Repository

    Cui, Xuefeng; Kuwahara, Hiroyuki; Li, Shuai Cheng; Gao, Xin

    2015-01-01

    Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria

  15. PDB2CD visualises dynamics within protein structures.

    Science.gov (United States)

    Janes, Robert W

    2017-10-01

    Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.

  16. DNA mimic proteins: functions, structures, and bioinformatic analysis.

    Science.gov (United States)

    Wang, Hao-Ching; Ho, Chun-Han; Hsu, Kai-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J

    2014-05-13

    DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.

  17. Liquid-gas phase transition and isospin fractionation in intermediate energy heavy ion collisions

    International Nuclear Information System (INIS)

    Xing Yongzhong; Liu Jianye; Guo Wenjun

    2004-01-01

    The liquid-gas phase transition in the heavy ion collisions and nuclear matter has been an important topic and got achievements, such as, based on the studies by H.Q. Song et al the critical temperature of liquid-gas phase transition enhances with increasing the mass of system and reduces as the increase of the neutron proton ratio of system. As authors know that both the liquid-gas phase transition and the isospin fractionation occur in the spinodal instability region at the nuclear density below the normal nuclear density. In particular, these two dynamical processes lead to the separation of nuclear matter into the liquid phase and gas phase. In this case to compare their dynamical behaviors is interested. The authors investigate the dependence of isospin fractionation degree on the mass and neutron proton ratio of system by using the isospin dependent quantum molecular dynamics model. The authors found that the degree of isospin fractionation (N/Z) n /(N/Z) imf decreases with increasing the mass of the system. This is just similar to the enhance of the critical temperature of liquid-gas phase transition T c as the increase of system mass. Because the enhance of T c is not favorable for the liquid-gas transition taking place, which reduces the isospin fractionation process and leads to decrease of (N/Z) n /(N/Z) imf . However the degree of isospin fractionation enhances with increasing the neutron proton ratio of the system. It is just corresponding to the reduce of T c of the liquid-gas phase transition as the increase of the isospin fractionation of the system. Because the reduce of T c enhances the liquid-gas phase transition process and also prompts the isospin fractionation process leading the increase of the isospin fractionation degree. To sum up, there are very similar dynamical behaviors for the degree of isospin fractionation and the critical temperature of the liquid-gas phase transition. So dynamical properties of the liquid-gas phase transition can

  18. Reactor for tracking catalyst nanoparticles in liquid at high temperature under a high-pressure gas phase with X-ray absorption spectroscopy.

    Science.gov (United States)

    Nguyen, Luan; Tao, Franklin Feng

    2018-02-01

    Structure of catalyst nanoparticles dispersed in liquid phase at high temperature under gas phase of reactant(s) at higher pressure (≥5 bars) is important for fundamental understanding of catalytic reactions performed on these catalyst nanoparticles. Most structural characterizations of a catalyst performing catalysis in liquid at high temperature under gas phase at high pressure were performed in an ex situ condition in terms of characterizations before or after catalysis since, from technical point of view, access to the catalyst nanoparticles during catalysis in liquid phase at high temperature under high pressure reactant gas is challenging. Here we designed a reactor which allows us to perform structural characterization using X-ray absorption spectroscopy including X-ray absorption near edge structure spectroscopy and extended X-ray absorption fine structure spectroscopy to study catalyst nanoparticles under harsh catalysis conditions in terms of liquid up to 350 °C under gas phase with a pressure up to 50 bars. This reactor remains nanoparticles of a catalyst homogeneously dispersed in liquid during catalysis and X-ray absorption spectroscopy characterization.

  19. Relation between native ensembles and experimental structures of proteins

    DEFF Research Database (Denmark)

    Best, R. B.; Lindorff-Larsen, Kresten; DePristo, M. A.

    2006-01-01

    Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of "high-sequence similarity Protein Data Bank" (HSP) structures and consider the extent to which such ensembles represent the structural...... Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest...... heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein...

  20. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    Energy Technology Data Exchange (ETDEWEB)

    Carr, J. K.; Roy, S.; Skinner, J. L. [Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Wisconsin 53706 (United States); Zabuga, A. V.; Rizzo, T. R. [Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne (Switzerland)

    2014-06-14

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala){sub 5}-Lys-H{sup +} in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly {sup 13}C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and {sup 13}C{sup 18}O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm{sup −1} for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

  1. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    International Nuclear Information System (INIS)

    Carr, J. K.; Roy, S.; Skinner, J. L.; Zabuga, A. V.; Rizzo, T. R.

    2014-01-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala) 5 -Lys-H + in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13 C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13 C 18 O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm −1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides

  2. Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

    Science.gov (United States)

    Carr, J. K.; Zabuga, A. V.; Roy, S.; Rizzo, T. R.; Skinner, J. L.

    2014-01-01

    The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed “maps,” which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H+ in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly 13C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and 13C18O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm−1 for both frequencies and couplings, having larger errors only for the frequencies of terminal amides. PMID:24929378

  3. Current strategies for protein production and purification enabling membrane protein structural biology.

    Science.gov (United States)

    Pandey, Aditya; Shin, Kyungsoo; Patterson, Robin E; Liu, Xiang-Qin; Rainey, Jan K

    2016-12-01

    Membrane proteins are still heavily under-represented in the protein data bank (PDB), owing to multiple bottlenecks. The typical low abundance of membrane proteins in their natural hosts makes it necessary to overexpress these proteins either in heterologous systems or through in vitro translation/cell-free expression. Heterologous expression of proteins, in turn, leads to multiple obstacles, owing to the unpredictability of compatibility of the target protein for expression in a given host. The highly hydrophobic and (or) amphipathic nature of membrane proteins also leads to challenges in producing a homogeneous, stable, and pure sample for structural studies. Circumventing these hurdles has become possible through the introduction of novel protein production protocols; efficient protein isolation and sample preparation methods; and, improvement in hardware and software for structural characterization. Combined, these advances have made the past 10-15 years very exciting and eventful for the field of membrane protein structural biology, with an exponential growth in the number of solved membrane protein structures. In this review, we focus on both the advances and diversity of protein production and purification methods that have allowed this growth in structural knowledge of membrane proteins through X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM).

  4. Tuning Catalytic Performance through a Single or Sequential Post-Synthesis Reaction(s) in a Gas Phase

    Energy Technology Data Exchange (ETDEWEB)

    Shan, Junjun [Department; Department; Zhang, Shiran [Department; Department; Choksi, Tej [Department; Nguyen, Luan [Department; Department; Bonifacio, Cecile S. [Department; Li, Yuanyuan [Department; Zhu, Wei [Department; Department; College; Tang, Yu [Department; Department; Zhang, Yawen [College; Yang, Judith C. [Department; Greeley, Jeffrey [Department; Frenkel, Anatoly I. [Department; Tao, Franklin [Department; Department

    2016-12-05

    Catalytic performance of a bimetallic catalyst is determined by geometric structure and electronic state of the surface or even the near-surface region of the catalyst. Here we report that single and sequential postsynthesis reactions of an as-synthesized bimetallic nanoparticle catalyst in one or more gas phases can tailor surface chemistry and structure of the catalyst in a gas phase, by which catalytic performance of this bimetallic catalyst can be tuned. Pt–Cu regular nanocube (Pt–Cu RNC) and concave nanocube (Pt–Cu CNC) are chosen as models of bimetallic catalysts. Surface chemistry and catalyst structure under different reaction conditions and during catalysis were explored in gas phase of one or two reactants with ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) and extended X-ray absorption fine structure (EXAFS) spectroscopy. The newly formed surface structures of Pt–Cu RNC and Pt–Cu CNC catalysts strongly depend on the reactive gas(es) used in the postsynthesis reaction(s). A reaction of Pt–Cu RNC-as synthesized with H2 at 200 °C generates a near-surface alloy consisting of a Pt skin layer, a Cu-rich subsurface, and a Pt-rich deep layer. This near-surface alloy of Pt–Cu RNC-as synthesized-H2 exhibits a much higher catalytic activity in CO oxidation in terms of a low activation barrier of 39 ± 4 kJ/mol in contrast to 128 ± 7 kJ/mol of Pt–Cu RNC-as synthesized. Here the significant decrease of activation barrier demonstrates a method to tune catalytic performances of as-synthesized bimetallic catalysts. A further reaction of Pt–Cu RNC-as synthesized-H2 with CO forms a Pt–Cu alloy surface, which exhibits quite different catalytic performance in CO oxidation. It suggests the capability of generating a different surface by using another gas. The capability of tuning surface chemistry and structure of bimetallic catalysts was also demonstrated in restructuring of Pt–Cu CNC-as synthesized.

  5. GAS PHASE SYNTHESIS OF (ISO)QUINOLINE AND ITS ROLE IN THE FORMATION OF NUCLEOBASES IN THE INTERSTELLAR MEDIUM

    International Nuclear Information System (INIS)

    Parker, Dorian S. N.; Kaiser, Ralf I.; Kostko, Oleg; Troy, Tyler P.; Ahmed, Musahid; Mebel, Alexander M.; Tielens, Alexander G. G. M.

    2015-01-01

    Nitrogen-substituted polycyclic aromatic hydrocarbons (NPAHs) have been proposed to play a key role in the astrochemical evolution of the interstellar medium, yet the formation mechanisms of even their simplest prototypes—quinoline and isoquinoline—remain elusive. Here, we reveal a novel concept that under high temperature conditions representing circumstellar envelopes of carbon stars, (iso)quinoline can be synthesized via the reaction of pyridyl radicals with two acetylene molecules. The facile gas phase formation of (iso)quinoline in circumstellar envelopes defines a hitherto elusive reaction class synthesizing aromatic structures with embedded nitrogen atoms that are essential building blocks in contemporary biological-structural motifs. Once ejected from circumstellar shells and incorporated into icy interstellar grains in cold molecular clouds, these NPAHs can be functionalized by photo processing forming nucleobase-type structures as sampled in the Murchison meteorite

  6. Predicting nucleic acid binding interfaces from structural models of proteins.

    Science.gov (United States)

    Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

    2012-02-01

    The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

  7. Ion pairs in non-redundant protein structures

    Indian Academy of Sciences (India)

    Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent–protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together.

  8. Droplet model of pyrocarbon deposition from the gas phase. [HTGR

    Energy Technology Data Exchange (ETDEWEB)

    Linke, J; Koizlik, K; Luhleich, H; Nickel, H

    1975-01-15

    Based on extensive earlier work a model has been developed to describe the formation of carbon by pyrolysis of gaseous hydrocarbons. One of the central statements of this model is the assumption of the existence of a quasi liquid carbon phase during deposition process.This model is described and is discussed as are the consequences for the material properties and structural parameters which arise from it. To review the droplet model, statically deposited pyrocarbon is examined by characterization methods suitable to analyze just these structural parameters.The results prove the model conceptions to be realistic.

  9. The structure and function of endophilin proteins

    DEFF Research Database (Denmark)

    Kjaerulff, Ole; Brodin, Lennart; Jung, Anita

    2011-01-01

    Members of the BAR domain protein superfamily are essential elements of cellular traffic. Endophilins are among the best studied BAR domain proteins. They have a prominent function in synaptic vesicle endocytosis (SVE), receptor trafficking and apoptosis, and in other processes that require...

  10. BLAST-based structural annotation of protein residues using Protein Data Bank.

    Science.gov (United States)

    Singh, Harinder; Raghava, Gajendra P S

    2016-01-25

    In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

  11. The contact activation proteins: a structure/function overview

    NARCIS (Netherlands)

    Meijers, J. C.; McMullen, B. A.; Bouma, B. N.

    1992-01-01

    In recent years, extensive knowledge has been obtained on the structure/function relationships of blood coagulation proteins. In this overview, we present recent developments on the structure/function relationships of the contact activation proteins: factor XII, high molecular weight kininogen,

  12. A gas-phase reactor powered by solar energy and ethanol for H2 production

    International Nuclear Information System (INIS)

    Ampelli, Claudio; Genovese, Chiara; Passalacqua, Rosalba; Perathoner, Siglinda; Centi, Gabriele

    2014-01-01

    In the view of H 2 as the future energy vector, we presented here the development of a homemade photo-reactor working in gas phase and easily interfacing with fuel cell devices, for H 2 production by ethanol dehydrogenation. The process generates acetaldehyde as the main co-product, which is more economically advantageous with respect to the low valuable CO 2 produced in the alternative pathway of ethanol photoreforming. The materials adopted as photocatalysts are based on TiO 2 substrates but properly modified with noble (Au) and not-noble (Cu) metals to enhance light harvesting in the visible region. The samples were characterized by BET surface area analysis, Transmission Electron Microscopy (TEM) and UV–visible Diffusive Reflectance Spectroscopy, and finally tested in our homemade photo-reactor by simulated solar irradiation. We discussed about the benefits of operating in gas phase with respect to a conventional slurry photo-reactor (minimization of scattering phenomena, no metal leaching, easy product recovery, etc.). Results showed that high H 2 productivity can be obtained in gas phase conditions, also irradiating titania photocatalysts doped with not-noble metals. - Highlights: • A gas-phase photoreactor for H 2 production by ethanol dehydrogenation was developed. • The photocatalytic behaviours of Au and Cu metal-doped TiO 2 thin layers are compared. • Benefits of operating in gas phase with respect to a slurry reactor are presented. • Gas phase conditions and use of not-noble metals are the best economic solution

  13. De novo protein structure determination using sparse NMR data

    International Nuclear Information System (INIS)

    Bowers, Peter M.; Strauss, Charlie E.M.; Baker, David

    2000-01-01

    We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models are built from these fragments by minimizing an energy function that favors hydrophobic burial, strand pairing, and satisfaction of NOE constraints. Models generated using this procedure with ∼1 NOE constraint per residue are in some cases closer to the corresponding X-ray structures than the published NMR solution structures. The method requires only the sparse constraints available during initial stages of NMR structure determination, and thus holds promise for increasing the speed with which protein solution structures can be determined

  14. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

    KAUST Repository

    Cui, Xuefeng

    2016-06-15

    Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.

  15. Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces

    International Nuclear Information System (INIS)

    Tuncbag, Nurcan; Gursoy, Attila; Keskin, Ozlem

    2011-01-01

    The vast majority of the chores in the living cell involve protein–protein interactions. Providing details of protein interactions at the residue level and incorporating them into protein interaction networks are crucial toward the elucidation of a dynamic picture of cells. Despite the rapid increase in the number of structurally known protein complexes, we are still far away from a complete network. Given experimental limitations, computational modeling of protein interactions is a prerequisite to proceed on the way to complete structural networks. In this work, we focus on the question 'how do proteins interact?' rather than 'which proteins interact?' and we review structure-based protein–protein interaction prediction approaches. As a sample approach for modeling protein interactions, PRISM is detailed which combines structural similarity and evolutionary conservation in protein interfaces to infer structures of complexes in the protein interaction network. This will ultimately help us to understand the role of protein interfaces in predicting bound conformations

  16. DFT Study of dimers of dimethyl sulfoxide in gas phase

    Directory of Open Access Journals (Sweden)

    Reza Fazaeli

    2014-10-01

    Full Text Available Density functional (DFT calculations at M05-2x/aug-cc-pVDZ level were used to analyze the interactions between dimethyl sulfoxide (DMSO dimers. The structures obtained have been ana-lyzed with the Atoms in Molecules (AIMs and Natural Bond Orbital (NBO methodologies. Four minima were located on the potential energy surface of the dimers. Three types of interac-tions are observed, CH•••O, CH•••S hydrogen bonds and orthogonal interaction between the lone pair of the oxygen with the electron-deficient region of the sulfur atom. Stabilization energies of dimers including BSSE and ZPE are in the range 27–40 kJmol-1. The most stable conformers of dimers at DFT level is cyclic structure with antiparallel orientation of S=O groups pairing with three C–H∙∙∙O and a S∙∙∙O interactions.

  17. Research in Korea on Gas Phase Synthesis and Control of Nanoparticles

    International Nuclear Information System (INIS)

    Choi, Mansoo

    2001-01-01

    Research activity into the gas phase synthesis of nanoparticles has witnessed rapid growth on a worldwide basis, which is also reflected by Korean research efforts. Nanoparticle research is inherently a multi-disciplinary activity involving both science and engineering. In this paper, the recent studies undertaken in Korea on the gas phase synthesis and control of nanoparticles are reviewed. Studies on the synthesis of various kinds of nanoparticles are first discussed with a focus on the different types of reactors used. Recent experimental and theoretical studies and newly developed methods of measuring and modeling nanoparticle growth are also reviewed

  18. FORTRAN program for calculating liquid-phase and gas-phase thermal diffusion column coefficients

    International Nuclear Information System (INIS)

    Rutherford, W.M.

    1980-01-01

    A computer program (COLCO) was developed for calculating thermal diffusion column coefficients from theory. The program, which is written in FORTRAN IV, can be used for both liquid-phase and gas-phase thermal diffusion columns. Column coefficients for the gas phase can be based on gas properties calculated from kinetic theory using tables of omega integrals or on tables of compiled physical properties as functions of temperature. Column coefficients for the liquid phase can be based on compiled physical property tables. Program listings, test data, sample output, and users manual are supplied for appendices

  19. Direct gas-phase epoxidation of propylene to propylene oxide through radical reactions: A theoretical study

    Science.gov (United States)

    Kizilkaya, Ali Can; Fellah, Mehmet Ferdi; Onal, Isik

    2010-03-01

    The gas-phase radical chain reactions which utilize O 2 as the oxidant to produce propylene oxide (PO) are investigated through theoretical calculations. The transition states and energy profiles were obtained for each path. The rate constants were also calculated. The energetics for the competing pathways indicate that PO can be formed selectively due to its relatively low activation barrier (9.3 kcal/mol) which is in a good agreement with the experimental value (11 kcal/mol) of gas-phase propylene epoxidation. The formation of the acrolein and combustion products have relatively high activation barriers and are not favored. These results also support the recent experimental findings.

  20. Acrolein Production by Gas-Phase Glycerol Dehydration Using PO₄/Nb₂O5 Catalysts.

    Science.gov (United States)

    Lee, Kyu Am; Ryoo, HeeKyoung; Ma, Byung Chol; Kim, Youngchul

    2018-02-01

    In this study, modified niobium oxide were prepared to study the addictive effects on the catalytic performance for gas-phase glycerol dehydration. The catalysts were characterized by N2 adsorption/desorption, XRD, NH3-TPD, FT-IR. The amount of phosphoric acid was up to 50 wt% in niobium. As a result, the highest glycerol conversion was achieved over 20 wt% PO4/Nb2O5. It indicates that the optimal amount of phosphoric acid leads the catalyst to have appropriate acidity which is an important factor for gas-phase glycerol dehydration.

  1. Gas phase THz spectroscopy of toxic agent simulant compounds using the AILES synchrotron beamline

    Science.gov (United States)

    Cuisset, A.; Smirnova, I.; Bocquet, R.; Hindle, F.; Mouret, G.; Yang, C.; Pirali, O.; Roy, P.

    2010-02-01

    A new study is currently underway aiming at recording and assigning the gas phase rovibrational spectra of several organophosphorus and organosulphur compounds in the THz frequency domain. Thanks to the exceptional properties of flux, brilliance and spectral range of the AILES beamline coupled to the FTIR spectrometer, the gas phase vibrational spectra of low volatility organophosphorous compounds have been recorded across the entire THz frequency range. High resolution FTIR spectroscopy was used to record the pure rotational and the low-frequency rovibrational spectrum of DMSO. A comparison between the spectra measured with the AILES beamline and the spectra obtained with optoelectronic THz sources is possible.

  2. Studies of gas phase ion/molecule reactions by Fourier transform ion cyclotron resonance mass spectrometry

    International Nuclear Information System (INIS)

    Kleingeld, J.C.

    1984-01-01

    An important field in which Fourier-transform ion cyclotron resonance has useful applications is that of gas phase ion chemistry, the subject of this thesis. First, the general picture of ion-molecule reactions in the gas phase is discussed. Next, some positive ion-molecule reactions are described, whereas the remaining chapters deal with negative ion-molecule reactions. Most of these studies have been performed using the FT-ICR method. Reactions involving H 3 O - and NH 4 - ions are described whereas the other chapters deal with larger organic complexes. (Auth.)

  3. Fischer Indole Synthesis in the Gas Phase, the Solution Phase, and at the Electrospray Droplet Interface.

    Science.gov (United States)

    Bain, Ryan M; Ayrton, Stephen T; Cooks, R Graham

    2017-07-01

    Previous reports have shown that reactions occurring in the microdroplets formed during electrospray ionization can, under the right conditions, exhibit significantly greater rates than the corresponding bulk solution-phase reactions. The observed acceleration under electrospray ionization could result from a solution-phase, a gas-phase, or an interfacial reaction. This study shows that a gas-phase ion/molecule (or ion/ion) reaction is not responsible for the observed rate enhancement in the particular case of the Fischer indole synthesis. The results show that the accelerated reaction proceeds in the microdroplets, and evidence is provided that an interfacial process is involved. Graphical Abstract GRAPHICAL ABSTRACT TEXT HERE] -->.

  4. Optical processes in the performance and recovery of gas-phase switches

    International Nuclear Information System (INIS)

    Gundersen, M.

    1982-01-01

    In this paper several optical processes that may be used to affect gas-phase switch performance and operation are discussed, and approaches using a laser to increase recovery rates of switches are presented. In the latter the laser is used during the recovery phase rather than the conductive or closure phase. This papper suggests that it should be possible to use a low-power laser (e.g., one that is technologically feasible to use as part of a switch) to assist in opening the switch by quenching excited atomic and/or molecular species. The application of laser-induced energy extraction to gas-phase switches is also discussed

  5. The electron spectrum of UF6 recorded in the gas phase

    Science.gov (United States)

    Mârtensson, N.; Malmquist, P.-Å.; Svensson, S.; Johansson, B.

    1984-06-01

    Gas phase core and valence electron spectra from UF6, excited by AlKα monochromatized x rays, in the binding energy range 0-1000 eV are presented. It is shown that the AlKα excited valence electron spectrum can be used to reassign the highest occupied molecular orbital (HOMO) in UF6. Many-body effects on the core levels are discussed and core level lifetimes are determined. The shift between solid phase and gas phase electron binding energies for core lines is used to discuss the U5 f population in UF6.

  6. Structure of synaptophysin: a hexameric MARVEL-domain channel protein.

    Science.gov (United States)

    Arthur, Christopher P; Stowell, Michael H B

    2007-06-01

    Synaptophysin I (SypI) is an archetypal member of the MARVEL-domain family of integral membrane proteins and one of the first synaptic vesicle proteins to be identified and cloned. Most all MARVEL-domain proteins are involved in membrane apposition and vesicle-trafficking events, but their precise role in these processes is unclear. We have purified mammalian SypI and determined its three-dimensional (3D) structure by using electron microscopy and single-particle 3D reconstruction. The hexameric structure resembles an open basket with a large pore and tenuous interactions within the cytosolic domain. The structure suggests a model for Synaptophysin's role in fusion and recycling that is regulated by known interactions with the SNARE machinery. This 3D structure of a MARVEL-domain protein provides a structural foundation for understanding the role of these important proteins in a variety of biological processes.

  7. Sampling Realistic Protein Conformations Using Local Structural Bias

    DEFF Research Database (Denmark)

    Hamelryck, Thomas Wim; Kent, John T.; Krogh, A.

    2006-01-01

    The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which...... are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded...... in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications...

  8. Rapid and reliable protein structure determination via chemical shift threading.

    Science.gov (United States)

    Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

    2018-01-01

    Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

  9. Is protein structure prediction still an enigma?

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-29

    Dec 29, 2008 ... Computer methods for protein analysis address this problem since they study the .... neighbor methods, molecular dynamic simulation, and approaches .... fuzzy clustering, neural net works, logistic regression, decision tree ...

  10. Solution structure and dynamics of melanoma inhibitory activity protein

    International Nuclear Information System (INIS)

    Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

    2002-01-01

    Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

  11. X-ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser

    DEFF Research Database (Denmark)

    Küpper, Jochen; Stern, Stephan; Holmegaard, Lotte

    2014-01-01

    We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive...... imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e. g., structural......-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules....

  12. Function and structure of GFP-like proteins in the protein data bank.

    Science.gov (United States)

    Ong, Wayne J-H; Alvarez, Samuel; Leroux, Ivan E; Shahid, Ramza S; Samma, Alex A; Peshkepija, Paola; Morgan, Alicia L; Mulcahy, Shawn; Zimmer, Marc

    2011-04-01

    The RCSB protein databank contains 266 crystal structures of green fluorescent proteins (GFP) and GFP-like proteins. This is the first systematic analysis of all the GFP-like structures in the pdb. We have used the pdb to examine the function of fluorescent proteins (FP) in nature, aspects of excited state proton transfer (ESPT) in FPs, deformation from planarity of the chromophore and chromophore maturation. The conclusions reached in this review are that (1) The lid residues are highly conserved, particularly those on the "top" of the β-barrel. They are important to the function of GFP-like proteins, perhaps in protecting the chromophore or in β-barrel formation. (2) The primary/ancestral function of GFP-like proteins may well be to aid in light induced electron transfer. (3) The structural prerequisites for light activated proton pumps exist in many structures and it's possible that like bioluminescence, proton pumps are secondary functions of GFP-like proteins. (4) In most GFP-like proteins the protein matrix exerts a significant strain on planar chromophores forcing most GFP-like proteins to adopt non-planar chromophores. These chromophoric deviations from planarity play an important role in determining the fluorescence quantum yield. (5) The chemospatial characteristics of the chromophore cavity determine the isomerization state of the chromophore. The cavities of highlighter proteins that can undergo cis/trans isomerization have chemospatial properties that are common to both cis and trans GFP-like proteins.

  13. A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

    Science.gov (United States)

    Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

    2010-08-01

    The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

  14. Tuning structure of oppositely charged nanoparticle and protein complexes

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Sugam, E-mail: sugam@barc.gov.in; Aswal, V. K., E-mail: sugam@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400085 (India); Callow, P. [Institut Laue Langevin, DS/LSS, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9 (France)

    2014-04-24

    Small-angle neutron scattering (SANS) has been used to probe the structures of anionic silica nanoparticles (LS30) and cationic lyszyme protein (M.W. 14.7kD, I.P. ∼ 11.4) by tuning their interaction through the pH variation. The protein adsorption on nanoparticles is found to be increasing with pH and determined by the electrostatic attraction between two components as well as repulsion between protein molecules. We show the strong electrostatic attraction between nanoparticles and protein molecules leads to protein-mediated aggregation of nanoparticles which are characterized by fractal structures. At pH 5, the protein adsorption gives rise to nanoparticle aggregation having surface fractal morphology with close packing of nanoparticles. The surface fractals transform to open structures of mass fractal morphology at higher pH (7 and 9) on approaching isoelectric point (I.P.)

  15. Studying Membrane Protein Structure and Function Using Nanodiscs

    DEFF Research Database (Denmark)

    Huda, Pie

    The structure and dynamic of membrane proteins can provide valuable information about general functions, diseases and effects of various drugs. Studying membrane proteins are a challenge as an amphiphilic environment is necessary to stabilise the protein in a functionally and structurally relevant...... form. This is most typically achieved through the use of detergent based reconstitution systems. However, time and again such systems fail to provide a suitable environment causing aggregation and inactivation. Nanodiscs are self-assembled lipoproteins containing two membrane scaffold proteins...... and a lipid bilayer in defined nanometer size, which can act as a stabiliser for membrane proteins. This enables both functional and structural investigation of membrane proteins in a detergent free environment which is closer to the native situation. Understanding the self-assembly of nanodiscs is important...

  16. Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

    Directory of Open Access Journals (Sweden)

    Ulf Hensen

    Full Text Available Proteins are usually described and classified according to amino acid sequence, structure or function. Here, we develop a minimally biased scheme to compare and classify proteins according to their internal mobility patterns. This approach is based on the notion that proteins not only fold into recurring structural motifs but might also be carrying out only a limited set of recurring mobility motifs. The complete set of these patterns, which we tentatively call the dynasome, spans a multi-dimensional space with axes, the dynasome descriptors, characterizing different aspects of protein dynamics. The unique dynamic fingerprint of each protein is represented as a vector in the dynasome space. The difference between any two vectors, consequently, gives a reliable measure of the difference between the corresponding protein dynamics. We characterize the properties of the dynasome by comparing the dynamics fingerprints obtained from molecular dynamics simulations of 112 proteins but our approach is, in principle, not restricted to any specific source of data of protein dynamics. We conclude that: 1. the dynasome consists of a continuum of proteins, rather than well separated classes. 2. For the majority of proteins we observe strong correlations between structure and dynamics. 3. Proteins with similar function carry out similar dynamics, which suggests a new method to improve protein function annotation based on protein dynamics.

  17. Host Proteins Determine MRSA Biofilm Structure and Integrity

    DEFF Research Database (Denmark)

    Dreier, Cindy; Nielsen, Astrid; Jørgensen, Nis Pedersen

    Human extracellular matrix (hECM) proteins aids the initial attachment and initiation of an infection, by specific binding to bacterial cell surface proteins. However, the importance of hECM proteins in structure, integrity and antibiotic resilience of a biofilm is unknown. This study aims...... to determine how specific hECM proteins affect S. aureus USA300 JE2 biofilms. Biofilms were grown in the presence of synovial fluid from rheumatoid arteritis patients to mimic in vivo conditions, where bacteria incorporate hECM proteins into the biofilm matrix. Difference in biofilm structure, with and without...... addition of hECM to growth media, was visualized by confocal laser scanning microscopy. Two enzymatic degradation experiments were used to study biofilm matrix composition and importance of hECM proteins: enzymatic removal of specific hECM proteins from growth media, before biofilm formation, and enzymatic...

  18. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

    2015-04-15

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  19. Using linear algebra for protein structural comparison and classification.

    Science.gov (United States)

    Gomide, Janaína; Melo-Minardi, Raquel; Dos Santos, Marcos Augusto; Neshich, Goran; Meira, Wagner; Lopes, Júlio César; Santoro, Marcelo

    2009-07-01

    In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.

  20. Using linear algebra for protein structural comparison and classification

    Directory of Open Access Journals (Sweden)

    Janaína Gomide

    2009-01-01

    Full Text Available In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD and Latent Semantic Indexing (LSI techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.

  1. Mainstream Smoke Gas Phase Filtration Performance of Adsorption Materials Evaluated With A Puff-by-Puff Multiplex GC-MS Method

    Directory of Open Access Journals (Sweden)

    Xue L

    2014-12-01

    Full Text Available The mainstream smoke filtration performance of activated carbon, silica gel and polymeric aromatic resins for gas-phase components was evaluated using a puff-by-puff multiplex gas chromatography-mass spectrometry (GC-MS analysis method (1. The sample 1R4F Kentucky reference cigarettes were modified by placing the adsorbents in a plug/space/plug filter configuration. Due to differences in surface area and structural characteristics, the adsorbent materials studied showed different levels of filtration activities for the twenty-six constituents monitored. Activated carbon had significant adsorption activity for all the gas-phase smoke constituents observed except ethane and carbon dioxide, while silica gel had significant activities for polar components such as aldehydes, acrolein, ketones, and diacetyl. XAD-16 polyaromatic resins showed varied levels of activity for aromatic compounds, cyclic dienes and ketones.

  2. Structural Mass Spectrometry of Proteins Using Hydroxyl Radical Based Protein Footprinting

    OpenAIRE

    Wang, Liwen; Chance, Mark R.

    2011-01-01

    Structural MS is a rapidly growing field with many applications in basic research and pharmaceutical drug development. In this feature article the overall technology is described and several examples of how hydroxyl radical based footprinting MS can be used to map interfaces, evaluate protein structure, and identify ligand dependent conformational changes in proteins are described.

  3. Aqueous-gas phase partitioning and hydrolysis of organic iodides

    International Nuclear Information System (INIS)

    Glowa, G.A.; Wren, J.C.

    2003-01-01

    The volatility and decomposition of organic iodides in a reactor containment building are important parameters to consider when assessing the potential consequences of a nuclear reactor accident. However, there are few experimental data available for the volatilities (often reported as partition coefficients) or few rate constants regarding the decomposition (via hydrolysis) of organic iodides. The partition coefficients and hydrolysis rate constants of eight organic iodides, having a range of molecular structures, have been measured in the current studies. This data, and data accumulated in the literature, have been reviewed and discussed to provide guidelines for appropriate organization of organic iodides for the purpose of modelling iodine behaviour under postulated nuclear reactor accident conditions. After assessment of the partition coefficients and their temperature dependences of many classes of organic compounds, it was found that organic iodides could be divided into two categories based upon their volatility relative to molecular iodine. Similarly, hydrolysis rates and their temperature dependences are assigned to the two categories of organic iodides. (author)

  4. Gas-phase Crystallization of Titanium Dioxide Nanoparticles

    International Nuclear Information System (INIS)

    Ahonen, P.P.; Moisala, A.; Tapper, U.; Brown, D.P.; Jokiniemi, J.K.; Kauppinen, E.I.

    2002-01-01

    We have investigated the development of crystal morphology and phase in ultrafine titanium dioxide particles. The particles were produced by a droplet-to-particle method starting from propanolic titanium tetraisopropoxide solution, and calcined in a vertical aerosol reactor in air. Mobility size classified 40-nm diameter particles were conveyed to the aerosol reactor to investigate particle size changes at 20-1200 deg. C with 5-1-s residence time. In addition, polydisperse particles were used to study morphology and phase formation by electron microscopy. According to differential mobility analysis, the particle diameter was reduced to 21-23-nm at 600 deg. C and above. Precursor decomposition occurred between 20 deg. C and 500 deg. C. The increased mobility particle size at 700 deg. C and above was observed to coincide with irregular particles at 700 deg. C and 800 deg. C and faceted particles between 900 deg. C and 1200 deg. C, according to transmission electron microscopy. The faceted anatase particles were observed to approach a minimized surface energy by forming {101} and {001} crystallographic surfaces. Anatase phase was observed at 500-1200 deg. C and above 600 deg. C the particles were single crystals. Indications of minor rutile formation were observed at 1200 deg. C. The relatively stable anatase phase vs. temperature is attributed to the defect free structure of the observed particles and a lack of crystal-crystal attachment points

  5. PSPP: a protein structure prediction pipeline for computing clusters.

    Directory of Open Access Journals (Sweden)

    Michael S Lee

    2009-07-01

    Full Text Available Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high-throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user's own high-performance computing cluster.The pipeline consists of a Perl core that integrates more than 20 individual software packages and databases, most of which are freely available from other research laboratories. The query protein sequences are first divided into domains either by domain boundary recognition or Bayesian statistics. The structures of the individual domains are then predicted using template-based modeling or ab initio modeling. The predicted models are scored with a statistical potential and an all-atom force field. The top-scoring ab initio models are annotated by structural comparison against the Structural Classification of Proteins (SCOP fold database. Furthermore, secondary structure, solvent accessibility, transmembrane helices, and structural disorder are predicted. The results are generated in text, tab-delimited, and hypertext markup language (HTML formats. So far, the pipeline has been used to study viral and bacterial proteomes.The standalone pipeline that we introduce here, unlike protein structure prediction Web servers, allows users to devote their own computing assets to process a potentially unlimited number of queries as well as perform

  6. Order from the disorder: hierarchical nanostructures self-assembled from the gas phase (Conference Presentation)

    Science.gov (United States)

    Di Fonzo, Fabio

    2017-02-01

    The assembly of nanoscale building blocks in engineered mesostructures is one of the fundamental goals of nanotechnology. Among the various processes developed to date, self-assembly emerges as one of the most promising, since it relays solely on basic physico-chemical forces. Our research is focused on a new type of self-assembly strategy from the gas-phase: Scattered Ballistic Deposition (SBD). SBD arises from the interaction of a supersonic molecular beam with a static gas and enables the growth of quasi-1D hierarchical mesostructures. Overall, they resemble a forest composed of individual, high aspect-ratio, tree-like structures, assembled from amorphous or crystalline nanoparticles. SBD is a general occurring phenomenon and can be obtained with different vapour or cluster sources. In particular, SBD by Pulsed Laser Deposition is a convenient physical vapor technique that allows the generation of supersonic plasma jets from any inorganic material irrespective of melting temperature, preserving even the most complex stoichiometries. One of the advantages of PLD over other vapour deposition techniques is extremely wide operational pressure range, from UHV to ambient pressure. These characteristics allowed us to develop quasi-1D hierarchical nanostructures from different transition metal oxides, semiconductors and metals. The precise control offered by the SBD-PLD technique over material properties at the nanoscale allowed us to fabricate ultra-thin, high efficiency hierarchical porous photonic crystals with Bragg reflectivity up to 85%. In this communication we will discuss the application of these materials to solar energy harvesting and storage, stimuli responsive photonic crystals and smart surfaces with digital control of their wettability behaviour.

  7. Do medium heavy fragments give evidence for a liquid-gas phase transition

    International Nuclear Information System (INIS)

    Trockel, R.; Hildenbrand, K.D.; Lynen, U.; Mueller, W.F.J.; Rabe, H.J.; Sann, H.; Stelzer, H.; Wada, R.; Brummund, N.; Glasow, R.; Kampert, K.H.; Santo, R.; Pelte, D.; Pochodzalla, J.; Eckert, E.

    1985-09-01

    Light and medium heavy fragments have been measured in light ion induced reactions at intermediate energies. The energy spectra have been parametrized with moving source fits. The resulting temperatures and yields do not confirm the expectations of a liquid-gas phase transition. (orig.)

  8. Electron Attachment to the Gas Phase DNA Bases Cytosine and Thymine

    Czech Academy of Sciences Publication Activity Database

    Denifl, S.; Ptasiňska, S.; Probst, M.; Hrušák, Jan; Scheier, P.; Märk, T. D.

    2004-01-01

    Roč. 108, č. 31 (2004), s. 6562-6569 ISSN 1089-5639 R&D Projects: GA ČR GA203/02/0737 Institutional research plan: CEZ:AV0Z4040901 Keywords : gas-phase * cytosine * thymine Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.639, year: 2004

  9. How Pt nanoparticles affect TiO2-induced gas-phase photocatalytic oxidation reactions

    NARCIS (Netherlands)

    Fraters, B.D.; Amrollahi Buky, Rezvaneh; Mul, Guido

    2015-01-01

    The effect of Pt nanoparticles on the gas-phase photocatalytic oxidation activity of TiO2 is shown to be largely dependent on the molecular functionality of the substrate. We demonstrate that Pt nanoparticles decrease rates in photocatalytic oxidation of propane, whereas a strong beneficial effect

  10. A gas phase work station for the Brazilian National Synchrotron Laboratory

    International Nuclear Information System (INIS)

    Souza, G.G.B. de

    1988-01-01

    A gas phase work station which has been proposed to the Brazilian National Synchrotron Laboratory is described with emphasis on the broad spectrum of physical and chemical processes which can be studied with the incorporated instrumentation. (A.C.A.S.) [pt

  11. Gas-phase polynuclear aromatic hydrocarbons (PAH) in vehicle exhaust: A method for collection and analysis

    International Nuclear Information System (INIS)

    Seigl, W.O.; Chladek, E.

    1990-01-01

    Gas-phase polynuclear aromatic hydrocarbons (PAH) are emitted at low levels in vehicle exhaust compared to other hydrocarbon emissions. A method has been developed involving the trapping of gas phase emissions on Tenax, a macrorecticular porous polymer, followed by thermal desorption onto a capillary gas chromatography column. Gas chromatography/mass spectrometry (GC/MS) was used for the chemical analysis. A detection limit of 0.05 ng was achieved for several gas-phase PAH. This high sensitivity enables the speciation and quantitation of gas-phase PAH collected from a dilution tube during standard driving (test) cycles. The method was demonstrated for the analysis of 9 PAH in the exhaust from a 1987 vehicle (with and without catalyst) during the hot start transient phase of the EPA urban dynamometer driving schedule. The PAH measured include naphthalene, 2-methyl- and 1-methylnaphthalene, biphenyl, fluorene, phenanthrene, anthracene, fluoranthene and pyrene. The four most abundant PAH observed are naphthalene, 2-methyl and 1-methylnaphthalene, and biphenyl, in that order

  12. C-terminal peptide extension via gas-phase ion/ion reactions

    Science.gov (United States)

    Peng, Zhou; McLuckey, Scott A.

    2015-01-01

    The formation of peptide bonds is of great importance from both a biological standpoint and in routine organic synthesis. Recent work from our group demonstrated the synthesis of peptides in the gas-phase via ion/ion reactions with sulfo-NHS reagents, which resulted in conjugation of individual amino acids or small peptides to the N-terminus of an existing ‘anchor’ peptide. Here, we demonstrate a complementary approach resulting in the C-terminal extension of peptides. Individual amino acids or short peptides can be prepared as reagents by incorporating gas phase-labile protecting groups to the reactive C-terminus and then converting the N-terminal amino groups to the active ketenimine reagent. Gas-phase ion/ion reactions between the anionic reagents and doubly protonated “anchor” peptide cations results in extension of the “anchor” peptide with new amide bond formation at the C-terminus. We have demonstrated that ion/ion reactions can be used as a fast, controlled, and efficient means for C-terminal peptide extension in the gas phase. PMID:26640400

  13. ECO LOGIC INTERNATIONAL GAS-PHASE CHEMICAL REDUCTION PROCESS - THE THERMAL DESORPTION UNIT - APPLICATIONS ANALYSIS REPORT

    Science.gov (United States)

    ELI ECO Logic International, Inc.'s Thermal Desorption Unit (TDU) is specifically designed for use with Eco Logic's Gas Phase Chemical Reduction Process. The technology uses an externally heated bath of molten tin in a hydrogen atmosphere to desorb hazardous organic compounds fro...

  14. DEMONSTRATION BULLETIN: GAS-PHASE CHEMICAL REDUCTION - ECO LOGIC INTERNATIONAL, INC.

    Science.gov (United States)

    The patented Eco Logic Process employs a gas-phase reduction reaction of hydrogen with organic and chlorinated organic compounds at elevated temperatures to convert aqueous and oily hazardous contaminants into a hydrocarbon-rich gas product. After passing through a scrubber, the ...

  15. Gas phase hydrogen peroxide production in atmospheric pressure glow discharges operating in He - H2O

    NARCIS (Netherlands)

    Vasko, C.A.; Veldhuizen, van E.M.; Bruggeman, P.J.

    2013-01-01

    The gas phase production of hydrogen peroxide (H2O2) in a RF atmospheric pressure glow discharge with helium and water vapour has been investigated as a function of the gas flow. It is shown that the production of H2O2 is through the recombination of two OH radicals in a three body collision and the

  16. Highly Selective Continuous Gas-Phase Methoxycarbonylation of Ethylene with Supported Ionic Liquid Phase (SILP) Catalysts

    DEFF Research Database (Denmark)

    Khokarale, Santosh Govind; Garcia Suárez, Eduardo José; Fehrmann, Rasmus

    2017-01-01

    Supported ionic liquid phase (SILP) technology was applied for the first time to the Pd-catalyzed continuous, gas-phase methoxycarbonylation of ethylene to selectively produce methyl propanoate (MP) in high yields. The influence of catalyst and reaction parameters such as, for example, ionic liquid...

  17. Gas-phase salt bridge interactions between glutamic acid and arginine

    NARCIS (Netherlands)

    Jaeqx, S.; Oomens, J.; Rijs, A.M.

    2013-01-01

    The gas-phase side chain-side chain (SC-SC) interaction and possible proton transfer between glutamic acid (Glu) and arginine (Arg) residues are studied under low-temperature conditions in an overall neutral peptide. Conformation-specific IR spectra, obtained with the free electron laser FELIX, in

  18. Humidity independent mass spectrometry for gas phase chemical analysis via ambient proton transfer reaction.

    Science.gov (United States)

    Zhu, Hongying; Huang, Guangming

    2015-03-31

    In this work, a humidity independent mass spectrometric method was developed for rapid analysis of gas phase chemicals. This method is based upon ambient proton transfer reaction between gas phase chemicals and charged water droplets, in a reaction chamber with nearly saturate humidity under atmospheric pressure. The humidity independent nature enables direct and rapid analysis of raw gas phase samples, avoiding time- and sample-consuming sample pretreatments in conventional mass spectrometry methods to control sample humidity. Acetone, benzene, toluene, ethylbenzene and meta-xylene were used to evaluate the analytical performance of present method. The limits of detection for benzene, toluene, ethylbenzene and meta-xylene are in the range of ∼0.1 to ∼0.3 ppbV; that of benzene is well below the present European Union permissible exposure limit for benzene vapor (5 μg m(-3), ∼1.44 ppbV), with linear ranges of approximately two orders of magnitude. The majority of the homemade device contains a stainless steel tube as reaction chamber and an ultrasonic humidifier as the source of charged water droplets, which makes this cheap device easy to assemble and facile to operate. In addition, potential application of this method was illustrated by the real time identification of raw gas phase chemicals released from plants at different physiological stages. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Ab initio study of gas phase and water-assisted tautomerization of ...

    Indian Academy of Sciences (India)

    WINTEC

    Water-assisted tautomerization in maleimide and formamide showed that difference in energy barrier reduces to 2⋅83 kcal/mol from 10⋅41 kcal/mol (in gas phase) at B3LYP level, which resulted that maleimide readily undergoes tautomerization in water molecule. Keywords. Ab Initio calculations; maleimide; formamide; ...

  20. Continuous gas-phase hydroformylation of 1-butene using supported ionic liquid phase (SILP) catalysts

    DEFF Research Database (Denmark)

    Haumann, Marco; Dentler, Katharina; Joni, Joni

    2007-01-01

    The concept of supported ionic liquid phase (SILP) catalysis has been extended to 1-butene hydroformylation. A rhodium-sulfoxantphos complex was dissolved in [BMIM][n-C8H17OSO3] and this solution was highly dispersed on silica. Continuous gas-phase experiments in a fixed-bed reactor revealed...

  1. Gas-phase UF6 enrichment monitor for enrichment plant safeguards

    International Nuclear Information System (INIS)

    Strittmatter, R.B.; Tape, J.W.

    1980-03-01

    An in-line enrichment monitor is being developed to provide real-time enrichment data for the gas-phase UF 6 feed stream of an enrichment plant. The nondestructive gamma-ray assay method can be used to determine the enrichment of natural UF 6 with a relative precision of better than 1% for a wide range of pressures

  2. Mid-IR spectra of different conformers of phenylalanine in the gas phase

    NARCIS (Netherlands)

    von Helden, G.; Compagnon, I.; Blom, M. N.; Frankowski, M.; Erlekam, U.; Oomens, J.; Brauer, B.; Gerber, R. B.; Meijer, G.

    2008-01-01

    The experimental mid- and far-IR spectra of six conformers of phenylalanine in the gas phase are presented. The experimental spectra are compared to spectra calculated at the B3LYP and at the MP2 level. The differences between B3LYP and MP2 IR spectra are found to be small. The agreement between

  3. Operando Spectroscopy of the Gas-Phase Aldol Condensation of Propanal over Solid Base Catalysts

    NARCIS (Netherlands)

    Hernández-giménez, Ana M.; Ruiz-martínez, Javier; Puértolas, Begoña; Pérez-ramírez, Javier; Bruijnincx, Pieter C. A.; Weckhuysen, Bert M.

    2017-01-01

    The gas-phase aldol condensation of propanal, taken as model for the aldehyde components in bio-oils, has been studied with a combined operando set-up allowing to perform FT-IR & UV–Vis diffuse reflectance spectroscopy (DRS) with on-line mass spectrometry (MS). The selected solid base catalysts, a

  4. Gas-Phase Oxidation of Aqueous Ethanol by Nanoparticle Vanadia/Anatase Catalysts

    DEFF Research Database (Denmark)

    Jørgensen, Betina; Kristensen, Steffen Buus; Kunov-Kruse, Andreas Jonas

    2009-01-01

    The gas-phase oxidation of aqueous ethanol with dioxygen has been examined with a new nanoparticle V2O5/TiO2 catalyst. Product selectivity could to a large extent be controlled by small alterations of reaction parameters, allowing production of acetaldehyde at a selectivity higher than 90%, near...

  5. Study of Iodine Behavior in the Gas Phase during a Severe Accident

    International Nuclear Information System (INIS)

    Kim, Hanchul; Cho, Yeonghun; Ryu, Myunghyun

    2014-01-01

    Among the iodine species, the organic iodides produced from the reaction between iodine and organics such as paint, are not easily trapped by the filters during the containment venting following a severe accident. Korea Institute of Nuclear Safety (KINS) has been studying this issue, joining international research programs such as ISTP-EPICUR, OECDBIP and OECD-STEM. In the course of this study, a simple iodine model, RAIM (Radio-Active Iodine chemistry Model) has been developed (Oh et al., 2011), based on the IMOD methodology, and other previous studies. This paper deals with our recent activities on this study, including the development of the model for the iodine reactions in gas phase. Iodine reactions in gas phase were modeled and added to the RAIM code, taking into account several relevant reactions such as formation of ARP, iodine oxide, and organic iodides in gas phase. RAIM was then applied to analyze the S2-6-5-2 test for which iodine-loaded coupons were tested in gas phase. The analysis results show a reasonable estimation of volatile iodine concentration with the desorption rate constant of about 10 -6 s -1 , while those of the other iodine species overestimated for the whole period of the test. It reveals the need to determine appropriate values for the rate constants for formation of iodine oxides and organic iodides

  6. Gas-phase synthesis of magnesium nanoparticles : A high-resolution transmission electron microscopy study

    NARCIS (Netherlands)

    Kooi, B.J.; Palasantzas, G.; de Hosson, J.T.M.

    2006-01-01

    Magnesium nanoparticles with size above 10 nm, prepared by gas-phase syntheses, were investigated by high-resolution transmission electron microscopy. The dominant particle shape is a hexagonal prism terminated by Mg(0002) and Mg{1010} facets. Oxidation of Mg yields a MgO shell (similar to 3 nm

  7. Supported Rh-phosphine complex catalysts for continuous gas-phase decarbonylation of aldehydes

    DEFF Research Database (Denmark)

    Malcho, Phillip; Garcia-Suarez, Eduardo J.; Mentzel, Uffe Vie

    2014-01-01

    Heterogeneous silica supported rhodium-phosphine complex catalysts are employed for the first time in the catalytic decarbonylation of aldehydes in continuous gas-phase. The reaction protocol is exemplified for the decarbonylation of p-tolualdehyde to toluene and further extended to other aromatic...

  8. Hydrocarbon fuels from gas phase decarboxylation of hydrolyzed free fatty acid

    KAUST Repository

    Wang, Weicheng; Roberts, William L.; Stikeleather, Larry F.

    2012-01-01

    Gas phase decarboxylation of hydrolyzed free fatty acid (FFA) from canola oil has beeninvestigated in two fix-bed reactors by changing reaction parameters such as temperatures,FFA feed rates, and H 2-to-FFA molar ratios. FFA, which contains mostly C

  9. Gas phase polymerization of propylene. Reaction kinetics and molecular weight distribution

    NARCIS (Netherlands)

    Meier, G.B.; Weickert, G.; van Swaaij, Willibrordus Petrus Maria

    2001-01-01

    Gas-phase polymerizations have been executed at different temperatures, pressures, and hydrogen concentrations using Me2Si[Ind]2ZrCl2 / methylaluminoxane / SiO2(Pennsylvania Quarts) as a catalyst. The reaction rate curves have been described by a kinetic model, which takes into account the initially

  10. Why do disk galaxies present a common gas-phase metallicity gradient?

    Science.gov (United States)

    Chang, R.; Zhang, Shuhui; Shen, Shiyin; Yin, Jun; Hou, Jinliang

    2017-03-01

    CALIFA data show that isolated disk galaxies present a common gas-phase metallicity gradient, with a characteristic slope of -0.1dex/re between 0.3 and 2 disk effective radius re (Sanchez et al. 2014). Here we construct a simple model to investigate which processes regulate the formation and evolution.

  11. Gas-phase photoemission with soft x-rays: cross sections and angular distributions

    International Nuclear Information System (INIS)

    Shirley, D.A.; Kobrin, P.H.; Truesdale, C.M.; Lindle, D.W.; Ferrett, T.A.; Heimann, P.A.; Becker, U.; Kerkhoff, H.G.; Southworth, S.H.

    1983-09-01

    A summary is presented of typical gas-phase photoemission studies based on synchrotron radiation in the 50-5000 eV range, using beam lines at the Stanford Synchrotron Radiation Laboratory. Three topics are addressed: atomic inner-shell photoelectron cross sections and asymmetries, correlation peaks in rare gases, and core-level shape resonances in molecules

  12. Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry.

    Science.gov (United States)

    Wang, Guanbo; Kaltashov, Igor A

    2014-08-05

    Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting factors. While the limitations imposed by the physical size of the proteins gradually become more relaxed as the sensitivity, resolution and dynamic range of modern MS instrumentation continue to improve at an ever accelerating pace, the presence of the disulfide linkages remains a much less forgiving limitation even for the proteins of relatively modest size. To circumvent this problem, we introduce an online chemical reduction step following completion and quenching of the HDX reactions and prior to the top-down MS measurements of deuterium occupancy of individual backbone amides. Application of the new methodology to the top-down HDX MS characterization of a small (99 residue long) disulfide-containing protein β2-microglobulin allowed the backbone amide protection to be probed with nearly a single-residue resolution across the entire sequence. The high-resolution backbone protection pattern deduced from the top-down HDX MS measurements carried out under native conditions is in excellent agreement with the crystal structure of the protein and high-resolution NMR data, suggesting that introduction of the chemical reduction step to the top-down routine does not trigger hydrogen scrambling either during the electrospray ionization process or in the gas phase prior to the protein ion dissociation.

  13. Bayesian comparison of protein structures using partial Procrustes distance.

    Science.gov (United States)

    Ejlali, Nasim; Faghihi, Mohammad Reza; Sadeghi, Mehdi

    2017-09-26

    An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.

  14. Structural and Functional Annotation of Hypothetical Proteins of O139

    Directory of Open Access Journals (Sweden)

    Md. Saiful Islam

    2015-06-01

    Full Text Available In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

  15. Structural study of surfactant-dependent interaction with protein

    Energy Technology Data Exchange (ETDEWEB)

    Mehan, Sumit; Aswal, Vinod K., E-mail: vkaswal@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085 (India); Kohlbrecher, Joachim [Laboratory for Neutron Scattering, Paul Scherrer Institut, CH-5232 PSI Villigen (Switzerland)

    2015-06-24

    Small-angle neutron scattering (SANS) has been used to study the complex structure of anionic BSA protein with three different (cationic DTAB, anionic SDS and non-ionic C12E10) surfactants. These systems form very different surfactant-dependent complexes. We show that the structure of protein-surfactant complex is initiated by the site-specific electrostatic interaction between the components, followed by the hydrophobic interaction at high surfactant concentrations. It is also found that hydrophobic interaction is preferred over the electrostatic interaction in deciding the resultant structure of protein-surfactant complexes.

  16. Diffusion Monte Carlo simulations of gas phase and adsorbed D2-(H2)n clusters

    Science.gov (United States)

    Curotto, E.; Mella, M.

    2018-03-01

    We have computed ground state energies and analyzed radial distributions for several gas phase and adsorbed D2(H2)n and HD(H2)n clusters. An external model potential designed to mimic ionic adsorption sites inside porous materials is used [M. Mella and E. Curotto, J. Phys. Chem. A 121, 5005 (2017)]. The isotopic substitution lowers the ground state energies by the expected amount based on the mass differences when these are compared with the energies of the pure clusters in the gas phase. A similar impact is found for adsorbed aggregates. The dissociation energy of D2 from the adsorbed clusters is always much higher than that of H2 from both pure and doped aggregates. Radial distributions of D2 and H2 are compared for both the gas phase and adsorbed species. For the gas phase clusters, two types of hydrogen-hydrogen interactions are considered: one based on the assumption that rotations and translations are adiabatically decoupled and the other based on nonisotropic four-dimensional potential. In the gas phase clusters of sufficiently large size, we find the heavier isotopomer more likely to be near the center of mass. However, there is a considerable overlap among the radial distributions of the two species. For the adsorbed clusters, we invariably find the heavy isotope located closer to the attractive interaction source than H2, and at the periphery of the aggregate, H2 molecules being substantially excluded from the interaction with the source. This finding rationalizes the dissociation energy results. For D2-(H2)n clusters with n ≥12 , such preference leads to the desorption of D2 from the aggregate, a phenomenon driven by the minimization of the total energy that can be obtained by reducing the confinement of (H2)12. The same happens for (H2)13, indicating that such an effect may be quite general and impact on the absorption of quantum species inside porous materials.

  17. The Stability of CI02 as a Product of Gas Phase Decontamination Treatments

    International Nuclear Information System (INIS)

    Simmons, D. W.

    1994-01-01

    The gas phase decontamination project is investigating the use of chlorine trifluoride (ClF 3 ) to fluorinate nonvolatile uranium deposits to produce uranium hexafluoride (UF 6 ) gas. The potential existence of chlorine dioxide (ClO 2 ) during gas phase decontamination with ClF 3 has been the subject of recent safety discussions. Some of the laboratory data collected during feasibility studies of the gas phase process has been evaluated for the presence of ClO 2 in the product gas stream. The preliminary evidence to date can be summarized as follows: (1) ClO 2 was not detected in the flow loop in the absence of ClF 3 ; (2) ClO 2 was not detected in the static reactors in the absence of both ClF 3 and ClF; and (3) ClO 2 was detected in a static reactor in the absence of all fluorinating gases. The experimental evidence suggests that ClO 2 will not exist in the presence of ClF 3 , ClF, or UF 6 . The data analyzed to date is insufficient to determine the stability of ClO 2 in the presence of ClO 2 F. Thermodynamic calculations of the ClF 3 + H 2 O system support the experimental evidence, and suggest that ClO 2 will not exist in the presence of ClO 2 F. Additional experimental efforts are needed to provide a better understanding of the gas phase ClF 3 treatments and the product gases. However, preliminary evidence to date suggests that ClO 2 should not be present as a product during the normal operations of the gas phase decontamination project

  18. The Stability of CI02 as a Product of Gas Phase Decontamination Treatments

    Energy Technology Data Exchange (ETDEWEB)

    D. W. Simmons

    1994-09-01

    The gas phase decontamination project is investigating the use of chlorine trifluoride (ClF{sub 3}) to fluorinate nonvolatile uranium deposits to produce uranium hexafluoride (UF{sub 6}) gas. The potential existence of chlorine dioxide (ClO{sub 2}) during gas phase decontamination with ClF{sub 3} has been the subject of recent safety discussions. Some of the laboratory data collected during feasibility studies of the gas phase process has been evaluated for the presence of ClO{sub 2} in the product gas stream. The preliminary evidence to date can be summarized as follows: (1) ClO{sub 2} was not detected in the flow loop in the absence of ClF{sub 3}; (2) ClO{sub 2} was not detected in the static reactors in the absence of both ClF{sub 3} and ClF; and (3) ClO{sub 2} was detected in a static reactor in the absence of all fluorinating gases. The experimental evidence suggests that ClO{sub 2} will not exist in the presence of ClF{sub 3}, ClF, or UF{sub 6}. The data analyzed to date is insufficient to determine the stability of ClO{sub 2} in the presence of ClO{sub 2}F. Thermodynamic calculations of the ClF{sub 3} + H{sub 2}O system support the experimental evidence, and suggest that ClO{sub 2} will not exist in the presence of ClO{sub 2}F. Additional experimental efforts are needed to provide a better understanding of the gas phase ClF{sub 3} treatments and the product gases. However, preliminary evidence to date suggests that ClO{sub 2} should not be present as a product during the normal operations of the gas phase decontamination project.

  19. Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

    Directory of Open Access Journals (Sweden)

    Bradley Michael E

    2006-02-01

    Full Text Available Abstract Background When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1 multiple sequence alignments, 2 mapping of alignment sites to crystal structure sites, 3 phylogenetic trees, 4 inferred ancestral sequences at internal tree nodes, and 5 amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. Conclusion We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural

  20. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

    KAUST Repository

    Najibi, Seyed Morteza

    2017-02-08

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  1. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

    KAUST Repository

    Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z.; Gao, Xin

    2017-01-01

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  2. Generation, Detection and characterization of Gas-Phase Transition Metal containing Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Steimle, Timothy [Arizona State Univ., Tempe, AZ (United States)

    2015-12-15

    The objective of this project was to generate, detect, and characterize small, gas-phase, metal containing molecules. In addition to being relevant to high temperature chemical environments (e.g. plasmas and combustion), gas-phase experiments on metal containing molecules serve as the most direct link to a molecular-level theoretical model for catalysis. Catalysis (i.e. the addition of a small about of recoverable material to control the rate and direction of a chemical reaction) is critical to the petroleum and pharmaceutical industries as well as environmental remediation. Currently, the majority of catalytic materials are based on very expensive metals such as platinum (Pt), palladium (Pd), iridium (Ir,) rhenium (Re), and rhodium (Rh). For example, the catalyst used for converting linear hydrocarbon molecules (e.g. hexane) to cyclic molecules (e.g. cyclohexane) is a mixture of Pt and Re suspended on alumina. It enables straight chain alkanes to be converted into branched-chain alkanes, cyclohexanes and aromatic hydrocarbons which are used, amongst other things, to enhance the octane number of petrol. A second example is the heterogeneous catalysis used in automobile exhaust systems to: a) decrease nitrogen oxide; b) reduce carbon monoxide; and c) oxidize unburned hydrocarbons. The exhaust is vented through a high-surface area chamber lined with Pt, Pd, and Rh. For example, the carbon monoxide is catalytically converted to carbon dioxide by reaction with oxygen. The research results from this work have been published in readily accessible journals1-28. The ground and excited electronic state properties of small metal containing molecules that we determine were: a) electronic state distributions and lifetimes, b) vibrational frequencies, c) bond lengths and angles, d) hyperfine interactions, e) permanent electric dipole moments, mel, and f) magnetic dipoles, μm. In general terms, μel, gives insight into the charge distribution and mm into

  3. 3D complex: a structural classification of protein complexes.

    Directory of Open Access Journals (Sweden)

    Emmanuel D Levy

    2006-11-01

    Full Text Available Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes.

  4. Protein structure determination by exhaustive search of Protein Data Bank derived databases.

    Science.gov (United States)

    Stokes-Rees, Ian; Sliz, Piotr

    2010-12-14

    Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.

  5. Topological properties of complex networks in protein structures

    Science.gov (United States)

    Kim, Kyungsik; Jung, Jae-Won; Min, Seungsik

    2014-03-01

    We study topological properties of networks in structural classification of proteins. We model the native-state protein structure as a network made of its constituent amino-acids and their interactions. We treat four structural classes of proteins composed predominantly of α helices and β sheets and consider several proteins from each of these classes whose sizes range from amino acids of the Protein Data Bank. Particularly, we simulate and analyze the network metrics such as the mean degree, the probability distribution of degree, the clustering coefficient, the characteristic path length, the local efficiency, and the cost. This work was supported by the KMAR and DP under Grant WISE project (153-3100-3133-302-350).

  6. Relationship between Molecular Structure Characteristics of Feed Proteins and Protein In vitro Digestibility and Solubility.

    Science.gov (United States)

    Bai, Mingmei; Qin, Guixin; Sun, Zewei; Long, Guohui

    2016-08-01

    The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller's dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR) spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as α-helices and β-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area) of feed proteins were correlated with their the in vitro digestibility and solubility (p≤0.003); moreover, the relatively quantitative amounts of α-helices, random coils, and α-helix to β-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility (p≤0.004). On the other hand, the percentage of β-sheet structures was negatively correlated with protein in vitro digestibility (pdigestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins.

  7. A Numerical Study on Effect of Gas-Phase Radiative Heat Loss on Extinction of Hydrogen Diffusion Flames

    International Nuclear Information System (INIS)

    Sohn, Chae Hoon

    2007-01-01

    Extinction characteristics of hydrogen-air diffusion flames are investigated numerically by adopting counterflow flame configuration. At various pressures, effect of radiative heat loss on flame extinction is examined. Only gas-phase radiation is considered here. Radiative heat loss depends on flame thickness, temperature, H 2 O concentration, and pressure. From flame structures at various pressures, flame thickness decreases with pressure, but its gradient decreases at high pressure. Flame temperature and mole fraction of H 2 O increase slightly with pressure. Accordingly, as pressure increases, radiative heat loss becomes dominant. When radiative heat loss is considered, radiation-induced extinction is observed at low strain rate in addition to transport-induced extinction. As pressure increases, flammable region shifts to the high-temperature region and then, shrunk to the point on the coordinate plane of flame temperature and strain rate

  8. The gas-phase on-line production of vanadium oxytrihalides, VOX3 and their identification by infrared spectroscopy

    International Nuclear Information System (INIS)

    Zidan, M. D.; Allaf, A. W.

    2001-01-01

    A new route has been devised, leading to the production of VOX 3 molecules where X=F, Br and I by an on-line process using vanadium oxytrichloride, VOCl 3 as a starting compound passed over the following heated salts NaF, KBr and KI at 375, 700 and 550 centigrade, respectively. The products have been characterized by the IR spectra of their vapors. the low resolution gas phase on-line Fourier transform infrared spectra reported for the first time show strong bands with PQR type structure, centered at 1058, 1035, 1030 and 1025 cm -1 to the υ 1 (a 1 ), the O=V stretching fundamental mode of VOF 3 , VOCl 3 , VOBr 3 and VOI 3 , respectively. (Author)

  9. Density Functional Theory Study of Competitive Reaction Pathways of Ti+ with Fluorinated Acetone in the Gas Phase

    International Nuclear Information System (INIS)

    Hong, Kiryong; Kim, Tae Kyu

    2012-01-01

    We investigate the doublet and quartet potential energy surfaces associated with the gas-phase reaction between Ti + and CF 3 COCH 3 for two plausible reaction pathways, TiF 2 + and TiO + formation pathways by using the density functional theory (DFT) method. The molecular structures of intermediates and transition states involved in these reaction pathways are optimized at the DFT level by using the PBE0 functional. All transition states are identified by using the intrinsic reaction coordinate (IRC) method, and the resulting reaction coordinates describe how Ti + activates CF 3 COCH 3 and produces TiF 2 + and TiO + as products. On the basis of presented results, we propose the most favorable reaction pathway in the reaction between Ti + and CF 3 COCH 3

  10. Effects of NMR spectral resolution on protein structure calculation.

    Directory of Open Access Journals (Sweden)

    Suhas Tikole

    Full Text Available Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.

  11. Structural and Function Prediction of Musa acuminata subsp. Malaccensis Protein

    Directory of Open Access Journals (Sweden)

    Anum Munir

    2016-03-01

    Full Text Available Hypothetical proteins (HPs are the proteins whose presence has been anticipated, yet in vivo function has not been built up. Illustrating the structural and functional privileged insights of these HPs might likewise prompt a superior comprehension of the protein-protein associations or networks in diverse types of life. Bananas (Musa acuminata spp., including sweet and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister grouped to the all-around considered Poales, which incorporate oats. Bananas are crucial for nourishment security in numerous tropical and subtropical nations and the most prominent organic product in industrialized nations. In the present study, the hypothetical protein of M. acuminata (Banana was chosen for analysis and modeling by distinctive bioinformatics apparatuses and databases. As indicated by primary and secondary structure analysis, XP_009393594.1 is a stable hydrophobic protein containing a noteworthy extent of α-helices; Homology modeling was done utilizing SWISS-MODEL server where the templates identity with XP_009393594.1 protein was less which demonstrated novelty of our protein. Ab initio strategy was conducted to produce its 3D structure. A few evaluations of quality assessment and validation parameters determined the generated protein model as stable with genuinely great quality. Functional analysis was completed by ProtFun 2.2, and KEGG (KAAS, recommended that the hypothetical protein is a transcription factor with cytoplasmic domain as zinc finger. The protein was observed to be vital for translation process, involved in metabolism, signaling and cellular processes, genetic information processing and Zinc ion binding. It is suggested that further test approval would help to anticipate the structures and functions of other uncharacterized proteins of different plants and living being.

  12. Structural basis for target protein recognition by the protein disulfide reductase thioredoxin

    DEFF Research Database (Denmark)

    Maeda, Kenji; Hägglund, Per; Finnie, Christine

    2006-01-01

    Thioredoxin is ubiquitous and regulates various target proteins through disulfide bond reduction. We report the structure of thioredoxin (HvTrxh2 from barley) in a reaction intermediate complex with a protein substrate, barley alpha-amylase/subtilisin inhibitor (BASI). The crystal structure...... of this mixed disulfide shows a conserved hydrophobic motif in thioredoxin interacting with a sequence of residues from BASI through van der Waals contacts and backbone-backbone hydrogen bonds. The observed structural complementarity suggests that the recognition of features around protein disulfides plays...... a major role in the specificity and protein disulfide reductase activity of thioredoxin. This novel insight into the function of thioredoxin constitutes a basis for comprehensive understanding of its biological role. Moreover, comparison with structurally related proteins shows that thioredoxin shares...

  13. Structural studies of human glioma pathogenesis-related protein 1

    Energy Technology Data Exchange (ETDEWEB)

    Asojo, Oluwatoyin A., E-mail: oasojo@unmc.edu [College of Medicine, Nebraska Medical Center, Omaha, NE 68198-6495 (United States); Koski, Raymond A.; Bonafé, Nathalie [L2 Diagnostics LLC, 300 George Street, New Haven, CT 06511 (United States); College of Medicine, Nebraska Medical Center, Omaha, NE 68198-6495 (United States)

    2011-10-01

    Structural analysis of a truncated soluble domain of human glioma pathogenesis-related protein 1, a membrane protein implicated in the proliferation of aggressive brain cancer, is presented. Human glioma pathogenesis-related protein 1 (GLIPR1) is a membrane protein that is highly upregulated in brain cancers but is barely detectable in normal brain tissue. GLIPR1 is composed of a signal peptide that directs its secretion, a conserved cysteine-rich CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) domain and a transmembrane domain. GLIPR1 is currently being investigated as a candidate for prostate cancer gene therapy and for glioblastoma targeted therapy. Crystal structures of a truncated soluble domain of the human GLIPR1 protein (sGLIPR1) solved by molecular replacement using a truncated polyalanine search model of the CAP domain of stecrisp, a snake-venom cysteine-rich secretory protein (CRISP), are presented. The correct molecular-replacement solution could only be obtained by removing all loops from the search model. The native structure was refined to 1.85 Å resolution and that of a Zn{sup 2+} complex was refined to 2.2 Å resolution. The latter structure revealed that the putative binding cavity coordinates Zn{sup 2+} similarly to snake-venom CRISPs, which are involved in Zn{sup 2+}-dependent mechanisms of inflammatory modulation. Both sGLIPR1 structures have extensive flexible loop/turn regions and unique charge distributions that were not observed in any of the previously reported CAP protein structures. A model is also proposed for the structure of full-length membrane-bound GLIPR1.

  14. Structure and function of nanoparticle-protein conjugates

    International Nuclear Information System (INIS)

    Aubin-Tam, M-E; Hamad-Schifferli, K

    2008-01-01

    Conjugation of proteins to nanoparticles has numerous applications in sensing, imaging, delivery, catalysis, therapy and control of protein structure and activity. Therefore, characterizing the nanoparticle-protein interface is of great importance. A variety of covalent and non-covalent linking chemistries have been reported for nanoparticle attachment. Site-specific labeling is desirable in order to control the protein orientation on the nanoparticle, which is crucial in many applications such as fluorescence resonance energy transfer. We evaluate methods for successful site-specific attachment. Typically, a specific protein residue is linked directly to the nanoparticle core or to the ligand. As conjugation often affects the protein structure and function, techniques to probe structure and activity are assessed. We also examine how molecular dynamics simulations of conjugates would complete those experimental techniques in order to provide atomistic details on the effect of nanoparticle attachment. Characterization studies of nanoparticle-protein complexes show that the structure and function are influenced by the chemistry of the nanoparticle ligand, the nanoparticle size, the nanoparticle material, the stoichiometry of the conjugates, the labeling site on the protein and the nature of the linkage (covalent versus non-covalent)

  15. Pushing the frontiers of atomic models for protein tertiary structure ...

    Indian Academy of Sciences (India)

    as an NP complete or NP hard problem.4,5 This notwith- standing, the dire need for tertiary structures of proteins in drug discovery and other areas6–8 has propelled the development of a multitude of computational recipes. In this article, we focus on ab initio/de novo strategies,. Bhageerath in particular, for protein tertiary ...

  16. Computing a new family of shape descriptors for protein structures

    DEFF Research Database (Denmark)

    Røgen, Peter; Sinclair, Robert

    2003-01-01

    The large-scale 3D structure of a protein can be represented by the polygonal curve through the carbon a atoms of the protein backbone. We introduce an algorithm for computing the average number of times that a given configuration of crossings on such polygonal curves is seen, the average being...

  17. Simulation of Protein Structure, Dynamics and Function in Organic Media

    National Research Council Canada - National Science Library

    Daggett, Valerie

    1998-01-01

    The overall goal of our ONR-sponsored research is to pursue realistic molecular modeling strudies pertinnent to the related properties of protein stability, dynamics, structure, function, and folding in aqueous solution...

  18. Protein structure estimation from NMR data by matrix completion.

    Science.gov (United States)

    Li, Zhicheng; Li, Yang; Lei, Qiang; Zhao, Qing

    2017-09-01

    Knowledge of protein structures is very important to understand their corresponding physical and chemical properties. Nuclear Magnetic Resonance (NMR) spectroscopy is one of the main methods to measure protein structure. In this paper, we propose a two-stage approach to calculate the structure of a protein from a highly incomplete distance matrix, where most data are obtained from NMR. We first randomly "guess" a small part of unobservable distances by utilizing the triangle inequality, which is crucial for the second stage. Then we use matrix completion to calculate the protein structure from the obtained incomplete distance matrix. We apply the accelerated proximal gradient algorithm to solve the corresponding optimization problem. Furthermore, the recovery error of our method is analyzed, and its efficiency is demonstrated by several practical examples.

  19. Modeling membrane protein structure through site-directed ESR spectroscopy

    NARCIS (Netherlands)

    Kavalenka, A.A.

    2009-01-01

    Site-directed spin labeling (SDSL) electron spin resonance (ESR) spectroscopy is a
    relatively new biophysical tool for obtaining structural information about proteins. This
    thesis presents a novel approach, based on powerful spectral analysis techniques (multicomponent
    spectral

  20. Computational design of proteins with novel structure and functions

    International Nuclear Information System (INIS)

    Yang Wei; Lai Lu-Hua

    2016-01-01

    Computational design of proteins is a relatively new field, where scientists search the enormous sequence space for sequences that can fold into desired structure and perform desired functions. With the computational approach, proteins can be designed, for example, as regulators of biological processes, novel enzymes, or as biotherapeutics. These approaches not only provide valuable information for understanding of sequence–structure–function relations in proteins, but also hold promise for applications to protein engineering and biomedical research. In this review, we briefly introduce the rationale for computational protein design, then summarize the recent progress in this field, including de novo protein design, enzyme design, and design of protein–protein interactions. Challenges and future prospects of this field are also discussed. (topical review)

  1. Potato leafroll virus structural proteins manipulate overlapping, yet distinct protein interaction networks during infection.

    Science.gov (United States)

    DeBlasio, Stacy L; Johnson, Richard; Sweeney, Michelle M; Karasev, Alexander; Gray, Stewart M; MacCoss, Michael J; Cilia, Michelle

    2015-06-01

    Potato leafroll virus (PLRV) produces a readthrough protein (RTP) via translational readthrough of the coat protein amber stop codon. The RTP functions as a structural component of the virion and as a nonincorporated protein in concert with numerous insect and plant proteins to regulate virus movement/transmission and tissue tropism. Affinity purification coupled to quantitative MS was used to generate protein interaction networks for a PLRV mutant that is unable to produce the read through domain (RTD) and compared to the known wild-type PLRV protein interaction network. By quantifying differences in the protein interaction networks, we identified four distinct classes of PLRV-plant interactions: those plant and nonstructural viral proteins interacting with assembled coat protein (category I); plant proteins in complex with both coat protein and RTD (category II); plant proteins in complex with the RTD (category III); and plant proteins that had higher affinity for virions lacking the RTD (category IV). Proteins identified as interacting with the RTD are potential candidates for regulating viral processes that are mediated by the RTP such as phloem retention and systemic movement and can potentially be useful targets for the development of strategies to prevent infection and/or viral transmission of Luteoviridae species that infect important crop species. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Binding free energy analysis of protein-protein docking model structures by evERdock.

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-14

    To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

  3. Constraining cyclic peptides to mimic protein structure motifs

    DEFF Research Database (Denmark)

    Hill, Timothy A.; Shepherd, Nicholas E.; Diness, Frederik

    2014-01-01

    peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides...... and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic pepti-domimetics that refine peptide structure and confer biological properties....

  4. Overcoming bottlenecks in the membrane protein structural biology pipeline.

    Science.gov (United States)

    Hardy, David; Bill, Roslyn M; Jawhari, Anass; Rothnie, Alice J

    2016-06-15

    Membrane proteins account for a third of the eukaryotic proteome, but are greatly under-represented in the Protein Data Bank. Unfortunately, recent technological advances in X-ray crystallography and EM cannot account for the poor solubility and stability of membrane protein samples. A limitation of conventional detergent-based methods is that detergent molecules destabilize membrane proteins, leading to their aggregation. The use of orthologues, mutants and fusion tags has helped improve protein stability, but at the expense of not working with the sequence of interest. Novel detergents such as glucose neopentyl glycol (GNG), maltose neopentyl glycol (MNG) and calixarene-based detergents can improve protein stability without compromising their solubilizing properties. Styrene maleic acid lipid particles (SMALPs) focus on retaining the native lipid bilayer of a membrane protein during purification and biophysical analysis. Overcoming bottlenecks in the membrane protein structural biology pipeline, primarily by maintaining protein stability, will facilitate the elucidation of many more membrane protein structures in the near future. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  5. Illuminating structural proteins in viral "dark matter" with metaproteomics.

    Science.gov (United States)

    Brum, Jennifer R; Ignacio-Espinoza, J Cesar; Kim, Eun-Hae; Trubl, Gareth; Jones, Robert M; Roux, Simon; VerBerkmoes, Nathan C; Rich, Virginia I; Sullivan, Matthew B

    2016-03-01

    Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional "viral dark matter." Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional dark matter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over one-half of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore, four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world's oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Together, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter.

  6. Functional diversification of structurally alike NLR proteins in plants.

    Science.gov (United States)

    Chakraborty, Joydeep; Jain, Akansha; Mukherjee, Dibya; Ghosh, Suchismita; Das, Sampa

    2018-04-01

    In due course of evolution many pathogens alter their effector molecules to modulate the host plants' metabolism and immune responses triggered upon proper recognition by the intracellular nucleotide-binding oligomerization domain containing leucine-rich repeat (NLR) proteins. Likewise, host plants have also evolved with diversified NLR proteins as a survival strategy to win the battle against pathogen invasion. NLR protein indeed detects pathogen derived effector proteins leading to the activation of defense responses associated with programmed cell death (PCD). In this interactive process, genome structure and plasticity play pivotal role in the development of innate immunity. Despite being quite conserved with similar biological functions in all eukaryotes, the intracellular NLR immune receptor proteins happen to be structurally distinct. Recent studies have made progress in identifying transcriptional regulatory complexes activated by NLR proteins. In this review, we attempt to decipher the intracellular NLR proteins mediated surveillance across the evolutionarily diverse taxa, highlighting some of the recent updates on NLR protein compartmentalization, molecular interactions before and after activation along with insights into the finer role of these receptor proteins to combat invading pathogens upon their recognition. Latest information on NLR sensors, helpers and NLR proteins with integrated domains in the context of plant pathogen interactions are also discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. New set-up for high-quality soft-X-ray absorption spectroscopy of large organic molecules in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Holch, Florian; Huebner, Dominique [Universitaet Wuerzburg, Experimentelle Physik VII, Am and Roentgen Reasearch Center for Complex Materials (RCCM) Hubland, 97074 Wuerzburg (Germany); Fink, Rainer [Universitaet Erlangen-Nuernberg, ICMM and CENEM, Egerlandstrasse 3, 91058 Erlangen (Germany); Schoell, Achim, E-mail: achim.schoell@physik.uni-wuerzburg.de [Universitaet Wuerzburg, Experimentelle Physik VII, Am and Roentgen Reasearch Center for Complex Materials (RCCM) Hubland, 97074 Wuerzburg (Germany); Umbach, Eberhard [Karlsruhe Institute of Technology, 76021 Karlsruhe (Germany)

    2011-11-15

    Highlights: {yields} We present a new set-up for x-ray absorption (NEXAFS) on large molecules in the gas-phase. {yields} The cell has a confined volume and can be heated. {yields} The spectra can be acquired fast, are of very high quality with respect tosignal-to-noise ratio and energy resolution. {yields} This allowsthe analysis of spectroscopic details (e.g. solid state effects by comparing gas- and condensed phase data). - Abstract: We present a new experimental set-up for the investigation of large (>128 amu) organic molecules in the gas-phase by means of near-edge X-ray absorption fine structure spectroscopy in the soft X-ray range. Our approach uses a gas cell, which is sealed off against the surrounding vacuum and which can be heated above the sublimation temperature of the respective molecular compound. Using a confined volume rather than a molecular beam yields short acquisition times and intense signals due to the high molecular density, which can be tuned by the container temperature. In turn, the resulting spectra are of very high quality with respect to signal-to-noise ratio and energy resolution, which are the essential aspects for the analysis of fine spectroscopic details. Using the examples of ANQ, NTCDA, and PTCDA, specific challenges of gas phase measurements on large organic molecules with high sublimation temperatures are addressed in detail with respect to the presented set-up and possible ways to tackle them are outlined.

  8. Combining neural networks for protein secondary structure prediction

    DEFF Research Database (Denmark)

    Riis, Søren Kamaric

    1995-01-01

    In this paper structured neural networks are applied to the problem of predicting the secondary structure of proteins. A hierarchical approach is used where specialized neural networks are designed for each structural class and then combined using another neural network. The submodels are designed...... by using a priori knowledge of the mapping between protein building blocks and the secondary structure and by using weight sharing. Since none of the individual networks have more than 600 adjustable weights over-fitting is avoided. When ensembles of specialized experts are combined the performance...

  9. A generative, probabilistic model of local protein structure

    DEFF Research Database (Denmark)

    Boomsma, Wouter; Mardia, Kanti V.; Taylor, Charles C.

    2008-01-01

    Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. One of the key remaining challenges is an efficient probabilistic exploration of the structural space that correctly reflects the relative...... conformational stabilities. Here, we present a fully probabilistic, continuous model of local protein structure in atomic detail. The generative model makes efficient conformational sampling possible and provides a framework for the rigorous analysis of local sequence-structure correlations in the native state...

  10. SCOWLP classification: Structural comparison and analysis of protein binding regions

    Directory of Open Access Journals (Sweden)

    Anders Gerd

    2008-01-01

    Full Text Available Abstract Background Detailed information about protein interactions is critical for our understanding of the principles governing protein recognition mechanisms. The structures of many proteins have been experimentally determined in complex with different ligands bound either in the same or different binding regions. Thus, the structural interactome requires the development of tools to classify protein binding regions. A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering protein interaction networks, understanding protein function, rational engineering and design. Description Protein binding regions (PBRs might be ideally described as well-defined separated regions that share no interacting residues one another. However, PBRs are often irregular, discontinuous and can share a wide range of interacting residues among them. The criteria to define an individual binding region can be often arbitrary and may differ from other binding regions within a protein family. Therefore, the rational behind protein interface classification should aim to fulfil the requirements of the analysis to be performed. We extract detailed interaction information of protein domains, peptides and interfacial solvent from the SCOWLP database and we classify the PBRs of each domain family. For this purpose, we define a similarity index based on the overlapping of interacting residues mapped in pair-wise structural alignments. We perform our classification with agglomerative hierarchical clustering using the complete-linkage method. Our classification is calculated at different similarity cut-offs to allow flexibility in the analysis of PBRs, feature especially interesting for those protein families with conflictive binding regions

  11. Sequential Release of Proteins from Structured Multishell Microcapsules.

    Science.gov (United States)

    Shimanovich, Ulyana; Michaels, Thomas C T; De Genst, Erwin; Matak-Vinkovic, Dijana; Dobson, Christopher M; Knowles, Tuomas P J

    2017-10-09

    In nature, a wide range of functional materials is based on proteins. Increasing attention is also turning to the use of proteins as artificial biomaterials in the form of films, gels, particles, and fibrils that offer great potential for applications in areas ranging from molecular medicine to materials science. To date, however, most such applications have been limited to single component materials despite the fact that their natural analogues are composed of multiple types of proteins with a variety of functionalities that are coassembled in a highly organized manner on the micrometer scale, a process that is currently challenging to achieve in the laboratory. Here, we demonstrate the fabrication of multicomponent protein microcapsules where the different components are positioned in a controlled manner. We use molecular self-assembly to generate multicomponent structures on the nanometer scale and droplet microfluidics to bring together the different components on the micrometer scale. Using this approach, we synthesize a wide range of multiprotein microcapsules containing three well-characterized proteins: glucagon, insulin, and lysozyme. The localization of each protein component in multishell microcapsules has been detected by labeling protein molecules with different fluorophores, and the final three-dimensional microcapsule structure has been resolved by using confocal microscopy together with image analysis techniques. In addition, we show that these structures can be used to tailor the release of such functional proteins in a sequential manner. Moreover, our observations demonstrate that the protein release mechanism from multishell capsules is driven by the kinetic control of mass transport of the cargo and by the dissolution of the shells. The ability to generate artificial materials that incorporate a variety of different proteins with distinct functionalities increases the breadth of the potential applications of artificial protein-based materials

  12. Structuring oil by protein building blocks

    NARCIS (Netherlands)

    Vries, de Auke

    2017-01-01

    Over the recent years, structuring of oil into ‘organogels’ or ‘oleogels’ has gained much attention amongst colloid-, material,- and food scientists. Potentially, these oleogels could be used as an alternative for saturated- and trans fats in food products. To develop oleogels as a

  13. Mass Spectrometry Coupled Experiments and Protein Structure Modeling Methods

    Directory of Open Access Journals (Sweden)

    Lee Sael

    2013-10-01

    Full Text Available With the accumulation of next generation sequencing data, there is increasing interest in the study of intra-species difference in molecular biology, especially in relation to disease analysis. Furthermore, the dynamics of the protein is being identified as a critical factor in its function. Although accuracy of protein structure prediction methods is high, provided there are structural templates, most methods are still insensitive to amino-acid differences at critical points that may change the overall structure. Also, predicted structures are inherently static and do not provide information about structural change over time. It is challenging to address the sensitivity and the dynamics by computational structure predictions alone. However, with the fast development of diverse mass spectrometry coupled experiments, low-resolution but fast and sensitive structural information can be obtained. This information can then be integrated into the structure prediction process to further improve the sensitivity and address the dynamics of the protein structures. For this purpose, this article focuses on reviewing two aspects: the types of mass spectrometry coupled experiments and structural data that are obtainable through those experiments; and the structure prediction methods that can utilize these data as constraints. Also, short review of current efforts in integrating experimental data in the structural modeling is provided.

  14. Chaperonin Structure - The Large Multi-Subunit Protein Complex

    Directory of Open Access Journals (Sweden)

    Irena Roterman

    2009-03-01

    Full Text Available The multi sub-unit protein structure representing the chaperonins group is analyzed with respect to its hydrophobicity distribution. The proteins of this group assist protein folding supported by ATP. The specific axial symmetry GroEL structure (two rings of seven units stacked back to back - 524 aa each and the GroES (single ring of seven units - 97 aa each polypeptide chains are analyzed using the hydrophobicity distribution expressed as excess/deficiency all over the molecule to search for structure-to-function relationships. The empirically observed distribution of hydrophobic residues is confronted with the theoretical one representing the idealized hydrophobic core with hydrophilic residues exposure on the surface. The observed discrepancy between these two distributions seems to be aim-oriented, determining the structure-to-function relation. The hydrophobic force field structure generated by the chaperonin capsule is presented. Its possible influence on substrate folding is suggested.

  15. NMR structural studies of peptides and proteins in membranes

    Energy Technology Data Exchange (ETDEWEB)

    Opella, S J [Pennsylvania Univ., Philadelphia, PA (United States). Dept. of Chemistry

    1994-12-31

    The use of NMR methodology in structural studies is described as applicable to larger proteins, considering that the majority of membrane proteins is constructed from a limited repertoire of structural and dynamic elements. The membrane associated domains of these proteins are made up of long hydrophobic membrane spanning helices, shorter amphipathic bridging helices in the plane of the bilayer, connecting loops with varying degrees of mobility, and mobile N- and C- terminal sections. NMR studies have been successful in identifying all of these elements and their orientations relative to each other and the membrane bilayer 19 refs., 9 figs.

  16. High throughput platforms for structural genomics of integral membrane proteins.

    Science.gov (United States)

    Mancia, Filippo; Love, James

    2011-08-01

    Structural genomics approaches on integral membrane proteins have been postulated for over a decade, yet specific efforts are lagging years behind their soluble counterparts. Indeed, high throughput methodologies for production and characterization of prokaryotic integral membrane proteins are only now emerging, while large-scale efforts for eukaryotic ones are still in their infancy. Presented here is a review of recent literature on actively ongoing structural genomics of membrane protein initiatives, with a focus on those aimed at implementing interesting techniques aimed at increasing our rate of success for this class of macromolecules. Copyright © 2011 Elsevier Ltd. All rights reserved.

  17. Mining protein loops using a structural alphabet and statistical exceptionality

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2010-02-01

    Full Text Available Abstract Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times. Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words. These structural words have low structural variability (mean RMSd of 0.85 Å. As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues and long loops. Moreover, half of

  18. Mining protein loops using a structural alphabet and statistical exceptionality.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

    2010-02-04

    Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of

  19. Structural protein relationships among eastern equine encephalitis viruses.

    Science.gov (United States)

    Strizki, J M; Repik, P M

    1994-11-01

    We have re-evaluated the relationships among the polypeptides of eastern equine encephalitis (EEE) viruses using SDS-PAGE and peptide mapping of individual virion proteins. Four to five distinct polypeptide bands were detected upon SDS-PAGE analysis of viruses: the E1, E2 and C proteins normally associated with alphavirus virions, as well as an additional more rapidly-migrating E2-associated protein and a high M(r) (HMW) protein. In contrast with previous findings by others, the electrophoretic profiles of the virion proteins of EEE viruses displayed a marked correlation with serotype. The protein profiles of the 33 North American (NA)-serotype viruses examined were remarkably homogeneous, with variation detected only in the E1 protein of two isolates. In contrast, considerable heterogeneity was observed in the migration profiles of both the E1 and E2 glycoproteins of the 13 South American (SA)-type viruses examined. Peptide mapping of individual virion proteins using limited proteolysis with Staphylococcus aureus V8 protease confirmed that, in addition to the homogeneity evident among NA-type viruses and relative heterogeneity among SA-type viruses, the E1 and E2 proteins of NA- and SA-serotype viruses exhibited serotype-specific structural variation. The C protein was highly conserved among isolates of both virus serotypes. Endoglycosidase analyses of intact virions did not reveal substantial glycosylation differences between the glycoproteins of NA- and SA-serotype viruses. Both the HMW protein and the E2 protein (doublet) of EEE virus appeared to contain, at least in part, high-mannose type N-linked oligosaccharides. No evidence of O-linked glycans was found on either the E1 or the E2 glycoprotein. Despite the observed structural differences between proteins of NA- and SA-type viruses, Western blot analyses utilizing polyclonal antibodies indicated that immunoreactive epitopes appeared to be conserved.

  20. An Algebro-Topological Description of Protein Domain Structure

    Science.gov (United States)

    Penner, Robert Clark; Knudsen, Michael; Wiuf, Carsten; Andersen, Jørgen Ellegaard

    2011-01-01

    The space of possible protein structures appears vast and continuous, and the relationship between primary, secondary and tertiary structure levels is complex. Protein structure comparison and classification is therefore a difficult but important task since structure is a determinant for molecular interaction and function. We introduce a novel mathematical abstraction based on geometric topology to describe protein domain structure. Using the locations of the backbone atoms and the hydrogen bonds, we build a combinatorial object – a so-called fatgraph. The description is discrete yet gives rise to a 2-dimensional mathematical surface. Thus, each protein domain corresponds to a particular mathematical surface with characteristic topological invariants, such as the genus (number of holes) and the number of boundary components. Both invariants are global fatgraph features reflecting the interconnectivity of the domain by hydrogen bonds. We introduce the notion of robust variables, that is variables that are robust towards minor changes in the structure/fatgraph, and show that the genus and the number of boundary components are robust. Further, we invesigate the distribution of different fatgraph variables and show how only four variables are capable of distinguishing different folds. We use local (secondary) and global (tertiary) fatgraph features to describe domain structures and illustrate that they are useful for classification of domains in CATH. In addition, we combine our method with two other methods thereby using primary, secondary, and tertiary structure information, and show that we can identify a large percentage of new and unclassified structures in CATH. PMID:21629687

  1. N3 and O2 Protonated Conformers of the Cytosine Mononucleotides Coexist in the Gas Phase

    Science.gov (United States)

    Wu, R. R.; Hamlow, L. A.; He, C. C.; Nei, Y.-w.; Berden, G.; Oomens, J.; Rodgers, M. T.

    2017-08-01

    The gas-phase conformations of the protonated forms of the DNA and RNA cytosine mononucleotides, [pdCyd+H]+ and [pCyd+H]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy over the IR fingerprint and hydrogen-stretching regions complemented by electronic structure calculations. The low-energy conformations of [pdCyd+H]+ and [pCyd+H]+ and their relative stabilities are computed at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparisons of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers allow the conformers present in the experiments to be determined. Similar to that found in previous IRMPD action spectroscopy studies of the protonated forms of the cytosine nucleosides, [dCyd+H]+ and [Cyd+H]+, both N3 and O2 protonated cytosine mononucleotides exhibiting an anti orientation of cytosine are found to coexist in the experimental population. The 2'-hydroxyl substituent does not significantly influence the most stable conformations of [pCyd+H]+ versus those of [pdCyd+H]+, as the IRMPD spectral profiles of [pdCyd+H]+ and [pCyd+H]+ are similar. However, the presence of the 2'-hydroxyl substituent does influence the relative intensities of the measured IRMPD bands. Comparisons to IRMPD spectroscopy studies of the deprotonated forms of the cytosine mononucleotides, [pdCyd-H]- and [pCyd-H]-, provide insight into the effects of protonation versus deprotonation on the conformational features of the nucleobase and sugar moieties. Likewise, comparisons to results of IRMPD spectroscopy studies of the protonated cytosine nucleosides provide insight into the influence of the phosphate moiety on structure. Comparison with previous ion mobility results shows the superiority of IRMPD spectroscopy for distinguishing various protonation sites.

  2. Linking structural features of protein complexes and biological function.

    Science.gov (United States)

    Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

    2015-09-01

    Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

  3. A computer graphics program system for protein structure representation.

    Science.gov (United States)

    Ross, A M; Golub, E E

    1988-01-01

    We have developed a computer graphics program system for the schematic representation of several protein secondary structure analysis algorithms. The programs calculate the probability of occurrence of alpha-helix, beta-sheet and beta-turns by the method of Chou and Fasman and assign unique predicted structure to each residue using a novel conflict resolution algorithm based on maximum likelihood. A detailed structure map containing secondary structure, hydrophobicity, sequence identity, sequence numbering and the location of putative N-linked glycosylation sites is then produced. In addition, helical wheel diagrams and hydrophobic moment calculations can be performed to further analyze the properties of selected regions of the sequence. As they require only structure specification as input, the graphics programs can easily be adapted for use with other secondary structure prediction schemes. The use of these programs to analyze protein structure-function relationships is described and evaluated. PMID:2832829

  4. Crystal structure of Homo sapiens protein LOC79017

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Euiyoung; Bingman, Craig A.; Aceti, David J.; Phillips, Jr., George N. (UW)

    2010-02-08

    LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of them have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).

  5. Deprotonated imidodiphosphate in AMPPNP-containing protein structures

    International Nuclear Information System (INIS)

    Dauter, Miroslawa; Dauter, Zbigniew

    2011-01-01

    In certain AMPPNP-containing protein structures, the nitrogen bridging the two terminal phosphate groups can be deprotonated. Many different proteins utilize the chemical energy provided by the cofactor adenosine triphosphate (ATP) for their proper function. A number of structures in the Protein Data Bank (PDB) contain adenosine 5′-(β,γ-imido)triphosphate (AMPPNP), a nonhydrolysable analog of ATP in which the bridging O atom between the two terminal phosphate groups is substituted by the imido function. Under mild conditions imides do not have acidic properties and thus the imide nitrogen should be protonated. However, an analysis of protein structures containing AMPPNP reveals that the imide group is deprotonated in certain complexes if the negative charges of the phosphate moieties in AMPPNP are in part neutralized by coordinating divalent metals or a guanidinium group of an arginine

  6. EVA: continuous automatic evaluation of protein structure prediction servers.

    Science.gov (United States)

    Eyrich, V A; Martí-Renom, M A; Przybylski, D; Madhusudhan, M S; Fiser, A; Pazos, F; Valencia, A; Sali, A; Rost, B

    2001-12-01

    Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. http://cubic.bioc.columbia.edu/eva. eva@cubic.bioc.columbia.edu

  7. De novo protein structure generation from incomplete chemical shift assignments

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vernon, Robert; Baker, David [University of Washington, Department of Biochemistry and Howard Hughes Medical Institute (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2009-02-15

    NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

  8. Blind Test of Physics-Based Prediction of Protein Structures

    Science.gov (United States)

    Shell, M. Scott; Ozkan, S. Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A.

    2009-01-01

    We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences. PMID:19186130

  9. Relationship between Molecular Structure Characteristics of Feed Proteins and Protein Digestibility and Solubility

    Directory of Open Access Journals (Sweden)

    Mingmei Bai

    2016-08-01

    Full Text Available The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller’s dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as α-helices and β-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area of feed proteins were correlated with their the in vitro digestibility and solubility (p≤0.003; moreover, the relatively quantitative amounts of α-helices, random coils, and α-helix to β-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility (p≤0.004. On the other hand, the percentage of β-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001 and solubility (p = 0.002. These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the α-helix-to-β-sheet ratio can be used to predict the nutritional value of feed proteins.

  10. Characterization of structural proteins of hirame rhabdovirus, HRV

    Science.gov (United States)

    Nishizawa, Toyohiko; Yoshimizu, Mamoru; Winton, James; Ahne, Winfried; Kimura, Takahisa

    1991-01-01

    Structural proteins of hirame rhabdovirus (HRV) were analyzed by SDS-polyacrylarnide gel electrophoresis, western blotting, 2-dimensional gel electrophoresis, and Triton X-100 treatment. Purified HRV virions were composed of: polymerase (L), glycoprotein (G), nucleoprotein (N), and 2 matrix proteins (M1 and M2). Based upon their relative mobilities, the estimated molecular weights of the proteins were: L, 156 KDa; G, 68 KDa; N, 46.4 KDa; M1, 26.4 KDa; and M2, 19.9 KDa. The electrophorehc pattern formed by the structural proteins of HRV was clearly different from that formed by pike fry rhabdovirus, spring viremia of carp virus, eel virus of America, and eel virus European X which belong to the Vesiculovirus genus; however, it resembled the pattern formed by structural proteins of viral hemorrhagic septicemia virus (VHSV) and infectious hematopoietic necrosis virus (IHNV) which are members of the Lyssavirus genus. Among HRV, IHNV, and VHSV, differences were observed in the relative mobilities of the G, N, M1, and M2 proteins. Western blot analysis revealed that the G. N, and M2 proteins of HRV shared antigenic determinants with IHNV and VHSV, but not with any of the 4 fish vesiculoviruses tested. Cross-reactions between the M1 proteins of HRV, IHNV, or VHSV were not detected in this assay. Two-dimensional gel electrophoresis was used to show that HRV differed from IHNV or VHSV in the isoelectric point (PI) of the M1 and M2 proteins. In this system, 2 forms of the M1 protein of HRV and IHNV were observed.These subspecies of M1 had the same relative mobility but different p1 values. Treatment of purified virions with 2% Triton X-100 in Tris buffer containing NaCl removed the G, M1, and M2 proteins of IHNV, but HRV virions were more stable under these conditions.

  11. The vibrational spectra of N-phenylpyrrole in the gas phase, in argon matrices and in single crystals

    International Nuclear Information System (INIS)

    Schweke, D.; Brauer, B.; Gerber, R.B.; Haas, Y.

    2007-01-01

    The infrared spectrum of N-phenylpyrrole (PP) was measured in the gas phase and in an argon matrix, and the Raman spectrum was obtained in a single crystal. The measured matrix shifts are found to be small: many bands are not split, and the shifts from the gas phase values are less than 1%. Splitting to two sub-bands is observed for some bands, indicating the presence of two major trapping sites, in agreement with previous predictions. The spectra are analyzed with the help of harmonic calculations on the free molecule and on its adduct with one or two argon atoms, and anharmonic frequency calculations on the free molecule. Harmonic frequencies were obtained at the MP2/cc-pVDZ and DFT-B3LYP/cc-pVDZ levels. Anharmonic frequencies were obtained by the correlation-corrected vibrational self-consistent field (CC-VSCF) method with a variant of the PM3 semiempirical electronic structure method, calibrated for much improved spectroscopic accuracy. The potential surfaces used in the CC-VSCF calculation obtained by adjusting standard PM3 surfaces so that they provide harmonic frequencies that are comparable to those obtained at the DFT-B3LYP/cc-pVDZ level. Agreement between the experimental and theoretical results is in general very good, allowing the assignments of most bands. The harmonic frequency calculations of PP-Ar clusters, at the MP2/cc-pVDZ level show that the environment can greatly affect the intensities of some of the transitions, which is in accord with experiment

  12. Photodissociative Cross-Linking of Non-covalent Peptide-Peptide Ion Complexes in the Gas Phase

    Science.gov (United States)

    Nguyen, Huong T. H.; Andrikopoulos, Prokopis C.; Rulíšek, Lubomír; Shaffer, Christopher J.; Tureček, František

    2018-05-01

    We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H-X bonds of the target peptide. The cross-link positions were established from collision-induced dissociation tandem mass spectra (CID-MS3) providing sequence information on the covalent adducts. Effects of the amino acid residue (Pro or Phe) and its position in the target peptide sequence were evaluated. For proline-containing peptides, interactions resulting in covalent cross-links in these complexes became more prominent as proline was moved towards the C-terminus of the target peptide sequence. The photocross-linking yields of phenylalanine-containing peptides depended on the position of both phenylalanine and photoleucine. Density functional theory calculations were used to assign structures of low-energy conformers of the (GLPMG + GLL*LK + H)+ complex. Born-Oppenheimer molecular dynamics trajectory calculations were used to capture the thermal motion in the complexes within 100 ps and determine close contacts between the incipient carbene and the H-X bonds in the target peptide. This provided atomic-level resolution of potential cross-links that aided spectra interpretation and was in agreement with experimental data. [Figure not available: see fulltext.

  13. The effect of a micro bubble dispersed gas phase on hydrogen isotope transport in liquid metals under nuclear irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Fradera, J., E-mail: jfradera@ubu.es; Cuesta-López, S., E-mail: scuesta@ubu.es

    2013-12-15

    The present work intend to be a first step towards the understanding and quantification of the hydrogen isotope complex phenomena in liquid metals for nuclear technology. Liquid metals under nuclear irradiation in, e.g., breeding blankets of a nuclear fusion reactor would generate tritium which is to be extracted and recirculated as fuel. At the same time that tritium is bred, helium is also generated and may precipitate in the form of nano bubbles. Other liquid metal systems of a nuclear reactor involve hydrogen isotope absorption processes, e.g., tritium extraction system. Hence, hydrogen isotope absorption into gas bubbles modelling and control may have a capital importance regarding design, operation and safety. Here general models for hydrogen isotopes transport in liquid metal and absorption into gas phase, that do not depend on the mass transfer limiting regime, are exposed and implemented in OpenFOAM® CFD tool for 0D–3D simulations. Results for a 0D case show the impact of a He dispersed phase of nano bubbles on hydrogen isotopes inventory at different temperatures as well as the inventory evolution during a He nucleation event. In addition, 1D and 2D axisymmetric cases are exposed showing the effect of a He dispersed gas phase on hydrogen isotope permeation through a lithium lead eutectic alloy and the effect of vortical structures on hydrogen isotope transport at a backward facing step. Exposed results give a valuable insight on current nuclear technology regarding the importance of controlling hydrogen isotope transport and its interactions with nucleation event through gas absorption processes.

  14. Cold-set globular protein gels: Interactions, structure and rheology as a function of protein concentration.

    NARCIS (Netherlands)

    Alting, A.C.; Hamer, R.J.; Kruif, de C.G.

    2003-01-01

    We identified the contribution of covalent and noncovalent interactions to the scaling behavior of the structural and rheological properties in a cold gelling protein system. The system we studied consisted of two types of whey protein aggregates, equal in size but different in the amount of

  15. Identification of structural domains in proteins by a graph heuristic

    NARCIS (Netherlands)

    Wernisch, Lorenz; Hunting, M.M.G.; Wodak, Shoshana J.

    1999-01-01

    A novel automatic procedure for identifying domains from protein atomic coordinates is presented. The procedure, termed STRUDL (STRUctural Domain Limits), does not take into account information on secondary structures and handles any number of domains made up of contiguous or non-contiguous chain

  16. Connecting Protein Structure to Intermolecular Interactions: A Computer Modeling Laboratory

    Science.gov (United States)

    Abualia, Mohammed; Schroeder, Lianne; Garcia, Megan; Daubenmire, Patrick L.; Wink, Donald J.; Clark, Ginevra A.

    2016-01-01

    An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several…

  17. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  18. ICR studies of some anionic gas phase reactions and FTICR software design

    International Nuclear Information System (INIS)

    Noest, A.J.

    1983-01-01

    This thesis consists of two parts. Part one (Chs. 1-5) reports experimental results from mostly drift-cell ICR studies of negative ion-molecule reactions; part two (Chs. 6-11) concerns the design of software for an FTICR instrument. The author discusses successively: 1. ion cyclotron resonance spectrometry; 2. the gas phase allyl anion; 3. the (M-H) and (M-H2) anions from acetone; 4. negative ion-molecule reactions of aliphatic nitrites studied by cyclotron resonance; 5. homoconjugation versus charge-dipole interaction effects in the stabilization of carbanions in the gas phase; 6. the Fourier Transform ICR method; 7. the FTICR-software; 8. an efficient adaptive matcher filter for fast transient signals; 9. reduction of spectral peak height errors by time-domain weighing; 10. Chirp excitation; 11. Compact data storage. The book concludes with a Dutch and English summary (G.J.P.)

  19. Experimental redetermination of the gas-phase enthalpy of formation of ethyl 2-thiophenecarboxylate

    International Nuclear Information System (INIS)

    Santos, Ana Filipa L.O.M.; Ribeiro da Silva, Manuel A.V.

    2013-01-01

    The condensed phase standard (p° = 0.1 MPa) molar enthalpy of formation of ethyl-2-thiophenecarboxylate was derived from the remeasured standard molar energy of combustion, in oxygen, at T = 298.15 K, by rotating bomb combustion calorimetry and the standard molar enthalpy of vaporization, at T = 298.15 K, remeasured by Calvet microcalorimetry. Combining these two values, the following enthalpy of formation in the gas phase, at T = 298.15 K, was then derived for ethyl-2-thiophenecarboxylate: −(277.7 ± 2.9) kJ · mol −1 . The calculated gas-phase enthalpy of formation of the title compound, through the G3(MP2)//B3LYP approach was found to be 278.9 kJ · mol −1 , in excellent agreement with the experimental measured value

  20. Gas-phase infrared spectrum of phosphorus (III) oxycyanide, OPCN: experimental and theoretical investigations

    Science.gov (United States)

    Allaf, Abdul. W.; Kassem, M.; Alibrahim, M.; Boustani, Ihsan

    1999-03-01

    An attempt was made to observe the gas-phase infrared spectrum of Phosphorus (III) oxycyanide, OPCN for the first time. This molecule was produced by an on-line process using phosphorus (III) oxychloride, OPCl as precursor passed over heated AgCN. The products were characterised by the infrared spectra of their vapours. The low resolution gas-phase Fourier transform infrared spectrum shows two bands centered at 2165 and 1385 cm -1. These bands are assigned to, ν1 (CN stretch) and ν2 (OP stretch), respectively. Ab initio self-consistent-field (SCF) molecular orbital (MO) and Møller-Plesset second order perturbation theory (MP2) calculations were performed to determine the geometry, total energy and vibrational frequencies of OPCN.

  1. Gas-phase infrared spectrum of phosphorus (III) oxycyanide, OPCN: Experimental and theoretical and theoretical investigations

    International Nuclear Information System (INIS)

    Allaf, A.W.; Kassem, M.; Alibrahim, M.

    1999-01-01

    An attempt was made to observe the gas-phase infrared spectrum of phosphorus (III) oxycyanide, OPCN for the first time. This molecule was produced by on-line process using phosphorus (III) oxychloride, OPCI as precursor passed over heated Ag CN. The products were characterised by the infrared spectra of their vapours. The low resolution gas-phase Fourier transform infrared spectrum shows two bands at 2165 and 1385 cm -1 . These bands are assigned to ν 1 (C≡N stretch) and ν 2 (O=P stretch), respectively. Ab initio self-consistent-field (SCF) molecular orbital (MO) and Moeller - Plesset second order perturbation theory (MP2) calculations were performed to determine the geometry, total energy and vibrational frequencies of OPCN. (authors)

  2. Effect of duty-cycles on the air plasma gas-phase of dielectric barrier discharges

    Science.gov (United States)

    Barni, R.; Biganzoli, I.; Dell'Orto, E. C.; Riccardi, C.

    2015-10-01

    An experimental investigation concerning the effects of a duty-cycle in the supply of a dielectric barrier discharge in atmospheric pressure air has been performed. Electrical characteristics of the discharge have been measured, focusing mainly on the statistical properties of the current filaments and on dielectric surface charging, both affected by the frequent repetition of breakdown imposed by the duty-cycle. Information on the gas-phase composition was gathered too. In particular, a strong enhancement in the ozone formation rate is observed when suitable long pauses separate the active discharge phases. A simulation of the chemical kinetics in the gas-phase, based on a simplified discharge modeling, is briefly described in order to shed light on the observed increase in ozone production. The effect of a duty-cycle on surface modification of polymeric films in order to increase their wettability has been investigated too.

  3. Ab initio treatment of gas phase GeO{sup 2+} doubly charged ion

    Energy Technology Data Exchange (ETDEWEB)

    Mogren Al Mogren, M. [Chemistry Department, Faculty of Science, King Saud University, PO Box 2455, Riyadh 11451 (Saudi Arabia); Ben Abdallah, D. [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications – LSAMA, Université de Tunis, Tunis (Tunisia); Department of General Studies, Riyadh Corporation of Technology, Technical and Vocational Training Corporation, PO Box 42826, Riyadh 11551 (Saudi Arabia); Hochlaf, M., E-mail: hochlaf@univ-mlv.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France)

    2015-01-13

    Highlights: • Theoretical investigation of the novel gas-phase molecular species GeO{sup 2+}. • Spectroscopic parameters of this dication in its electronic ground and exited states. • Theoretical double ionization spectrum of GeO. - Abstract: Using multi reference configuration interaction methodology in connection with a large basis set, we show that GeO{sup 2+} is a metastable species either in the ground or in the electronically excited states. This confirms the observation of this dication in gas phase by mass spectrometry. In addition, we derived a set of accurate spectroscopic terms for GeO{sup 2+} bound states. At the MRCI/aug-cc-pV5Z level of theory, the adiabatic double ionization energy of GeO is computed to be ∼28.93 eV.

  4. Treatment of reduced sulphur compounds and SO2 by Gas Phase Advanced Oxidation

    DEFF Research Database (Denmark)

    Meusinger, Carl; Bluhme, Anders Brostrøm; Ingemar, Jonas L.

    2017-01-01

    Reduced sulphur compounds (RSCs) emitted from pig farms are a major problem for agriculture, due to their health and environmental impacts and foul odour. This study investigates the removal of RSCs, including H2S, and their oxidation product SO2 using Gas Phase Advanced Oxidation (GPAO). GPAO...... is a novel air cleaning technique which utilises accelerated atmospheric chemistry to oxidise pollutants before removing their oxidation products as particles. Removal efficiencies of 24.5% and 3.9% were found for 461 ppb of H2S and 714 ppb of SO2 in a laboratory system (volumetric flow Q = 75 m3/h......). A numerical model of the reactor system was developed to explore the basic features of the system; its output was in fair agreement with the experiment. The model verified the role of OH radicals in initiating the oxidation chemistry. All sulphur removed from the gas phase was detected as particulate matter...

  5. The Protein Model Portal--a comprehensive resource for protein structure and model information.

    Science.gov (United States)

    Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

    2013-01-01

    The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org.

  6. The Protein Model Portal—a comprehensive resource for protein structure and model information

    Science.gov (United States)

    Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

    2013-01-01

    The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org PMID:23624946

  7. Protein Structural Change Data - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PSCDB Protein Structural Change Data Data detail Data name Protein Structural Change Data DO...History of This Database Site Policy | Contact Us Protein Structural Change Data - PSCDB | LSDB Archive ...

  8. Protein 3D structure computed from evolutionary sequence variation.

    Directory of Open Access Journals (Sweden)

    Debora S Marks

    Full Text Available The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org. This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of

  9. Structure and Dynamic Properties of Membrane Proteins using NMR

    DEFF Research Database (Denmark)

    Rösner, Heike; Kragelund, Birthe

    2012-01-01

    conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....

  10. Perspective: Structural fluctuation of protein and Anfinsen's thermodynamic hypothesis

    Science.gov (United States)

    Hirata, Fumio; Sugita, Masatake; Yoshida, Masasuke; Akasaka, Kazuyuki

    2018-01-01

    The thermodynamics hypothesis, casually referred to as "Anfinsen's dogma," is described theoretically in terms of a concept of the structural fluctuation of protein or the first moment (average structure) and the second moment (variance and covariance) of the structural distribution. The new theoretical concept views the unfolding and refolding processes of protein as a shift of the structural distribution induced by a thermodynamic perturbation, with the variance-covariance matrix varying. Based on the theoretical concept, a method to characterize the mechanism of folding (or unfolding) is proposed. The transition state, if any, between two stable states is interpreted as a gap in the distribution, which is created due to an extensive reorganization of hydrogen bonds among back-bone atoms of protein and with water molecules in the course of conformational change. Further perspective to applying the theory to the computer-aided drug design, and to the material science, is briefly discussed.

  11. Protein structure prediction using bee colony optimization metaheuristic

    DEFF Research Database (Denmark)

    Fonseca, Rasmus; Paluszewski, Martin; Winter, Pawel

    2010-01-01

    of the proteins structure, an energy potential and some optimization algorithm that ¿nds the structure with minimal energy. Bee Colony Optimization (BCO) is a relatively new approach to solving opti- mization problems based on the foraging behaviour of bees. Several variants of BCO have been suggested......Predicting the native structure of proteins is one of the most challenging problems in molecular biology. The goal is to determine the three-dimensional struc- ture from the one-dimensional amino acid sequence. De novo prediction algorithms seek to do this by developing a representation...... our BCO method to generate good solutions to the protein structure prediction problem. The results show that BCO generally ¿nds better solutions than simulated annealing which so far has been the metaheuristic of choice for this problem....

  12. The nuclear liquid-gas phase transition: Present status and future perspectives

    International Nuclear Information System (INIS)

    Pochodzalla, J.; Imme, G.; Maddalena, V.

    1996-07-01

    More than two decades ago, the van der Waals behavior of the nucleon -nucleon force inspired the idea of a liquid-gas phase transition in nuclear matter. Heavy-ion reactions at relativistic energies offer the unique possibility for studying this phase transition in a finite, hadronic system. A general overview of this subject is given emphasizing the most recent results on nuclear calorimetry. (orig.)

  13. Gas Phase Transport, Adsorption and Surface Diffusion in Porous Glass Membrane

    Czech Academy of Sciences Publication Activity Database

    Yang, J.; Čermáková, Jiřina; Uchytil, Petr; Hamel, Ch.; Seidel-Morgenstern, A.

    2005-01-01

    Roč. 104, 2-4 (2005), s. 344-351 ISSN 0920-5861. [International Conference on Catalysis in Membrane Reactors /6./. Lahnstein, 06.07.2004-09.07.2004] R&D Projects: GA AV ČR(CZ) IAA4072402 Institutional research plan: CEZ:AV0Z40720504 Keywords : gas phase transport * vycor glass * adsorption Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.365, year: 2005

  14. Investigation of gas-phase decontamination of internally radioactively contaminated gaseous diffusion process equipment and piping

    International Nuclear Information System (INIS)

    Bundy, R.D.; Munday, E.B.

    1991-01-01

    Construction of the gaseous diffusion plants (GDPs) was begun during World War 2 to produce enriched uranium for defense purposes. These plants, which utilized UF 6 gas, were used primarily for this purpose through 1964. From 1959 through 1968, production shifted primarily to uranium enrichment to supply the nuclear power industry. Additional UF 6 -handling facilities were built in feed and fuel-processing plants associated with the uranium enrichment process. Two of the five process buildings at Oak ridge were shut down in 1964. Uranium enrichment activities at Oak Ridge were discontinued altogether in 1985. In 1987, the Department of Energy (DOE) decided to proceed with a permanent shutdown of the Oak Ridge Gaseous Diffusion Plant (ORGDP). DOE intends to begin decommissioning and decontamination (D ampersand D) of ORGDP early in the next century. The remaining two GDPs are expected to be shut down during the next 10 to 40 years and will also require D ampersand D, as will the other UF 6 -handling facilities. This paper presents an investigation of gas- phase decontamination of internally radioactively contaminated gaseous diffusion process equipment and piping using powerful fluorinating reagents that convert nonvolatile uranium compounds to volatile UF 6 . These reagents include ClF 3 , F 2 , and other compounds. The scope of D ampersand D at the GDPs, previous work of gas-phase decontamination, four concepts for using gas-phase decontamination, plans for further study of gas-phase decontamination, and the current status of this work are discussed. 13 refs., 15 figs

  15. Dynamics of gas-phase transient species studied by dissociative photodetachment of molecular anions

    OpenAIRE

    Lu, Zhou

    2007-01-01

    Gas-phase transient species, such as the CH₃CO₂ and HOCO free radicals, play important roles in combustion and environment chemistry. In this thesis work, the dynamics of these two radicals were studied by dissociative photodetachment (DPD) of the negative ions, CH₃CO₂-С and HOCO⁻, respectively. The experiments were carried out with a fast-ion-beam photoelectron-photofragment coincidence (PPC) spectrometer. Mass-selected molecular anions in a fast ion beam were intercepted by a linearly polar...

  16. Isospin and momentum dependence of liquid-gas phase transition in hot asymmetric nuclear matter

    International Nuclear Information System (INIS)

    Xu, Jun; Ma, Hongru; Chen, Liewen; Li, Baoan

    2008-01-01

    The liquid-gas phase transition in hot neutron-rich nuclear matter is investigated within a self-consistent thermal model using different interactions with or without isospin and/or momentum dependence. The boundary of the phase-coexistence region is shown to be sensitive to the density dependence of the nuclear symmetry energy as well as the isospin and momentum dependence of the nuclear interaction. (author)

  17. LIAD-fs: A novel method for studies of ultrafast processes in gas phase neutral biomolecules

    International Nuclear Information System (INIS)

    Calvert, C R; Kelly, O; Duffy, M J; Belshaw, L; King, R B; Williams, I D; Greenwood, J B

    2012-01-01

    A new experimental technique for femtosecond (fs) pulse studies of gas phase biomolecules is reported. Using Laser-Induced Acoustic Desorption (LIAD) to produce a plume of neutral molecules, a time-delayed fs pulse is employed for ionisation/fragmentation, with subsequent products extracted and mass analysed electrostatically. By varying critical laser pulse parameters, this technique can be used to implement control over molecular fragmentation for a range of small biomolecules, with specific studies of amino acids demonstrated.

  18. Method and apparatus for selective capture of gas phase analytes using metal .beta.-diketonate polymers

    Science.gov (United States)

    Harvey, Scott D [Kennewick, WA

    2011-06-21

    A process and sensor device are disclosed that employ metal .beta.-diketonate polymers to selectively capture gas-phase explosives and weaponized chemical agents in a sampling area or volume. The metal .beta.-diketonate polymers can be applied to surfaces in various analytical formats for detection of: improvised explosive devices, unexploded ordinance, munitions hidden in cargo holds, explosives, and chemical weapons in public areas.

  19. Thermodynamic Functions of Yttrium Trifluoride and Its Dimer in the Gas Phase

    Science.gov (United States)

    Osina, E. L.; Kovtun, D. M.

    2018-05-01

    New calculations of the functions for YF3 and Y2F6 in the gas phase using quantum-chemical calculations by MP2 and CCSD(T) methods are performed in connection with the ongoing work on obtaining reliable thermodynamic data of yttrium halides. The obtained values are entered in the database of the IVTANTERMO software complex. Equations approximating the temperature dependence of the reduced Gibbs energy in the T = 298.15-6000 K range of temperatures are presented.

  20. Crystal structure of secretory protein Hcp3 from Pseudomonas aeruginosa.

    Science.gov (United States)

    Osipiuk, Jerzy; Xu, Xiaohui; Cui, Hong; Savchenko, Alexei; Edwards, Aled; Joachimiak, Andrzej

    2011-03-01

    The Type VI secretion pathway transports proteins across the cell envelope of Gram-negative bacteria. Pseudomonas aeruginosa, an opportunistic Gram-negative bacterial pathogen infecting humans, uses the type VI secretion pathway to export specific effector proteins crucial for its pathogenesis. The HSI-I virulence locus encodes for several proteins that has been proposed to participate in protein transport including the Hcp1 protein, which forms hexameric rings that assemble into nanotubes in vitro. Two Hcp1 paralogues have been identified in the P. aeruginosa genome, Hsp2 and Hcp3. Here, we present the structure of the Hcp3 protein from P. aeruginosa. The overall structure of the monomer resembles Hcp1 despite the lack of amino-acid sequence similarity between the two proteins. The monomers assemble into hexamers similar to Hcp1. However, instead of forming nanotubes in head-to-tail mode like Hcp1, Hcp3 stacks its rings in head-to-head mode forming double-ring structures.

  1. Structural Elements Regulating AAA+ Protein Quality Control Machines.

    Science.gov (United States)

    Chang, Chiung-Wen; Lee, Sukyeong; Tsai, Francis T F

    2017-01-01

    Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.

  2. Models of protein-ligand crystal structures: trust, but verify.

    Science.gov (United States)

    Deller, Marc C; Rupp, Bernhard

    2015-09-01

    X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

  3. Rotational order–disorder structure of fluorescent protein FP480

    International Nuclear Information System (INIS)

    Pletnev, Sergei; Morozova, Kateryna S.; Verkhusha, Vladislav V.; Dauter, Zbigniew

    2009-01-01

    An analysis of the rotational order–disorder structure of fluorescent protein FP480 is presented. In the last decade, advances in instrumentation and software development have made crystallography a powerful tool in structural biology. Using this method, structural information can now be acquired from pathological crystals that would have been abandoned in earlier times. In this paper, the order–disorder (OD) structure of fluorescent protein FP480 is discussed. The structure is composed of tetramers with 222 symmetry incorporated into the lattice in two different ways, namely rotated 90° with respect to each other around the crystal c axis, with tetramer axes coincident with crystallographic twofold axes. The random distribution of alternatively oriented tetramers in the crystal creates a rotational OD structure with statistically averaged I422 symmetry, although the presence of very weak and diffuse additional reflections suggests that the randomness is only approximate

  4. Tertiary alphabet for the observable protein structural universe.

    Science.gov (United States)

    Mackenzie, Craig O; Zhou, Jianfu; Grigoryan, Gevorg

    2016-11-22

    Here, we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs). A TERM is a compact backbone fragment that captures the secondary, tertiary, and quaternary environments around a given residue, comprising one or more disjoint segments (three on average). We seek the set of universal TERMs that capture all structure in the Protein Data Bank (PDB), finding remarkable degeneracy. Only ∼600 TERMs are sufficient to describe 50% of the PDB at sub-Angstrom resolution. However, more rare geometries also exist, and the overall structural coverage grows logarithmically with the number of TERMs. We go on to show that universal TERMs provide an effective mapping between sequence and structure. We demonstrate that TERM-based statistics alone are sufficient to recapitulate close-to-native sequences given either NMR or X-ray backbones. Furthermore, sequence variability predicted from TERM data agrees closely with evolutionary variation. Finally, locations of TERMs in protein chains can be predicted from sequence alone based on sequence signatures emergent from TERM instances in the PDB. For multisegment motifs, this method identifies spatially adjacent fragments that are not contiguous in sequence-a major bottleneck in structure prediction. Although all TERMs recur in diverse proteins, some appear specialized for certain functions, such as interface formation, metal coordination, or even water binding. Structural biology has benefited greatly from previously observed degeneracies in structure. The decomposition of the known structural universe into a finite set of compact TERMs offers exciting opportunities toward better understanding, design, and prediction of protein structure.

  5. Shear viscosity of neutron-rich nucleonic matter near its liquid–gas phase transition

    International Nuclear Information System (INIS)

    Xu, Jun; Chen, Lie-Wen; Ko, Che Ming; Li, Bao-An; Ma, Yu Gang

    2013-01-01

    Within a relaxation time approach using free nucleon–nucleon cross sections modified by the in-medium nucleon masses that are determined from an isospin- and momentum-dependent effective nucleon–nucleon interaction, we investigate the specific shear viscosity (η/s) of neutron-rich nucleonic matter near its liquid–gas phase transition. It is found that as the nucleonic matter is heated at fixed pressure or compressed at fixed temperature, its specific shear viscosity shows a valley shape in the temperature or density dependence, with the minimum located at the boundary of the phase transition. Moreover, the value of η/s drops suddenly at the first-order liquid–gas phase transition temperature, reaching as low as 4–5 times the KSS bound of ℏ/4π. However, it varies smoothly for the second-order liquid–gas phase transition. Effects of the isospin degree of freedom and the nuclear symmetry energy on the value of η/s are also discussed

  6. Thermodynamic analysis of fuels in gas phase: ethanol, gasoline and ethanol - gasoline predicted by DFT method.

    Science.gov (United States)

    Neto, A F G; Lopes, F S; Carvalho, E V; Huda, M N; Neto, A M J C; Machado, N T

    2015-10-01

    This paper presents a theoretical study using density functional theory to calculate thermodynamics properties of major molecules compounds at gas phase of fuels like gasoline, ethanol, and gasoline-ethanol mixture in thermal equilibrium on temperature range up to 1500 K. We simulated a composition of gasoline mixture with ethanol for a thorough study of thermal energy, enthalpy, Gibbs free energy, entropy, heat capacity at constant pressure with respect to temperature in order to study the influence caused by ethanol as an additive to gasoline. We used semi-empirical computational methods as well in order to know the efficiency of other methods to simulate fuels through this methodology. In addition, the ethanol influence through the changes in percentage fractions of chemical energy released in combustion reaction and the variations on thermal properties for autoignition temperatures of fuels was analyzed. We verified how ethanol reduces the chemical energy released by gasoline combustion and how at low temperatures the gas phase fuels in thermal equilibrium have similar thermodynamic behavior. Theoretical results were compared with experimental data, when available, and showed agreement. Graphical Abstract Thermodynamic analysis of fuels in gas phase.

  7. Heavy haze in winter Beijing driven by fast gas phase oxidation

    Science.gov (United States)

    Lu, K.; Tan, Z.; Wang, H.; Li, X.; Wu, Z.; Chen, Q.; Wu, Y.; Ma, X.; Liu, Y.; Chen, X.; Shang, D.; Dong, H.; Zeng, L.; Shao, M.; Hu, M.; Fuchs, H.; Novelli, A.; Broch, S.; Hofzumahaus, A.; Holland, F.; Rohrer, F.; Bohn, B.; Georgios, G.; Schmitt, S. H.; Schlag, P.; Kiendler-Scharr, A.; Wahner, A.; Zhang, Y.

    2017-12-01

    Heavy haze conditions were frequently presented in the airsheds of Beijing and surrounding areas, especially during winter time. To explore the trace gas oxidation and the subsequent formation of aerosols, a comprehensive field campaign was performed at a regional site (in the campus of University of Chinese Academy of Science, UCAS) in Beijing winter 2016. Serious haze pollution processes were often observed with the fast increase of inorganic salt (especially nitrate) and these pollutions were always associated with enhanced humidity and the concentrations of PAN (PeroxyAcyl Nitrates) which is normally a marker of gas phase oxidations from NOx and VOCs. Moreover, based on the measurements of OH, HO2, RO2, total OH reactivity, N2O5, NO, NO2, SO2, particle concentrations/distributions/chemical compositions, and meteorological parameters, the gas phase oxidation rates that leads to the formation of sulfate, nitrate and secondary organic aerosols were estimated. These determined formation rates were clearly enhanced by several folds during pollution episodes compared to that of the clean air masses. Preliminary analysis result showed that the gas phase formation potential of nitrate and secondary organic aerosols were larger than the observed concentrations of nitrate and SOA of which the excess production may be explained by deposition and dilution.

  8. The Gas-Phase Formation of Methyl Formate in Hot Molecular Cores

    Science.gov (United States)

    Horn, Anne; Møllendal, Harald; Sekiguchi, Osamu; Uggerud, Einar; Roberts, Helen; Herbst, Eric; Viggiano, A. A.; Fridgen, Travis D.

    2004-08-01

    Methyl formate, HCOOCH3, is a well-known interstellar molecule prominent in the spectra of hot molecular cores. The current view of its formation is that it occurs in the gas phase from precursor methanol, which is synthesized on the surfaces of grain mantles during a previous colder era and evaporates while temperatures increase during the process of high-mass star formation. The specific reaction sequence thought to form methyl formate, the ion-molecule reaction between protonated methanol and formaldehyde followed by dissociative recombination of the protonated ion [HCO(H)OCH3]+, has not been studied in detail in the laboratory. We present here the results of both a quantum chemical study of the ion-molecule reaction between [CH3OH2]+ and H2CO as well as new experimental work on the system. In addition, we report theoretical and experimental studies for a variety of other possible gas-phase reactions leading to ion precursors of methyl formate. The studied chemical processes leading to methyl formate are included in a chemical model of hot cores. Our results show that none of these gas-phase processes produces enough methyl formate to explain its observed abundance.

  9. Conformational Preferences of Glycerol in the Gas Phase and in Water

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Keun Hong [Korea Military Academy, Seoul (Korea, Republic of); Byun, Byung Jin; Kang, Young Kee [Chungbuk National University, Cheongju (Korea, Republic of)

    2012-03-15

    The conformational study of glycerol has been carried out using the M06-2X/cc-pVTZ level of theory in the gas phase and the SMD M06-2X/cc-pVTZ level of theory in water in order to understand its conformational preferences and solvation effects. Most of the preferred conformers of glycerol have two C{sub 5} hydrogen bonds in the gas phase, as found by the analysis of calorimetric data. It has been known that the solvation drove the hydrogen bonds of glycerol to be weaker and its potential surface to be fatter and that glycerol exists as an ensemble of many feasible local minima in water. The calculated populations of glycerol in the gas phase and in water are consistent with the observed values, which are better than the previously calculated ones at the G2(MP2), CBS-QB3, and SM5.42 HF/6-31G(d) levels of theory

  10. Systematic Search for Chemical Reactions in Gas Phase Contributing to Methanol Formation in Interstellar Space.

    Science.gov (United States)

    Gamez-Garcia, Victoria G; Galano, Annia

    2017-10-05

    A massive search for chemical routes leading to methanol formation in gas phase has been conducted using computational chemistry, at the CBS-QB3 level of theory. The calculations were performed at five different temperatures (100, 80, 50, 20, and 10 K) and at three pressures (0.1, 0.01, and 0.001 atm) for each temperature. The search was focused on identifying reactions with the necessary features to be viable in the interstellar medium (ISM). A searching strategy was applied to that purpose, which allowed to reduce an initial set of 678 possible reactions to a subset of 11 chemical routes that are recommended, for the first time, as potential candidates for contributing to methanol formation in the gas phase of the ISM. They are all barrier-less, and thus they are expected to take place at collision rates. Hopefully, including these reactions in the currently available models, for the gas-phase methanol formation in the ISM, would help improving the predicted fractional abundance of this molecule in dark clouds. Further investigations, especially those dealing with grain chemistry and electronic excited states, would be crucial to get a complete picture of the methanol formation in the ISM.

  11. Gas-phase advanced oxidation as an integrated air pollution control technique

    Directory of Open Access Journals (Sweden)

    Getachew A. Adnew

    2016-03-01

    Full Text Available Gas-phase advanced oxidation (GPAO is an emerging air cleaning technology based on the natural self-cleaning processes that occur in the Earth’s atmosphere. The technology uses ozone, UV-C lamps and water vapor to generate gas-phase hydroxyl radicals that initiate oxidation of a wide range of pollutants. In this study four types of GPAO systems are presented: a laboratory scale prototype, a shipping container prototype, a modular prototype, and commercial scale GPAO installations. The GPAO systems treat volatile organic compounds, reduced sulfur compounds, amines, ozone, nitrogen oxides, particles and odor. While the method covers a wide range of pollutants, effective treatment becomes difficult when temperature is outside the range of 0 to 80 °C, for anoxic gas streams and for pollution loads exceeding ca. 1000 ppm. Air residence time in the system and the rate of reaction of a given pollutant with hydroxyl radicals determine the removal efficiency of GPAO. For gas phase compounds and odors including VOCs (e.g. C6H6 and C3H8 and reduced sulfur compounds (e.g. H2S and CH3SH, removal efficiencies exceed 80%. The method is energy efficient relative to many established technologies and is applicable to pollutants emitted from diverse sources including food processing, foundries, water treatment, biofuel generation, and petrochemical industries.

  12. Fragger: a protein fragment picker for structural queries.

    Science.gov (United States)

    Berenger, Francois; Simoncini, David; Voet, Arnout; Shrestha, Rojan; Zhang, Kam Y J

    2017-01-01

    Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.

  13. DNA nanotubes for NMR structure determination of membrane proteins.

    Science.gov (United States)

    Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

    2013-04-01

    Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

  14. The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from streptococcus pyogenes.

    Energy Technology Data Exchange (ETDEWEB)

    Chang, C.; Coggill, P.; Bateman, A.; Finn, R.; Cymborowski, M.; Otwinowski, Z.; Minor, W.; Volkart, L.; Joachimiak, A.; Wellcome Trust Sanger Inst.; Univ. of Virginia; UT Southwestern Medical Center

    2009-12-17

    Many Gram-positive lactic acid bacteria (LAB) produce anti-bacterial peptides and small proteins called bacteriocins, which enable them to compete against other bacteria in the environment. These peptides fall structurally into three different classes, I, II, III, with class IIa being pediocin-like single entities and class IIb being two-peptide bacteriocins. Self-protective cognate immunity proteins are usually co-transcribed with these toxins. Several examples of cognates for IIa have already been solved structurally. Streptococcus pyogenes, closely related to LAB, is one of the most common human pathogens, so knowledge of how it competes against other LAB species is likely to prove invaluable. We have solved the crystal structure of the gene-product of locus Spy-2152 from S. pyogenes, (PDB: 2fu2), and found it to comprise an anti-parallel four-helix bundle that is structurally similar to other bacteriocin immunity proteins. Sequence analyses indicate this protein to be a possible immunity protein protective against class IIa or IIb bacteriocins. However, given that S. pyogenes appears to lack any IIa pediocin-like proteins but does possess class IIb bacteriocins, we suggest this protein confers immunity to IIb-like peptides. Combined structural, genomic and proteomic analyses have allowed the identification and in silico characterization of a new putative immunity protein from S. pyogenes, possibly the first structure of an immunity protein protective against potential class IIb two-peptide bacteriocins. We have named the two pairs of putative bacteriocins found in S. pyogenes pyogenecin 1, 2, 3 and 4.

  15. Vibrational Spectra of Discrete UO22+ Halide Complexes in the Gas Phase

    International Nuclear Information System (INIS)

    Groenewold, G.S.; Van Stipdonk, Michael J.; Oomens, Jos; De Jong, Wibe A.; Gresham, Garold L.; Mcilwain, Michael

    2010-01-01

    The intrinsic binding of halide ions to the metal center in the uranyl molecule is a topic of ongoing research interest in both the actinide separations and theoretical communities. Investigations of structure in the condensed phases is frequently obfuscated by solvent interactions that can alter ligand binding and spectroscopic properties. The approach taken in this study is to move the uranyl halide complexes into the gas phase where they are free from solvent interactions, and then interrogate their vibrational spectroscopy using infrared multiple photon dissociation (IRMPD). The spectra of cationic coordination complexes having the composition (UO 2 (X)(ACO) 3 ) + (where X = F, Cl, Br and I; ACO = acetone) were acquired using electrospray for ion formation, and monitoring the ion signal from the photoelimination of ACO ligands. The studies showed that the asymmetric ν 3 UO 2 frequency was insensitive to halide identity as X was varied from Cl to I, suggesting that in these pseudo-octahedral complexes, changing the nucleophilicity of the halide did not appreciably alter its binding in the complex. The ν 3 peak in the spectrum of the F-containing complex was 9 cm -1 lower indicating stronger coordination in this complex. Similarly the ACO carbonyl stretches showed that the C=O frequency was relatively insensitive to the identity of the halide, although a modest shift to higher wavenumber was seen for the complexes with the more nucleophilic anions, consistent with the idea that they loosen solvent binding. Surprisingly, the ν 1 stretch was activated when the softer anions Cl, Br and I were present in the complexes. IR studies of the anionic complexes (UO 2 X 3 ) - (where X = Cl - , Br - and I - ) compared the ν 3 UO 2 modes versus halide, and showed that the ν 3 values decreased with increasing anion nucleophilicity. This observation was consistent with DFT calculations that indicated that (UO 2 X 2 ) - -X, and (UO 2 X 2 )·-X - dissociation energies

  16. Real time observation of the excimer formation dynamics of a gas phase benzene dimer by picosecond pump-probe spectroscopy.

    Science.gov (United States)

    Miyazaki, Mitsuhiko; Fujii, Masaaki

    2015-10-21

    We observed the real-time excimer (EXC) formation dynamics of a gas phase benzene dimer (Bz2) cluster after photo-excitation to the S1 state by applying an ionization detected picosecond transient absorption method for probing the visible EXC absorption for the first time. The time evolution of the EXC absorption from the S1 0(0) level shows a rise that is well fitted by a single exponential function with a time constant of 18 ± 2 ps. The structure of the Bz dimer has a T-shaped structure in the ground electronic state, and that in the EXC state is a parallel sandwich (SW) structure. Thus, the observed rise time corresponds to the structural change from the T to the SW structures, which directly shows the EXC formation. On the other hand, the EXC formation after excitation of the S1 6(1) vibrational level of the stem site showed a faster rise of the time constant of 10 ± 2 ps. Supposing equilibrium between the EXC and the local excited states, it followed that the intramolecular vibrational energy redistribution rate of the 6(1) level is largely enhanced and becomes faster than the EXC formation reaction.

  17. Constraint Logic Programming approach to protein structure prediction

    Directory of Open Access Journals (Sweden)

    Fogolari Federico

    2004-11-01

    Full Text Available Abstract Background The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Results Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics. Conclusions The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of Constraint Logic Programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space.

  18. Constraint Logic Programming approach to protein structure prediction.

    Science.gov (United States)

    Dal Palù, Alessandro; Dovier, Agostino; Fogolari, Federico

    2004-11-30

    The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics. The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of Constraint Logic Programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space.

  19. Oxidative potential of gas phase combustion emissions - An underestimated and potentially harmful component of air pollution from combustion processes

    Science.gov (United States)

    Stevanovic, S.; Vaughan, A.; Hedayat, F.; Salimi, F.; Rahman, M. M.; Zare, A.; Brown, R. A.; Brown, R. J.; Wang, H.; Zhang, Z.; Wang, X.; Bottle, S. E.; Yang, I. A.; Ristovski, Z. D.

    2017-06-01

    The oxidative potential (OP) of the gas phase is an important and neglected aspect of environmental toxicity. Whilst prolonged exposure to particulate matter (PM) associated reactive oxygen species (ROS) have been shown to lead to negative health effects, the potential for compounds in gas phase to cause similar effects is yet to be understood. In this study we describe: the significance of the gas phase OP generated through vehicle emissions; discuss the origin and evolution of species contributing to measured OP; and report on the impact of gas phase OP on human lung cells. The model aerosol for this study was exhaust emitted from a Euro III Common-rail diesel engine fuelled with different blends of diesel and biodiesel. The gas phase of these emissions was found to be potentially as hazardous as the particle phase. Fuel oxygen content was found to negatively correlate with the gas phase OP, and positively correlate with particle phase OP. This signifies a complex interaction between reactive species present in gas and particle phase. Furthermore, this interaction has an overarching effect on the OP of both particle and gas phase, and therefore the toxicity of combustion emissions.

  20. Structural Basis for Target Protein Regcognition by Thiredoxin

    DEFF Research Database (Denmark)

    Maeda, Kenji

    2007-01-01

    Ser) and a mutant of an in vitro substrate alpha-amylase/subtilisin inhibitor (BASI) (Cys144Ser), as a reaction intermediate-mimic of Trx-catalyzed disulfide reduction. The resultant structure showed a sequence of BASI residues along a conserved hydrophobic groove constituted of three loop segments...... of Trx-fold proteins glutaredoxin and glutathione transferase. This study suggests that the features of main chain conformation as well as charge property around disulfide bonds in protein substrates are important factors for interaction with Trx. Moreover, this study describes a detailed structural......Thioredoxin (Trx) is an ubiquitous protein disulfide reductase that possesses two redox active cysteines in the conserved active site sequence motif, Trp-CysN-Gly/Pro-Pro-CysC situated in the so called Trx-fold. The lack of insight into the protein substrate recognition mechanism of Trx has to date...