Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins.

Science.gov (United States)

Lakbub, Jude C; Shipman, Joshua T; Desaire, Heather

2018-04-01

Disulfide bonds are important structural moieties of proteins: they ensure proper folding, provide stability, and ensure proper function. With the increasing use of proteins for biotherapeutics, particularly monoclonal antibodies, which are highly disulfide bonded, it is now important to confirm the correct disulfide bond connectivity and to verify the presence, or absence, of disulfide bond variants in the protein therapeutics. These studies help to ensure safety and efficacy. Hence, disulfide bonds are among the critical quality attributes of proteins that have to be monitored closely during the development of biotherapeutics. However, disulfide bond analysis is challenging because of the complexity of the biomolecules. Mass spectrometry (MS) has been the go-to analytical tool for the characterization of such complex biomolecules, and several methods have been reported to meet the challenging task of mapping disulfide bonds in proteins. In this review, we describe the relevant, recent MS-based techniques and provide important considerations needed for efficient disulfide bond analysis in proteins. The review focuses on methods for proper sample preparation, fragmentation techniques for disulfide bond analysis, recent disulfide bond mapping methods based on the fragmentation techniques, and automated algorithms designed for rapid analysis of disulfide bonds from liquid chromatography-MS/MS data. Researchers involved in method development for protein characterization can use the information herein to facilitate development of new MS-based methods for protein disulfide bond analysis. In addition, individuals characterizing biotherapeutics, especially by disulfide bond mapping in antibodies, can use this review to choose the best strategies for disulfide bond assignment of their biologic products. Graphical Abstract This review, describing characterization methods for disulfide bonds in proteins, focuses on three critical components: sample preparation, mass

Phi ({Phi}) and psi ({Psi}) angles involved in malarial peptide bonds determine sterile protective immunity

Energy Technology Data Exchange (ETDEWEB)

Patarroyo, Manuel E., E-mail: mepatarr@gmail.com [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia); Universidad Nacional de Colombia, Bogota (Colombia); Moreno-Vranich, Armando; Bermudez, Adriana [Fundacion Instituto de Inmunologia de Colombia (FIDIC), Bogota (Colombia)

2012-12-07

Highlights: Black-Right-Pointing-Pointer Phi ({Phi}) and psi ({Psi}) angles determine sterile protective immunity. Black-Right-Pointing-Pointer Modified peptide's tendency to assume a regular conformation related to a PPII{sub L}. Black-Right-Pointing-Pointer Structural modifications in mHABPs induce Ab and protective immunity. Black-Right-Pointing-Pointer mHABP backbone atom's interaction with HLA-DR{beta}1{sup Asterisk-Operator} is stabilised by H-bonds. -- Abstract: Modified HABP (mHABP) regions interacting with HLA-DR{beta}1{sup Asterisk-Operator} molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their {Phi} and {Psi} torsion angles. These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by {sup 1}H-NMR and superimposed into HLA-DR{beta}1{sup Asterisk-Operator }-like Aotus monkey molecules; their phi ({Phi}) and psi ({Psi}) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII{sub L}) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them.

Deep learning methods for protein torsion angle prediction.

Science.gov (United States)

Li, Haiou; Hou, Jie; Adhikari, Badri; Lyu, Qiang; Cheng, Jianlin

2017-09-18

Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012, it has achieved success in a number of areas such as protein residue-residue contact prediction, secondary structure prediction, and fold recognition. In this work, we developed deep learning methods to improve the prediction of torsion (dihedral) angles of proteins. We design four different deep learning architectures to predict protein torsion angles. The architectures including deep neural network (DNN) and deep restricted Boltzmann machine (DRBN), deep recurrent neural network (DRNN) and deep recurrent restricted Boltzmann machine (DReRBM) since the protein torsion angle prediction is a sequence related problem. In addition to existing protein features, two new features (predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments) are used as input to each of the four deep learning architectures to predict phi and psi angles of protein backbone. The mean absolute error (MAE) of phi and psi angles predicted by DRNN, DReRBM, DRBM and DNN is about 20-21° and 29-30° on an independent dataset. The MAE of phi angle is comparable to the existing methods, but the MAE of psi angle is 29°, 2° lower than the existing methods. On the latest CASP12 targets, our methods also achieved the performance better than or comparable to a state-of-the art method. Our experiment demonstrates that deep learning is a valuable method for predicting protein torsion angles. The deep recurrent network architecture performs slightly better than deep feed-forward architecture, and the predicted residue contact number and the error distribution of torsion angles extracted from sequence fragments are useful features for improving prediction accuracy.

A single-layer wide-angle negative-index metamaterial at visible frequencies.

Science.gov (United States)

Burgos, Stanley P; de Waele, Rene; Polman, Albert; Atwater, Harry A

2010-05-01

Metamaterials are materials with artificial electromagnetic properties defined by their sub-wavelength structure rather than their chemical composition. Negative-index materials (NIMs) are a special class of metamaterials characterized by an effective negative index that gives rise to such unusual wave behaviour as backwards phase propagation and negative refraction. These extraordinary properties lead to many interesting functions such as sub-diffraction imaging and invisibility cloaking. So far, NIMs have been realized through layering of resonant structures, such as split-ring resonators, and have been demonstrated at microwave to infrared frequencies over a narrow range of angles-of-incidence and polarization. However, resonant-element NIM designs suffer from the limitations of not being scalable to operate at visible frequencies because of intrinsic fabrication limitations, require multiple functional layers to achieve strong scattering and have refractive indices that are highly dependent on angle of incidence and polarization. Here we report a metamaterial composed of a single layer of coupled plasmonic coaxial waveguides that exhibits an effective refractive index of -2 in the blue spectral region with a figure-of-merit larger than 8. The resulting NIM refractive index is insensitive to both polarization and angle-of-incidence over a +/-50 degree angular range, yielding a wide-angle NIM at visible frequencies.

A tensegrity model for hydrogen bond networks in proteins.

Science.gov (United States)

Bywater, Robert P

2017-05-01

Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger - covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance ("closure") is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins ("domains") as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating elements in fibrous proteins.

Widespread Disulfide Bonding in Proteins from Thermophilic Archaea

Directory of Open Access Journals (Sweden)

Julien Jorda

2011-01-01

Full Text Available Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaeal branch, which are essentially all hyperthermophilic, are universally rich in disulfide bonding while lesser degrees of disulfide bonding are found among the thermophilic Euryarchaea, excluding those that are methanogenic. The results help clarify which parts of the archaeal lineage are likely to yield more examples and additional specific data on protein disulfide bonding, as increasing genomic sequencing efforts are brought to bear.

Widespread disulfide bonding in proteins from thermophilic archaea.

Science.gov (United States)

Jorda, Julien; Yeates, Todd O

2011-01-01

Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaeal branch, which are essentially all hyperthermophilic, are universally rich in disulfide bonding while lesser degrees of disulfide bonding are found among the thermophilic Euryarchaea, excluding those that are methanogenic. The results help clarify which parts of the archaeal lineage are likely to yield more examples and additional specific data on protein disulfide bonding, as increasing genomic sequencing efforts are brought to bear.

Evaluation of Die-Attach Bonding Using High-Frequency Ultrasonic Energy for High-Temperature Application

Science.gov (United States)

Lee, Jong-Bum; Aw, Jie-Li; Rhee, Min-Woo

2014-09-01

Room-temperature die-attach bonding using ultrasonic energy was evaluated on Cu/In and Cu/Sn-3Ag metal stacks. The In and Sn-3Ag layers have much lower melting temperatures than the base material (Cu) and can be melted through the heat generated during ultrasonic bonding, forming intermetallic compounds (IMCs). Samples were bonded using different ultrasonic powers, bonding times, and forces and subsequently aged at 300°C for 500 h. After aging, die shear testing was performed and the fracture surfaces were inspected by scanning electron microscopy. Results showed that the shear strength of Cu/In joints reached an upper plateau after 100 h of thermal aging and remained stable with aging time, whereas that of the Cu/Sn-3Ag joints decreased with increasing aging time. η-Cu7In4 and (Cu,Au)11In9 IMCs were observed at the Cu/In joint, while Cu3Sn and (Ag,Cu)3Sn IMCs were found at the Cu/Sn-3Ag joint after reliability testing. As Cu-based IMCs have high melting temperatures, they are highly suitable for use in high-temperature electronics, but can be formed at room temperature using an ultrasonic approach.

A tensegrity model for hydrogen bond networks in proteins

Directory of Open Access Journals (Sweden)

Robert P. Bywater

2017-05-01

Full Text Available Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger − covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance (“closure” is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins (“domains” as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating

A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

Science.gov (United States)

Poznański, Jarosław; Poznańska, Anna; Shugar, David

2014-01-01

Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC')

Energy Technology Data Exchange (ETDEWEB)

Bonvin, Alexandre M.J.J.; Houben, Klaartje; Guenneugues, Marc; Kaptein, Robert; Boelens, Rolf [Utrecht University, Bijvoet Center for Biomolecular Research, NMR Spectroscopy (Netherlands)

2001-11-15

The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small {alpha}/{beta} protein chymotrypsin inhibitor 2. Dihedral angle restraints for the {phi} and {psi} angles of 32 out of 64 residues could be obtained from secondary chemical shift analysis with the TALOS program (Corneliscu et al., 1999a). This information was supplemented by 18 hydrogen-bond restraints derived from experimentally measured cross-hydrogen bond {sup 3hb}J{sub NC'} coupling constants. These experimental data were sufficient to generate structures that are as close as 1.0 A backbone rmsd from the crystal structure. The fold is, however, not uniquely defined and several solutions are generated that cannot be distinguished on the basis of violations or energetic considerations. Correct folds could be identified by combining clustering methods with knowledge-based potentials derived from structural databases.

Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings - an assessment of the interrelation of NMR restraints

Energy Technology Data Exchange (ETDEWEB)

Jensen, Pernille Rose; Axelsen, Jacob Bock [University of Copenhagen, Institute of Molecular Biology (Denmark); Lerche, Mathilde Hauge [Amersham Health (Sweden); Poulsen, Flemming M. [University of Copenhagen, Institute of Molecular Biology (Denmark)], E-mail: fmp@apk.molbio.ku.dk

2004-01-15

We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on {sup 1}H{sup N}-{sup 15}N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of {sup 13}CO-{sup 13}C{sup {alpha}} and {sup 15}N-{sup 13}CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 A resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone.

Hydrogen bonds of DsrD protein revealed by neutron crystallography

International Nuclear Information System (INIS)

Chatake, Toshiyuki; Higuchi, Yoshiki; Mizuno, Nobuhiro; Tanaka, Ichiro; Niimura, Nobuo; Morimoto, Yukio

2008-01-01

Hydrogen bonds of DNA-binding protein DsrD have been determined by neutron diffraction. In terms of proton donors and acceptors, DsrD protein shows striking differences from other proteins. The features of hydrogen bonds in DsrD protein from sulfate-reducing bacteria have been investigated by neutron protein crystallography. The function of DsrD has not yet been elucidated clearly, but its X-ray crystal structure revealed that it comprises a winged-helix motif and shows the highest structural homology to the DNA-binding proteins. Since any neutron structure of a DNA recognition protein has not yet been obtained, here detailed information on the hydrogen bonds in the winged-helix-motif protein is given and the following features found. (i) The number of hydrogen bonds per amino acid of DsrD is relatively fewer than for other proteins for which neutron structures were determined previously. (ii) Hydrogen bonds are localized between main-chain and main-chain atoms; there are few hydrogen bonds between main-chain and side-chain atoms and between side-chain and side-chain atoms. (iii) Hydrogen bonds inducted by protonation of specific amino acid residues (Glu50) seem to play an essential role in the dimerization of DsrD. The former two points are related to the function of the DNA-binding protein; the three-dimensional structure was mainly constructed by hydrogen bonds in main chains, while the side chains appeared to be used for another role. The latter point would be expected to contribute to the crystal growth of DsrD

Widespread Disulfide Bonding in Proteins from Thermophilic Archaea

OpenAIRE

Jorda, Julien; Yeates, Todd O.

2011-01-01

Disulfide bonds are generally not used to stabilize proteins in the cytosolic compartments of bacteria or eukaryotic cells, owing to the chemically reducing nature of those environments. In contrast, certain thermophilic archaea use disulfide bonding as a major mechanism for protein stabilization. Here, we provide a current survey of completely sequenced genomes, applying computational methods to estimate the use of disulfide bonding across the Archaea. Microbes belonging to the Crenarchaea...

A Protein Data Bank survey reveals shortening of intermolecular hydrogen bonds in ligand-protein complexes when a halogenated ligand is an H-bond donor.

Directory of Open Access Journals (Sweden)

Jarosław Poznański

Full Text Available Halogen bonding in ligand-protein complexes is currently widely exploited, e.g. in drug design or supramolecular chemistry. But little attention has been directed to other effects that may result from replacement of a hydrogen by a strongly electronegative halogen. Analysis of almost 30000 hydrogen bonds between protein and ligand demonstrates that the length of a hydrogen bond depends on the type of donor-acceptor pair. Interestingly, lengths of hydrogen bonds between a protein and a halogenated ligand are visibly shorter than those estimated for the same family of proteins in complexes with non-halogenated ligands. Taking into account the effect of halogenation on hydrogen bonding is thus important when evaluating structural and/or energetic parameters of ligand-protein complexes. All these observations are consistent with the concept that halogenation increases the acidity of the proximal amino/imino/hydroxyl groups and thus makes them better, i.e. stronger, H-bond donors.

Small angle scattering from protein/sugar conjugates

Science.gov (United States)

Jackson, Andrew; White, John

2006-11-01

The Maillard reaction between free amine groups on proteins and sugars is well known. We have examined the effect of the reaction of the casein group of milk proteins with sugars on their nanoscale structure and aggregation. The small angle neutron scattering from beta casein and sodium caseinate and their sugar conjugates have been studied as a function of solution concentration. At high conjugate concentration (greater than ca. 5 mg/ml) the addition of sugar reduces supra-micellar aggregation of the protein whilst at lower concentration, where the protein is expected to be deaggregated already, little effect is seen. Guinier analysis of the scattering data show a radius of gyration of around 75 A˚ for beta casein in solution and around 80 A˚ for the sucrose conjugate.

Phi (Φ) and psi (Ψ) angles involved in malarial peptide bonds determine sterile protective immunity.

Science.gov (United States)

Patarroyo, Manuel E; Moreno-Vranich, Armando; Bermúdez, Adriana

2012-12-07

Modified HABP (mHABP) regions interacting with HLA-DRβ1(∗) molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their Φ and Ψ torsion angles. These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by (1)H-NMR and superimposed into HLA-DRβ1(∗)-like Aotus monkey molecules; their phi (Φ) and psi (Ψ) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII(L)) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them. Copyright © 2012 Elsevier Inc. All rights reserved.

Understanding the influence of low-frequency vibrations on the hydrogen bonds of acetic acid and acetamide dimers.

Science.gov (United States)

Copeland, Christopher; Menon, Omkaran; Majumdar, D; Roszak, Szczepan; Leszczynski, Jerzy

2017-09-20

Low-frequency vibrations coupled to high-frequency modes are known to influence the hydrogen bond strengths in a weakly interacting dimer. In this context, various acetic acid and acetamide dimers were analyzed using Møller-Plesset second-order perturbation (MP2) and density functional theory (DFT)-based approaches with explicit anharmonicity corrections. The computed low-frequency fundamentals as well as the high-frequency modes, which were found to be related to hydrogen bonding (OH/NH stretching modes), were analyzed and their computed intensities were correlated with their hydrogen-bond strengths/binding energies. There are similarities in the nature of eight low-frequency fundamentals of these two dimers, and the in-plane bending and stretch-bend fundamentals of the different dimers of these two species (in this low-frequency region) have specific roles in their relative stability order. The computed linear correlations were further verified against the results from coupled cluster calculations including triple excitation (CCSD(T)), Gaussian-G4 (G4), Gaussian-G2-MP2 (G2MP2) and complete basis set (CBS-QB3) methods of high accuracy energy calculations. As a consequence of such linear correlations, an additive property of local fragment energies (responsible for hydrogen bonding) was found to be a valid approximation to predict the binding energies of such dimers and the idea was found to be extendable to the other homologues of these acids/amides.

A tensegrity model for hydrogen bond networks in proteins

OpenAIRE

Bywater, Robert P.

2017-01-01

Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger − c...

In-Depth Characterization of Protein Disulfide Bonds by Online Liquid Chromatography-Electrochemistry-Mass Spectrometry

Science.gov (United States)

Switzar, Linda; Nicolardi, Simone; Rutten, Julie W.; Oberstein, Saskia A. J. Lesnik; Aartsma-Rus, Annemieke; van der Burgt, Yuri E. M.

2016-01-01

Disulfide bonds are an important class of protein post-translational modifications, yet this structurally crucial modification type is commonly overlooked in mass spectrometry (MS)-based proteomics approaches. Recently, the benefits of online electrochemistry-assisted reduction of protein S-S bonds prior to MS analysis were exemplified by successful characterization of disulfide bonds in peptides and small proteins. In the current study, we have combined liquid chromatography (LC) with electrochemistry (EC) and mass analysis by Fourier transform ion cyclotron resonance (FTICR) MS in an online LC-EC-MS platform to characterize protein disulfide bonds in a bottom-up proteomics workflow. A key advantage of a LC-based strategy is the use of the retention time in identifying both intra- and interpeptide disulfide bonds. This is demonstrated by performing two sequential analyses of a certain protein digest, once without and once with electrochemical reduction. In this way, the "parent" disulfide-linked peptide detected in the first run has a retention time-based correlation with the EC-reduced peptides detected in the second run, thus simplifying disulfide bond mapping. Using this platform, both inter- and intra-disulfide-linked peptides were characterized in two different proteins, ß-lactoglobulin and ribonuclease B. In order to prevent disulfide reshuffling during the digestion process, proteins were digested at a relatively low pH, using (a combination of) the high specificity proteases trypsin and Glu-C. With this approach, disulfide bonds in ß-lactoglobulin and ribonuclease B were comprehensively identified and localized, showing that online LC-EC-MS is a useful tool for the characterization of protein disulfide bonds.

Small angle scattering from protein/sugar conjugates

International Nuclear Information System (INIS)

Jackson, Andrew; White, John

2006-01-01

The Maillard reaction between free amine groups on proteins and sugars is well known. We have examined the effect of the reaction of the casein group of milk proteins with sugars on their nanoscale structure and aggregation. The small angle neutron scattering from beta casein and sodium caseinate and their sugar conjugates have been studied as a function of solution concentration. At high conjugate concentration (greater than ca. 5mg/ml) the addition of sugar reduces supra-micellar aggregation of the protein whilst at lower concentration, where the protein is expected to be deaggregated already, little effect is seen. Guinier analysis of the scattering data show a radius of gyration of around 75A-bar for beta casein in solution and around 80A-bar for the sucrose conjugate

Small angle scattering from protein/sugar conjugates

Energy Technology Data Exchange (ETDEWEB)

Jackson, Andrew [Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia)]. E-mail: ajj@nist.gov; White, John [Research School of Chemistry, Australian National University, Canberra, ACT 0200 (Australia)

2006-11-15

The Maillard reaction between free amine groups on proteins and sugars is well known. We have examined the effect of the reaction of the casein group of milk proteins with sugars on their nanoscale structure and aggregation. The small angle neutron scattering from beta casein and sodium caseinate and their sugar conjugates have been studied as a function of solution concentration. At high conjugate concentration (greater than ca. 5mg/ml) the addition of sugar reduces supra-micellar aggregation of the protein whilst at lower concentration, where the protein is expected to be deaggregated already, little effect is seen. Guinier analysis of the scattering data show a radius of gyration of around 75A-bar for beta casein in solution and around 80A-bar for the sucrose conjugate.

Non-equilibrium hydrogen exchange for determination of H-bond strength and water accessibility in solid proteins.

Science.gov (United States)

Grohe, Kristof; Movellan, Kumar Tekwani; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus

2017-05-01

We demonstrate measurement of non-equilibrium backbone amide hydrogen-deuterium exchange rates (HDX) for solid proteins. The target of this study are the slowly exchanging residues in solid samples, which are associated with stable secondary-structural elements of proteins. These hydrogen exchange processes escape methods measuring equilibrium exchange rates of faster processes. The method was applied to a micro-crystalline preparation of the SH3 domain of chicken α-spectrin. Therefore, from a 100% back-exchanged micro-crystalline protein preparation, the supernatant buffer was exchanged by a partially deuterated buffer to reach a final protonation level of approximately 20% before packing the sample in a 1.3 mm rotor. Tracking of the HN peak intensities for 2 weeks reports on site-specific hydrogen bond strength and also likely reflects water accessibility in a qualitative manner. H/D exchange can be directly determined for hydrogen-bonded amides using 1 H detection under fast magic angle spinning. This approach complements existing methods and provides the means to elucidate interesting site-specific characteristics for protein functionality in the solid state.

Correlating Nitrile IR Frequencies to Local Electrostatics Quantifies Noncovalent Interactions of Peptides and Proteins.

Science.gov (United States)

Deb, Pranab; Haldar, Tapas; Kashid, Somnath M; Banerjee, Subhrashis; Chakrabarty, Suman; Bagchi, Sayan

2016-05-05

Noncovalent interactions, in particular the hydrogen bonds and nonspecific long-range electrostatic interactions are fundamental to biomolecular functions. A molecular understanding of the local electrostatic environment, consistently for both specific (hydrogen-bonding) and nonspecific electrostatic (local polarity) interactions, is essential for a detailed understanding of these processes. Vibrational Stark Effect (VSE) has proven to be an extremely useful method to measure the local electric field using infrared spectroscopy of carbonyl and nitrile based probes. The nitrile chemical group would be an ideal choice because of its absorption in an infrared spectral window transparent to biomolecules, ease of site-specific incorporation into proteins, and common occurrence as a substituent in various drug molecules. However, the inability of VSE to describe the dependence of IR frequency on electric field for hydrogen-bonded nitriles to date has severely limited nitrile's utility to probe the noncovalent interactions. In this work, using infrared spectroscopy and atomistic molecular dynamics simulations, we have reported for the first time a linear correlation between nitrile frequencies and electric fields in a wide range of hydrogen-bonding environments that may bridge the existing gap between VSE and H-bonding interactions. We have demonstrated the robustness of this field-frequency correlation for both aromatic nitriles and sulfur-based nitriles in a wide range of molecules of varying size and compactness, including small molecules in complex solvation environments, an amino acid, disordered peptides, and structured proteins. This correlation, when coupled to VSE, can be used to quantify noncovalent interactions, specific or nonspecific, in a consistent manner.

Sulfur dioxide induced aggregation of wine thaumatin-like proteins: Role of disulfide bonds.

Science.gov (United States)

Chagas, Ricardo; Laia, César A T; Ferreira, Ricardo B; Ferreira, Luísa M

2018-09-01

Aggregation of heat unstable wine proteins is responsible for the economically and technologically detrimental problem called wine protein haze. This is caused by the aggregation of thermally unfolded proteins that can precipitate in bottled wine. To study the influence of SO 2 in this phenomenon, wine proteins were isolated and thaumatins were identified has the most prone to aggregate in the presence of this compound. Isolated wine thaumatins aggregation was followed by dynamic light scattering (DLS), circular dichroism (CD), fluorescence spectroscopy and size exclusion chromatography (SEC). Our experimental results demonstrate that protein thermal unfolding after exposure of the protein to 70 °C does not present differences whether SO 2 is present or not. Conversely, when the protein solution is cooled to 15 °C (after heat stress) significant analytical changes can be observed between samples with and without SO 2 . A remarkable change of circular dichroism spectra in the region 220-230 nm is observed (which can be related to S-S torsion angles), as well as an increase in tryptophan fluorescence intensity (absence of fluorescence quenching by S-S bonds). Formation of covalently-linked dimeric and tetrameric protein species were also detected by SEC. The ability to dissolve the aggregates with 8 M urea seems to indicate that hydrophobic interactions are prevalent in the formed aggregates. Also, the reduction of these aggregates with tris (2-carboxyethyl) phosphine (TCEP) to only monomeric species reveals the presence of intermolecular S-S bonds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evidence for high-pressure-induced rupture of hydrogen bonds in LH2 photosynthetic antenna pigment-protein complexes

International Nuclear Information System (INIS)

Kangur, L; Leiger, K; Freiberg, A

2008-01-01

The bacteriochlorophyll a-containing LH2 light harvesting complex is an integral membrane protein that catalyzes the photosynthetic process in purple photosynthetic bacteria. The LH2 complexes from Rhodobacter sphaeroides show characteristic strong absorbance at 800 and 850 nm due to the bacteriochlorophyll a molecules confined in two separate areas of the protein. Using these cofactors as intrinsic probes to monitor changes in membrane protein structure, we investigate the response to high hydrostatic pressure up to 2.1 GPa of LH2 complexes embedded into natural membrane environment or extracted with detergent. We demonstrate that high pressure does induce significant alterations to the tertiary structure of the protein in proximity of the protein-bound bacteriochlorophyll a molecules, including breakage of the hydrogen bond they are involved in. The membrane-embedded complexes appear more resilient to damaging effects of the compression than the complexes extracted into detergent environment. This difference has tentatively been explained by more compact structure of the membrane-embedded complexes

Evidence for high-pressure-induced rupture of hydrogen bonds in LH2 photosynthetic antenna pigment-protein complexes

Energy Technology Data Exchange (ETDEWEB)

Kangur, L; Leiger, K; Freiberg, A [Institute of Physics, University of Tartu, Riia 142, Tartu 51014 (Estonia)

2008-07-15

The bacteriochlorophyll a-containing LH2 light harvesting complex is an integral membrane protein that catalyzes the photosynthetic process in purple photosynthetic bacteria. The LH2 complexes from Rhodobacter sphaeroides show characteristic strong absorbance at 800 and 850 nm due to the bacteriochlorophyll a molecules confined in two separate areas of the protein. Using these cofactors as intrinsic probes to monitor changes in membrane protein structure, we investigate the response to high hydrostatic pressure up to 2.1 GPa of LH2 complexes embedded into natural membrane environment or extracted with detergent. We demonstrate that high pressure does induce significant alterations to the tertiary structure of the protein in proximity of the protein-bound bacteriochlorophyll a molecules, including breakage of the hydrogen bond they are involved in. The membrane-embedded complexes appear more resilient to damaging effects of the compression than the complexes extracted into detergent environment. This difference has tentatively been explained by more compact structure of the membrane-embedded complexes.

Interplay between Peptide Bond Geometrical Parameters in Nonglobular Structural Contexts

Directory of Open Access Journals (Sweden)

Luciana Esposito

2013-01-01

Full Text Available Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides. Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-Cα-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-Cα-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles Δω/ψ in collagen-like models may have interesting implications for triple helix stability.

Interplay between peptide bond geometrical parameters in nonglobular structural contexts.

Science.gov (United States)

Esposito, Luciana; Balasco, Nicole; De Simone, Alfonso; Berisio, Rita; Vitagliano, Luigi

2013-01-01

Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides). Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-C(α)-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-C(α)-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles Δω/ψ in collagen-like models may have interesting implications for triple helix stability.

Vibrational characteristics of FRP-bonded concrete interfacial defects in a low frequency regime

Science.gov (United States)

Cheng, Tin Kei; Lau, Denvid

2014-04-01

As externally bonded fiber-reinforced polymer (FRP) is a critical load-bearing component of strengthened or retrofitted civil infrastructures, the betterment of structural health monitoring (SHM) methodology for such composites is imperative. Henceforth the vibrational characteristics of near surface interfacial defects involving delamination and trapped air pockets at the FRP-concrete interface are investigated in this study using a finite element approach. Intuitively, due to its lower interfacial stiffness compared with an intact interface, a damaged region is expected to have a set of resonance frequencies different from an intact region when excited by acoustic waves. It has been observed that, when excited acoustically, both the vibrational amplitudes and frequency peaks in the response spectrum of the defects demonstrate a significant deviation from an intact FRP-bonded region. For a thin sheet of FRP bonded to concrete with sizable interfacial defects, the fundamental mode under free vibration is shown to be relatively low, in the order of kHz. Due to the low resonance frequencies of the defects, the use of low-cost equipment for interfacial defect detection via response spectrum analysis is highly feasible.

At least 10% shorter C–H bonds in cryogenic protein crystal structures than in current AMBER forcefields

Energy Technology Data Exchange (ETDEWEB)

Pang, Yuan-Ping, E-mail: pang@mayo.edu

2015-03-06

High resolution protein crystal structures resolved with X-ray diffraction data at cryogenic temperature are commonly used as experimental data to refine forcefields and evaluate protein folding simulations. However, it has been unclear hitherto whether the C–H bond lengths in cryogenic protein structures are significantly different from those defined in forcefields to affect protein folding simulations. This article reports the finding that the C–H bonds in high resolution cryogenic protein structures are 10–14% shorter than those defined in current AMBER forcefields, according to 3709 C–H bonds in the cryogenic protein structures with resolutions of 0.62–0.79 Å. Also, 20 all-atom, isothermal–isobaric, 0.5-μs molecular dynamics simulations showed that chignolin folded from a fully-extended backbone formation to the native β-hairpin conformation in the simulations using AMBER forcefield FF12SB at 300 K with an aggregated native state population including standard error of 10 ± 4%. However, the aggregated native state population with standard error reduced to 3 ± 2% in the same simulations except that C–H bonds were shortened by 10–14%. Furthermore, the aggregated native state populations with standard errors increased to 35 ± 3% and 26 ± 3% when using FF12MC, which is based on AMBER forcefield FF99, with and without the shortened C–H bonds, respectively. These results show that the 10–14% bond length differences can significantly affect protein folding simulations and suggest that re-parameterization of C–H bonds according to the cryogenic structures could improve the ability of a forcefield to fold proteins in molecular dynamics simulations. - Highlights: • Cryogenic crystal structures are commonly used in computational studies of proteins. • C–H bonds in the cryogenic structures are shorter than those defined in forcefields. • A survey of 3709 C–H bonds shows that the cryogenic bonds are 10–14% shorter. • The

Joint Angle and Frequency Estimation Using Multiple-Delay Output Based on ESPRIT

Science.gov (United States)

Xudong, Wang

2010-12-01

This paper presents a novel ESPRIT algorithm-based joint angle and frequency estimation using multiple-delay output (MDJAFE). The algorithm can estimate the joint angles and frequencies, since the use of multiple output makes the estimation accuracy greatly improved when compared with a conventional algorithm. The useful behavior of the proposed algorithm is verified by simulations.

A Comparison of High Frequency Angle of Arrival and Ionosonde Data During a Traveling Ionospheric Disturbance

Science.gov (United States)

Knippling, K.; Nava, O.; Emmons, D. J., II; Dao, E. V.

2017-12-01

Geolocation techniques are used to track the source of uncooperative high frequency emitters. Traveling ionospheric disturbances (TIDs) make geolocation particularly difficult due to large perturbations in the local ionospheric electron density profiles. Angle of arrival(AoA) and ionosonde virtual height measurements collected at White Sands Missile Range, New Mexico in January, 2014 are analyzed during a medium scale TID (MSTID). MSTID characteristics are extracted from the measurements, and a comparison between the data sets is performed, providing a measure of the correlation as a function of distance between the ionosonde and AoA circuit midpoints. The results of this study may advance real-time geolocation techniques through the implementation of a time varying mirror model height.

High-frequency conductivity of photoionized plasma

Energy Technology Data Exchange (ETDEWEB)

Anakhov, M. V.; Uryupin, S. A., E-mail: uryupin@sci.lebedev.ru [National Research Nuclear University “MEPhI,” (Russian Federation)

2016-08-15

The tensor of the high-frequency conductivity of a plasma created via tunnel ionization of atoms in the field of linearly or circularly polarized radiation is derived. It is shown that the real part of the conductivity tensor is highly anisotropic. In the case of a toroidal velocity distribution of photoelectrons, the possibility of amplification of a weak high-frequency field polarized at a sufficiently large angle to the anisotropy axis of the initial nonequilibrium distribution is revealed.

Integrating angle-frequency domain synchronous averaging technique with feature extraction for gear fault diagnosis

Science.gov (United States)

Zhang, Shengli; Tang, J.

2018-01-01

Gear fault diagnosis relies heavily on the scrutiny of vibration responses measured. In reality, gear vibration signals are noisy and dominated by meshing frequencies as well as their harmonics, which oftentimes overlay the fault related components. Moreover, many gear transmission systems, e.g., those in wind turbines, constantly operate under non-stationary conditions. To reduce the influences of non-synchronous components and noise, a fault signature enhancement method that is built upon angle-frequency domain synchronous averaging is developed in this paper. Instead of being averaged in the time domain, the signals are processed in the angle-frequency domain to solve the issue of phase shifts between signal segments due to uncertainties caused by clearances, input disturbances, and sampling errors, etc. The enhanced results are then analyzed through feature extraction algorithms to identify the most distinct features for fault classification and identification. Specifically, Kernel Principal Component Analysis (KPCA) targeting at nonlinearity, Multilinear Principal Component Analysis (MPCA) targeting at high dimensionality, and Locally Linear Embedding (LLE) targeting at local similarity among the enhanced data are employed and compared to yield insights. Numerical and experimental investigations are performed, and the results reveal the effectiveness of angle-frequency domain synchronous averaging in enabling feature extraction and classification.

Hysteresis-free high-temperature precise bimorph actuators produced by direct bonding of lithium niobate wafers

Energy Technology Data Exchange (ETDEWEB)

Shur, V. Ya.; Baturin, I. S.; Mingaliev, E. A.; Zorikhin, D. V.; Udalov, A. R.; Greshnyakov, E. D. [Ferroelectric Laboratory, Institute of Natural Sciences, Ural Federal University, 51 Lenin Ave., 620000 Ekaterinburg (Russian Federation)

2015-02-02

The current paper presents a piezoelectric bimorph actuator produced by direct bonding of lithium niobate wafers with the mirrored Y and Z axes. Direct bonding technology allowed to fabricate bidomain plate with precise positioning of ideally flat domain boundary. By optimizing the cutting angle (128° Y-cut), the piezoelectric constant became as large as 27.3 pC/N. Investigation of voltage dependence of bending displacement confirmed that bimorph actuator has excellent linearity and hysteresis-free. Decrease of the applied voltage down to mV range showed the perfect linearity up to the sub-nm deflection amplitude. The frequency and temperature dependences of electromechanical transmission coefficient in wide temperature range (from 300 to 900 K) were investigated.

Small angle x-ray scattering from proteins in solution

International Nuclear Information System (INIS)

de Souza, C.F.; Torriani, I.L.; Bonafe, C.F.S.; Merrelles, N.C.; Vachette, P.

1989-01-01

In this work the authors report experiments performed with giant respiratory proteins from annelids (erythrocruorins), known to have a molecular weight in the order of four million Daltons. Preliminary x-ray scattering data was obtained using a conventional rotating anode source. High resolution small angle scattering curves were obtained with synchrotron radiation from the DCI storage ring at LURE. Data from solutions with several protein concentrations were analyzed in order to determine low resolution dimensional parameters, using Guinier plots from the smeared scattering curves and the inverse transformation method

Nitrile Probes of Electric Field Agree with Independently Measured Fields in Green Fluorescent Protein Even in the Presence of Hydrogen Bonding.

Science.gov (United States)

Slocum, Joshua D; Webb, Lauren J

2016-05-25

demonstrate that even in the presence of hydrogen bonding it is possible to relate nitrile absorption frequencies to electrostatic environment by comparing highly similar environments. GFP's intrinsic linear sensitivity to electric fields makes it a convenient model system for studying electrostatics in proteins that offers lessons for proteins without this visible fluorophore.

Full cyclic coordinate descent: solving the protein loop closure problem in Cα space

Directory of Open Access Journals (Sweden)

Hamelryck Thomas

2005-06-01

Full Text Available Abstract Background Various forms of the so-called loop closure problem are crucial to protein structure prediction methods. Given an N- and a C-terminal end, the problem consists of finding a suitable segment of a certain length that bridges the ends seamlessly. In homology modelling, the problem arises in predicting loop regions. In de novo protein structure prediction, the problem is encountered when implementing local moves for Markov Chain Monte Carlo simulations. Most loop closure algorithms keep the bond angles fixed or semi-fixed, and only vary the dihedral angles. This is appropriate for a full-atom protein backbone, since the bond angles can be considered as fixed, while the (φ, ψ dihedral angles are variable. However, many de novo structure prediction methods use protein models that only consist of Cα atoms, or otherwise do not make use of all backbone atoms. These methods require a method that alters both bond and dihedral angles, since the pseudo bond angle between three consecutive Cα atoms also varies considerably. Results Here we present a method that solves the loop closure problem for Cα only protein models. We developed a variant of Cyclic Coordinate Descent (CCD, an inverse kinematics method from the field of robotics, which was recently applied to the loop closure problem. Since the method alters both bond and dihedral angles, which is equivalent to applying a full rotation matrix, we call our method Full CCD (FCDD. FCCD replaces CCD's vector-based optimization of a rotation around an axis with a singular value decomposition-based optimization of a general rotation matrix. The method is easy to implement and numerically stable. Conclusion We tested the method's performance on sets of random protein Cα segments between 5 and 30 amino acids long, and a number of loops of length 4, 8 and 12. FCCD is fast, has a high success rate and readily generates conformations close to those of real loops. The presence of constraints

Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

International Nuclear Information System (INIS)

Langkilde, Annette; Kristensen, Søren M.; Lo Leggio, Leila; Mølgaard, Anne; Jensen, Jan H.; Houk, Andrew R.; Navarro Poulsen, Jens-Christian; Kauppinen, Sakari; Larsen, Sine

2008-01-01

The short hydrogen bonds in rhamnogalacturonan acetylesterase have been investigated by structure determination of an active-site mutant, 1 H NMR spectra and computational methods. Comparisons are made to database statistics. A very short carboxylic acid carboxylate hydrogen bond, buried in the protein, could explain the low-field (18 p.p.m.) 1 H NMR signal. An extremely low-field signal (at approximately 18 p.p.m.) in the 1 H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theoretical calculations of chemical shift values were used in the interpretation of the experimental 1 H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 Å resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 Å) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor–acceptor distances of different types of hydrogen bonds. The short hydrogen-bond interactions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK a values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are

A piezoelectric micro generator worked at low frequency and high acceleration based on PZT and phosphor bronze bonding.

Science.gov (United States)

Tang, Gang; Yang, Bin; Hou, Cheng; Li, Guimiao; Liu, Jingquan; Chen, Xiang; Yang, Chunsheng

2016-12-08

Recently, piezoelectric energy harvesters (PEHs) have been paid a lot of attention by many researchers to convert mechanical energy into electrical and low level vibration. Currently, most of PEHs worked under high frequency and low level vibration. In this paper, we propose a micro cantilever generator based on the bonding of bulk PZT wafer and phosphor bronze, which is fabricated by MEMS technology, such as mechanical chemical thinning and etching. The experimental results show that the open-circuit output voltage, output power and power density of this fabricated prototype are 35 V, 321 μW and 8664 μW cm -3 at the resonant frequency of 100.8 Hz, respectively, when it matches an optimal loading resistance of 140 kΩ under the excitation of 3.0 g acceleration. The fabricated micro generator can obtain the open-circuit stable output voltage of 61.2 V when the vibration acceleration arrives at 7.0 g. Meanwhile, when this device is pasted on the vibrating vacuum pump, the output voltage is about 11 V. It demonstrates that this novel proposed device can scavenge high vibration level energy at low frequency for powering the inertial sensors in internet of things application.

A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles

Directory of Open Access Journals (Sweden)

Maurer Till

2005-04-01

Full Text Available Abstract Background We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restraints defining the optimal local geometry of the structure weighted mean dihedral angles and their standard deviations are used which are calculated with an algorithm described earlier by Döker et al. (1999, BBRC, 257, 348–350. The overall long-range contacts are established via a small number of distance restraints between atoms involved in hydrogen bonds and backbone atoms of conserved residues. Employing the restraints generated by PERMOL three-dimensional structures are obtained using standard molecular dynamics programs such as DYANA or CNS. Results To test this modeling approach it has been used for predicting the structure of the histidine-containing phosphocarrier protein HPr from E. coli and the structure of the human peroxisome proliferator activated receptor γ (Ppar γ. The divergence between the modeled HPr and the previously determined X-ray structure was comparable to the divergence between the X-ray structure and the published NMR structure. The modeled structure of Ppar γ was also very close to the previously solved X-ray structure with an RMSD of 0.262 nm for the backbone atoms. Conclusion In summary, we present a new method for homology modeling capable of producing high-quality structure models. An advantage of the method is that it can be used in combination with incomplete NMR data to obtain reasonable structure models in accordance with the experimental data.

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.

Science.gov (United States)

Lyons, James; Dehzangi, Abdollah; Heffernan, Rhys; Sharma, Alok; Paliwal, Kuldip; Sattar, Abdul; Zhou, Yaoqi; Yang, Yuedong

2014-10-30

Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between C(αi-1)-C(αi)-C(αi+1) (θ) and a dihedral angle rotated about the C(αi)-C(αi+1) bond (τ). θ and τ angles, as the representative of structural properties of three to four amino-acid residues, offer a description of backbone conformations that is complementary to φ and ψ angles (single residue) and secondary structures (>3 residues). Here, we report the first machine-learning technique for sequence-based prediction of θ and τ angles. Predicted angles based on an independent test have a mean absolute error of 9° for θ and 34° for τ with a distribution on the θ-τ plane close to that of native values. The average root-mean-square distance of 10-residue fragment structures constructed from predicted θ and τ angles is only 1.9Å from their corresponding native structures. Predicted θ and τ angles are expected to be complementary to predicted ϕ and ψ angles and secondary structures for using in model validation and template-based as well as template-free structure prediction. The deep neural network learning technique is available as an on-line server called Structural Property prediction with Integrated DEep neuRal network (SPIDER) at http://sparks-lab.org. Copyright © 2014 Wiley Periodicals, Inc.

Microwave-assisted acid and base hydrolysis of intact proteins containing disulfide bonds for protein sequence analysis by mass spectrometry.

Science.gov (United States)

Reiz, Bela; Li, Liang

2010-09-01

Controlled hydrolysis of proteins to generate peptide ladders combined with mass spectrometric analysis of the resultant peptides can be used for protein sequencing. In this paper, two methods of improving the microwave-assisted protein hydrolysis process are described to enable rapid sequencing of proteins containing disulfide bonds and increase sequence coverage, respectively. It was demonstrated that proteins containing disulfide bonds could be sequenced by MS analysis by first performing hydrolysis for less than 2 min, followed by 1 h of reduction to release the peptides originally linked by disulfide bonds. It was shown that a strong base could be used as a catalyst for microwave-assisted protein hydrolysis, producing complementary sequence information to that generated by microwave-assisted acid hydrolysis. However, using either acid or base hydrolysis, amide bond breakages in small regions of the polypeptide chains of the model proteins (e.g., cytochrome c and lysozyme) were not detected. Dynamic light scattering measurement of the proteins solubilized in an acid or base indicated that protein-protein interaction or aggregation was not the cause of the failure to hydrolyze certain amide bonds. It was speculated that there were some unknown local structures that might play a role in preventing an acid or base from reacting with the peptide bonds therein. 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

Science.gov (United States)

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Large angle and high linearity two-dimensional laser scanner based on voice coil actuators

Science.gov (United States)

Wu, Xin; Chen, Sihai; Chen, Wei; Yang, Minghui; Fu, Wen

2011-10-01

A large angle and high linearity two-dimensional laser scanner with an in-house ingenious deflection angle detecting system is developed based on voice coil actuators direct driving mechanism. The specially designed voice coil actuators make the steering mirror moving at a sufficiently large angle. Frequency sweep method based on virtual instruments is employed to achieve the natural frequency of the laser scanner. The response shows that the performance of the laser scanner is limited by the mechanical resonances. The closed-loop controller based on mathematical model is used to reduce the oscillation of the laser scanner at resonance frequency. To design a qualified controller, the model of the laser scanner is set up. The transfer function of the model is identified with MATLAB according to the tested data. After introducing of the controller, the nonlinearity decreases from 13.75% to 2.67% at 50 Hz. The laser scanner also has other advantages such as large deflection mirror, small mechanical structure, and high scanning speed.

Ligand Bridging-Angle-Driven Assembly of Molecular Architectures Based on Quadruply Bonded Mo-Mo Dimers

Energy Technology Data Exchange (ETDEWEB)

Li, Jian-Rong; Yakovenko, Andrey A; Lu, Weigang; Timmons, Daren J; Zhuang, Wenjuan; Yuan, Daqiang; Zhou, Hong-Cai

2010-12-15

A systematic exploration of the assembly of Mo₂(O₂C-)₄-based metal–organic molecular architectures structurally controlled by the bridging angles of rigid organic linkers has been performed. Twelve bridging dicarboxylate ligands were designed to be of different sizes with bridging angles of 0, 60, 90, and 120° while incorporating a variety of nonbridging functional groups, and these ligands were used as linkers. These dicarboxylate linkers assemble with quadruply bonded Mo–Mo clusters acting as nodes to give 13 molecular architectures, termed metal–organic polygons/polyhedra with metal cluster node arrangements of a linear shape, triangle, octahedron, and cuboctahedron/anti-cuboctahedron. The syntheses of these complexes have been optimized and their structures determined by single-crystal X-ray diffraction. The results have shown that the shape and size of the resulting molecular architecture can be controlled by tuning the bridging angle and size of the linker, respectively. Functionalization of the linker can adjust the solubility of the ensuing molecular assembly but has little or no effect on the geometry of the product. Preliminary gas adsorption, spectroscopic, and electrochemical properties of selected members were also studied. The present work is trying to enrich metal-containing supramolecular chemistry through the inclusion of well-characterized quadruply bonded Mo–Mo units into the structures, which can widen the prospect of additional electronic functionality, thereby leading to novel properties.

Ligand bridging-angle-driven assembly of molecular architectures based on quadruply bonded Mo-Mo dimers.

Science.gov (United States)

Li, Jian-Rong; Yakovenko, Andrey A; Lu, Weigang; Timmons, Daren J; Zhuang, Wenjuan; Yuan, Daqiang; Zhou, Hong-Cai

2010-12-15

A systematic exploration of the assembly of Mo2(O2C-)4-based metal-organic molecular architectures structurally controlled by the bridging angles of rigid organic linkers has been performed. Twelve bridging dicarboxylate ligands were designed to be of different sizes with bridging angles of 0, 60, 90, and 120° while incorporating a variety of nonbridging functional groups, and these ligands were used as linkers. These dicarboxylate linkers assemble with quadruply bonded Mo-Mo clusters acting as nodes to give 13 molecular architectures, termed metal-organic polygons/polyhedra with metal cluster node arrangements of a linear shape, triangle, octahedron, and cuboctahedron/anti-cuboctahedron. The syntheses of these complexes have been optimized and their structures determined by single-crystal X-ray diffraction. The results have shown that the shape and size of the resulting molecular architecture can be controlled by tuning the bridging angle and size of the linker, respectively. Functionalization of the linker can adjust the solubility of the ensuing molecular assembly but has little or no effect on the geometry of the product. Preliminary gas adsorption, spectroscopic, and electrochemical properties of selected members were also studied. The present work is trying to enrich metal-containing supramolecular chemistry through the inclusion of well-characterized quadruply bonded Mo-Mo units into the structures, which can widen the prospect of additional electronic functionality, thereby leading to novel properties.

Bite angle effects of diphosphines in C-C and C-X bond forming cross coupling reactions

NARCIS (Netherlands)

Birkholz, M.N.; Freixa, Z.; van Leeuwen, P.W.N.M.

2009-01-01

Catalytic reactions of C-C and C-X bond formation are discussed in this critical review with particular emphasis on cross coupling reactions catalyzed by palladium and wide bite angle bidentate diphosphine ligands. Especially those studies have been collected that allow comparison of the ligand bite

Disulfide Linkage Characterization of Disulfide Bond-Containing Proteins and Peptides by Reducing Electrochemistry and Mass Spectrometry

DEFF Research Database (Denmark)

Cramer, Christian N; Haselmann, Kim F; Olsen, Jesper V

2016-01-01

in protein sequencing by tandem MS (MS/MS). Electrochemical (EC) reduction of disulfide bonds has recently been demonstrated to provide efficient reduction efficiencies, significantly enhancing sequence coverages in online coupling with MS characterization. In this study, the potential use of EC disulfide...... link between parent disulfide-linked fragments and free reduced peptides in an LC-EC-MS platform of nonreduced proteolytic protein digestions. Here we report the successful use of EC as a partial reduction approach in mapping of disulfide bonds of intact human insulin (HI) and lysozyme. In addition, we...... established a LC-EC-MS platform advantageous in disulfide characterization of complex and highly disulfide-bonded proteins such as human serum albumin (HSA) by online EC reduction of nonreduced proteolytic digestions....

The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules.

Science.gov (United States)

Sun, Weitao

2018-01-01

The global shape of a protein molecule is believed to be dominant in determining low-frequency deformational motions. However, how structure dynamics relies on residue interactions remains largely unknown. The global residue community structure and the local residue interactions are two important coexisting factors imposing significant effects on low-frequency normal modes. In this work, an algorithm for community structure partition is proposed by integrating Miyazawa-Jernigan empirical potential energy as edge weight. A sensitivity parameter is defined to measure the effect of local residue interaction on low-frequency movement. We show that community structure is a more fundamental feature of residue contact networks. Moreover, we surprisingly find that low-frequency normal mode eigenvectors are sensitive to some local critical residue interaction pairs (CRIPs). A fair amount of CRIPs act as bridges and hold distributed structure components into a unified tertiary structure by bonding nearby communities. Community structure analysis and CRIP detection of 116 catalytic proteins reveal that breaking up of a CRIP can cause low-frequency allosteric movement of a residue at the far side of protein structure. The results imply that community structure and CRIP may be the structural basis for low-frequency motions.

Disulphide bond formation in food protein aggregation and gelation

NARCIS (Netherlands)

Visschers, R.W.; Jongh, de H.H.J.

2005-01-01

In this short review we discuss the role of cysteine residues and cystine bridges for the functional aggregation of food proteins. We evaluate how formation and cleavage of disulphide bonds proceeds at a molecular level, and how inter- and intramolecular disulfide bonds can be detected and modified.

Contribution of Adsorbed Protein Films to Nanoscopic Vibrations Exhibited by Bacteria Adhering through Ligand-Receptor Bonds.

Science.gov (United States)

Song, Lei; Sjollema, Jelmer; Norde, Willem; Busscher, Henk J; van der Mei, Henny C

2015-09-29

Bacteria adhering to surfaces exhibit nanoscopic vibrations that depend on the viscoelasticity of the bond. The quantification of the nanoscopic vibrations of bacteria adhering to surfaces provides new opportunities to better understand the properties of the bond through which bacteria adhere and the mechanisms by which they resist detachment. Often, however, bacteria do not adhere to bare surfaces but to adsorbed protein films, on which adhesion involves highly specific ligand-receptor binding next to nonspecific DLVO interaction forces. Here we determine the contribution of adsorbed salivary protein and fibronectin films to vibrations exhibited by adhering streptococci and staphylococci, respectively. The streptococcal strain used has the ability to adhere to adsorbed salivary proteins films through antigen I/II ligand-receptor binding, while the staphylococcal strain used adheres to adsorbed fibronectin films through a proteinaceous ligand-receptor bond. In the absence of ligand-receptor binding, electrostatic interactions had a large impact on vibration amplitudes of adhering bacteria on glass. On an adsorbed salivary protein film, vibration amplitudes of adhering streptococci depended on the film softness as determined by QCM-D and were reduced after film fixation using glutaraldehyde. On a relatively stiff fibronectin film, cross-linking the film in glutaraldehyde hardly reduced its softness, and accordingly fibronectin film softness did not contribute to vibration amplitudes of adhering staphylococci. However, fixation of the staphylococcus-fibronectin bond further decreased vibration amplitudes, while fixation of the streptococcus bond hardly impacted vibration amplitudes. Summarizing, this study shows that both the softness of adsorbed protein films and the properties of the bond between an adhering bacterium and an adsorbed protein film play an important role in bacterial vibration amplitudes. These nanoscopic vibrations reflect the viscoelasticity of the

FR4-Based Electromagnetic Scanning Micromirror Integrated with Angle Sensor

Directory of Open Access Journals (Sweden)

Hongjie Lei

2018-05-01

Full Text Available This paper presents a flame retardant 4 (FR4-based electromagnetic scanning micromirror, which aims to overcome the limitations of conventional microelectromechanical systems (MEMS micromirrors for the large-aperture and low-frequency scanning applications. This micromirror is fabricated through a commercial printed circuit board (PCB technology at a low cost and with a short process cycle, before an aluminum-coated silicon mirror plate with a large aperture is bonded on the FR4 platform to provide a high surface quality. In particular, an electromagnetic angle sensor is integrated to monitor the motion of the micromirror in real time. A prototype has been assembled and tested. The results show that the micromirror can reach the optical scan angle of 11.2 ∘ with a low driving voltage of only 425 mV at resonance (361.8 Hz. At the same time, the signal of the integrated angle sensor also shows good signal-to-noise ratio, linearity and sensitivity. Finally, the reliability of the FR4 based micro-mirror has been tested. The prototype successfully passes both shock and vibration tests. Furthermore, the results of the long-term mechanical cycling test (50 million cycles suggest that the maximum variations of resonant frequency and scan angle are less than 0.3% and 6%, respectively. Therefore, this simple and robust micromirror has great potential in being useful in a number of optical microsystems, especially when large-aperture or low-frequency is required.

Protein disulfide bond generation in Escherichia coli DsbB–DsbA

International Nuclear Information System (INIS)

Inaba, Kenji

2008-01-01

The crystal structure of the DsbB–DsbA–ubiquinone ternary complex has revealed a mechanism of protein disulfide bond generation in Escherichia coli. Protein disulfide bond formation is catalyzed by a series of Dsb enzymes present in the periplasm of Escherichia coli. The crystal structure of the DsbB–DsbA–ubiquinone ternary complex provided important insights into mechanisms of the de novo disulfide bond generation cooperated by DsbB and ubiquinone and of the disulfide bond shuttle from DsbB to DsbA. The structural basis for prevention of the crosstalk between the DsbA–DsbB oxidative and the DsbC–DsbD reductive pathways has also been proposed

Conformational analysis by quantitative NOE measurements of the β-proton pairs across individual disulfide bonds in proteins

International Nuclear Information System (INIS)

Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune

2012-01-01

NOEs between the β-protons of cysteine residues across disulfide bonds in proteins provide direct information on the connectivities and conformations of these important cross-links, which are otherwise difficult to investigate. With conventional [U- 13 C, 15 N]-proteins, however, fast spin diffusion processes mediated by strong dipolar interactions between geminal β-protons prohibit the quantitative measurements and thus the analyses of long-range NOEs across disulfide bonds. We describe a robust approach for alleviating such difficulties, by using proteins selectively labeled with an equimolar mixture of (2R, 3S)-[β- 13 C; α,β- 2 H 2 ] Cys and (2R, 3R)-[β- 13 C; α,β- 2 H 2 ] Cys, but otherwise fully deuterated. Since either one of the prochiral methylene protons, namely β2 (proS) or β3 (proR), is always replaced with a deuteron and no other protons remain in proteins prepared by this labeling scheme, all four of the expected NOEs for the β-protons across disulfide bonds could be measured without any spin diffusion interference, even with long mixing times. Therefore, the NOEs for the β2 and β3 pairs across each of the disulfide bonds could be observed at high sensitivity, even though they are 25% of the theoretical maximum for each pair. With the NOE information, the disulfide bond connectivities can be unambiguously established for proteins with multiple disulfide bonds. In addition, the conformations around disulfide bonds, namely χ 2 and χ 3 , can be determined based on the precise proton distances of the four β-proton pairs, by quantitative measurements of the NOEs across the disulfide bonds. The feasibility of this method is demonstrated for bovine pancreatic trypsin inhibitor, which has three disulfide bonds.

Characteristics of enzyme hydrolyzing natural covalent bond between RNA and protein VPg of encephalomyocarditis virus

International Nuclear Information System (INIS)

Drygin, Yu.F.; Siyanova, E.Yu.

1986-01-01

The isolation and a preliminary characterization of the enzyme specifically hydrolyzing the phosphodiester bond between protein VPg and the RNA of encephalomyocarditis virus was the goal of the present investigation. The enzyme was isolated from a salt extract of Krebs II mouse ascites carcinoma cells by ion-exchange and affinity chromatography. It was found that the enzyme actually specifically cleaves the covalent bond between the RNA and protein, however, the isolation procedure does not free the enzyme from impurities which partially inhibit it. The enzyme cleaves the RNA-protein VPg complex of polio virus at a high rate, it is completely inactivated at 55 0 C, and is partially inhibited by EDTA

Variable-angle epifluorescence microscopy characterizes protein dynamics in the vicinity of plasma membrane in plant cells.

Science.gov (United States)

Chen, Tong; Ji, Dongchao; Tian, Shiping

2018-03-14

The assembly of protein complexes and compositional lipid patterning act together to endow cells with the plasticity required to maintain compositional heterogeneity with respect to individual proteins. Hence, the applications for imaging protein localization and dynamics require high accuracy, particularly at high spatio-temporal level. We provided experimental data for the applications of Variable-Angle Epifluorescence Microscopy (VAEM) in dissecting protein dynamics in plant cells. The VAEM-based co-localization analysis took penetration depth and incident angle into consideration. Besides direct overlap of dual-color fluorescence signals, the co-localization analysis was carried out quantitatively in combination with the methodology for calculating puncta distance and protein proximity index. Besides, simultaneous VAEM tracking of cytoskeletal dynamics provided more insights into coordinated responses of actin filaments and microtubules. Moreover, lateral motility of membrane proteins was analyzed by calculating diffusion coefficients and kymograph analysis, which represented an alternative method for examining protein motility. The present study presented experimental evidence on illustrating the use of VAEM in tracking and dissecting protein dynamics, dissecting endosomal dynamics, cell structure assembly along with membrane microdomain and protein motility in intact plant cells.

Selectively dispersed isotope labeling for protein structure determination by magic angle spinning NMR

Energy Technology Data Exchange (ETDEWEB)

Eddy, Matthew T. [Massachusetts Institute of Technology, Department of Chemistry (United States); Belenky, Marina [Brandeis University, Department of Chemistry (United States); Sivertsen, Astrid C. [Massachusetts Institute of Technology, Francis Bitter Magnet Laboratory (United States); Griffin, Robert G. [Massachusetts Institute of Technology, Department of Chemistry (United States); Herzfeld, Judith, E-mail: herzfeld@brandeis.edu [Brandeis University, Department of Chemistry (United States)

2013-10-15

The power of nuclear magnetic resonance spectroscopy derives from its site-specific access to chemical, structural and dynamic information. However, the corresponding multiplicity of interactions can be difficult to tease apart. Complimentary approaches involve spectral editing on the one hand and selective isotope substitution on the other. Here we present a new 'redox' approach to the latter: acetate is chosen as the sole carbon source for the extreme oxidation numbers of its two carbons. Consistent with conventional anabolic pathways for the amino acids, [1-{sup 13}C] acetate does not label {alpha} carbons, labels other aliphatic carbons and the aromatic carbons very selectively, and labels the carboxyl carbons heavily. The benefits of this labeling scheme are exemplified by magic angle spinning spectra of microcrystalline immunoglobulin binding protein G (GB1): the elimination of most J-couplings and one- and two-bond dipolar couplings provides narrow signals and long-range, intra- and inter-residue, recoupling essential for distance constraints. Inverse redox labeling, from [2-{sup 13}C] acetate, is also expected to be useful: although it retains one-bond couplings in the sidechains, the removal of CA-CO coupling in the backbone should improve the resolution of NCACX spectra.

Prediction of backbone dihedral angles and protein secondary structure using support vector machines

Directory of Open Access Journals (Sweden)

Hirst Jonathan D

2009-12-01

Full Text Available Abstract Background The prediction of the secondary structure of a protein is a critical step in the prediction of its tertiary structure and, potentially, its function. Moreover, the backbone dihedral angles, highly correlated with secondary structures, provide crucial information about the local three-dimensional structure. Results We predict independently both the secondary structure and the backbone dihedral angles and combine the results in a loop to enhance each prediction reciprocally. Support vector machines, a state-of-the-art supervised classification technique, achieve secondary structure predictive accuracy of 80% on a non-redundant set of 513 proteins, significantly higher than other methods on the same dataset. The dihedral angle space is divided into a number of regions using two unsupervised clustering techniques in order to predict the region in which a new residue belongs. The performance of our method is comparable to, and in some cases more accurate than, other multi-class dihedral prediction methods. Conclusions We have created an accurate predictor of backbone dihedral angles and secondary structure. Our method, called DISSPred, is available online at http://comp.chem.nottingham.ac.uk/disspred/.

Influence of frequency on shear fatigue strength of resin composite to enamel bonds using self-etch adhesives.

Science.gov (United States)

Takamizawa, Toshiki; Scheidel, Donal D; Barkmeier, Wayne W; Erickson, Robert L; Tsujimoto, Akimasa; Latta, Mark A; Miyazaki, Masashi

2016-09-01

The purpose of this study was to determine the influence of different frequency rates on of bond durability of self-etch adhesives to enamel using shear fatigue strength (SFS) testing. A two-step self-etch adhesive (OX, OptiBond XTR), and two single step self-etch adhesives (GB, G-ӕnial Bond and SU, Scotchbond Universal) were used in this study. The shear fatigue strength (SFS) to enamel was obtained. A staircase method was used to determine the SFS values with 50,000 cycles or until failure occurred. Fatigue testing was performed at frequencies of 5Hz, 10Hz, and 20Hz. For each test condition, 30 specimens were prepared for the SFS testing. Regardless of the bond strength test method, OX showed significantly higher SFS values than the two single-step self-etch adhesives. For each of the three individual self-etch adhesives, there was no significant difference in SFS depending on the frequency rate, although 20Hz results tended to be higher. Regardless of the self-etch adhesive system, frequencies of 5Hz, 10Hz, and 20Hz produced similar results in fatigue strength of resin composite bonded to enamel using 50,000 cycles or until bond failure. Accelerated fatigue testing provides valuable information regarding the long term durability of resin composite to enamel bonding using self-etch adhesive system. Copyright © 2016 Elsevier Ltd. All rights reserved.

ProteinAC: a frequency domain technique for analyzing protein dynamics

Science.gov (United States)

Bozkurt Varolgunes, Yasemin; Demir, Alper

2018-03-01

It is widely believed that the interactions of proteins with ligands and other proteins are determined by their dynamic characteristics as opposed to only static, time-invariant processes. We propose a novel computational technique, called ProteinAC (PAC), that can be used to analyze small scale functional protein motions as well as interactions with ligands directly in the frequency domain. PAC was inspired by a frequency domain analysis technique that is widely used in electronic circuit design, and can be applied to both coarse-grained and all-atom models. It can be considered as a generalization of previously proposed static perturbation-response methods, where the frequency of the perturbation becomes the key. We discuss the precise relationship of PAC to static perturbation-response schemes. We show that the frequency of the perturbation may be an important factor in protein dynamics. Perturbations at different frequencies may result in completely different response behavior while magnitude and direction are kept constant. Furthermore, we introduce several novel frequency dependent metrics that can be computed via PAC in order to characterize response behavior. We present results for the ferric binding protein that demonstrate the potential utility of the proposed techniques.

Angle-of-arrival-based gesture recognition using ultrasonic multi-frequency signals

KAUST Repository

Chen, Hui; Ballal, Tarig; Saad, Mohamed; Al-Naffouri, Tareq Y.

2017-01-01

transducer. The 2-D angles of the moving hand are estimated using multi-frequency signals captured by a fixed receiver array. A simple redundant dictionary matching classifier is designed to recognize gestures representing the numbers from `0' to `9

Control of concerted two bond versus single bond dissociation in CH3Co(CO)4 via an intermediate state using pump-dump laser pulses

Science.gov (United States)

Ambrosek, David; González, Leticia

2007-10-01

Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH3Co(CO)4 indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH3 and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.

Control of concerted two bond versus single bond dissociation in CH(3)Co(CO)(4) via an intermediate state using pump-dump laser pulses.

Science.gov (United States)

Ambrosek, David; González, Leticia

2007-10-07

Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH(3)Co(CO)(4) indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH(3) and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.

Photo-reduction on the rupture of disulfide bonds and the related protein assembling

Science.gov (United States)

Wang, Wei

It has been found that many proteins can self-assemble into nanoscale assemblies when they unfold or partially unfold under harsh conditions, such as low pH, high temperature, or the presence of denaturants, and so on. These nanoscale assemblies can have some applications such as the drug-delivery systems (DDSs). Here we report a study that a very physical way, the UV illumination, can be used to facilitate the formation of protein fibrils and nanoparticles under native conditions by breaking disulfide bonds in some disulfide-containing proteins. By controlling the intensity of UV light and the illumination time, we realized the preparation of self-assembly nanoparticles which encapsulate the anticancer drug doxorubicin (DOX) and can be used as the DDS for inhibiting the growth of tumor. The formation of fibrillary assemblies was also observed. The rupture of disulfide bonds through photo-reduction process due to the effect of tryptophan and tyrosine was studied, and the physical mechanism of the assembling of the related disulfide-containing proteins was also discussed. We thank the financial support from NSF of China and the 973 project.

Wire bonding in microelectronics

CERN Document Server

Harman, George G

2010-01-01

Wire Bonding in Microelectronics, Third Edition, has been thoroughly revised to help you meet the challenges of today's small-scale and fine-pitch microelectronics. This authoritative guide covers every aspect of designing, manufacturing, and evaluating wire bonds engineered with cutting-edge techniques. In addition to gaining a full grasp of bonding technology, you'll learn how to create reliable bonds at exceedingly high yields, test wire bonds, solve common bonding problems, implement molecular cleaning methods, and much more. Coverage includes: Ultrasonic bonding systems and technologies, including high-frequency systems Bonding wire metallurgy and characteristics, including copper wire Wire bond testing Gold-aluminum intermetallic compounds and other interface reactions Gold and nickel-based bond pad plating materials and problems Cleaning to improve bondability and reliability Mechanical problems in wire bonding High-yield, fine-pitch, specialized-looping, soft-substrate, and extreme-temperature wire bo...

Pairwise NMR experiments for the determination of protein backbone dihedral angle Φ based on cross-correlated spin relaxation

International Nuclear Information System (INIS)

Takahashi, Hideo; Shimada, Ichio

2007-01-01

Novel cross-correlated spin relaxation (CCR) experiments are described, which measure pairwise CCR rates for obtaining peptide dihedral angles Φ. The experiments utilize intra-HNCA type coherence transfer to refocus 2-bond J NCα coupling evolution and generate the N (i)-C α (i) or C'(i-1)-C α (i) multiple quantum coherences which are required for measuring the desired CCR rates. The contribution from other coherences is also discussed and an appropriate setting of the evolution delays is presented. These CCR experiments were applied to 15 N- and 13 C-labeled human ubiquitin. The relevant CCR rates showed a high degree of correlation with the Φ angles observed in the X-ray structure. By utilizing these CCR experiments in combination with those previously established for obtaining dihedral angle Ψ, we can determine high resolution structures of peptides that bind weakly to large target molecules

Measurements of the weak bonding interfacial stiffness by using air-coupled ultrasound

Directory of Open Access Journals (Sweden)

Wen-Lin Wu

2017-12-01

Full Text Available An air-coupled ultrasonic method, focusing on the problem that weak bonding interface is difficult to accurately measure using conventional nondestructive testing technique, is proposed to evaluate the bond integrity. Based on the spring model and the potential function theory, a theoretical model is established to predict the through-transmission spectrum in double-layer adhesive structure. The result of a theoretical algorithm shows that all the resonant transmission peaks move towards higher frequency with the increase of the interfacial stiffness. The reason for these movements is related to either the normal stiffness (KN or the transverse stiffness (KT. A method to optimize the measurement parameters (i.e. the incident angle and testing frequency is put forward through analyzing the relationship between the resonant transmission peaks and the interfacial spring stiffness at the frequency below 1MHz. The air-coupled ultrasonic testing experiments at the normal and oblique incident angle respectively are carried out to verify the theoretical analysis and to accurately measure the interfacial stiffness of double-layer adhesive composite plate. The experimental results are good agreement with the results from the theoretical algorithm, and the relationship between bonding time and interfacial stiffness is presented at the end of this paper.

On prediction of OH stretching frequencies in intramolecularly hydrogen bonded systems

DEFF Research Database (Denmark)

Hansen, Poul Erik; Spanget-Larsen, Jens

2012-01-01

OH stretching frequencies are investigated for a series of non-tautomerizing systems with intramolecular hydrogen bonds. Effective OH stretching wavenumbers are predicted by the application of empirical correlation procedures based on the results of B3LYP/6-31G(d) theoretical calculations...

Internal-strain effect on the valence band of strained silicon and its correlation with the bond angles

Energy Technology Data Exchange (ETDEWEB)

Inaoka, Takeshi, E-mail: inaoka@phys.u-ryukyu.ac.jp; Yanagisawa, Susumu; Kadekawa, Yukihiro [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213 (Japan)

2014-02-14

By means of the first-principles density-functional theory, we investigate the effect of relative atom displacement in the crystal unit cell, namely, internal strain on the valence-band dispersion of strained silicon, and find close correlation of this effect with variation in the specific bond angles due to internal strain. We consider the [111] ([110]) band dispersion for (111) ((110)) biaxial tensility and [111] ([110]) uniaxial compression, because remarkably small values of hole effective mass m* can be obtained in this dispersion. Under the practical condition of no normal stress, biaxial tensility (uniaxial compression) involves additional normal compression (tensility) and internal strain. With an increase in the internal-strain parameter, the energy separation between the highest and second-highest valence bands becomes strikingly larger, and the highest band with conspicuously small m* extends remarkably down to a lower energy region, until it intersects or becomes admixed with the second band. This is closely correlated with the change in the specific bond angles, and this change can reasonably explain the above enlargement of the band separation.

Reactive bonding mediated high mass loading of individualized single-walled carbon nanotubes in an elastomeric polymer

Science.gov (United States)

Zhao, Liping; Li, Yongjin; Qiu, Jishan; You, Jichun; Dong, Wenyong; Cao, Xiaojun

2012-09-01

A reactive chemical bonding strategy was developed for the incorporation of a high mass loading of individual single-wall carbon nanotubes (SWCNTs) into an elastomeric matrix using a reactive ionic liquid as a linker. This method simultaneously prevented the agglomeration of SWCNTs and caused strong interfacial bonding, while the electronic properties of the SWCNTs remained intact. As a result, the high conductivity of the carbon nanotubes (CNTs) and the flexibility of the elastomeric matrix were retained, producing optimum electrical and mechanical properties. A composite material with a loading of 20 wt% SWCNTs was fabricated with excellent mechanical properties and a high conductivity (9500 S m-1). The method could be used to form transparent thin conductive films that could tolerate over 800 bend cycles at a bending angle of 180° while maintaining a constant sheet resistance.A reactive chemical bonding strategy was developed for the incorporation of a high mass loading of individual single-wall carbon nanotubes (SWCNTs) into an elastomeric matrix using a reactive ionic liquid as a linker. This method simultaneously prevented the agglomeration of SWCNTs and caused strong interfacial bonding, while the electronic properties of the SWCNTs remained intact. As a result, the high conductivity of the carbon nanotubes (CNTs) and the flexibility of the elastomeric matrix were retained, producing optimum electrical and mechanical properties. A composite material with a loading of 20 wt% SWCNTs was fabricated with excellent mechanical properties and a high conductivity (9500 S m-1). The method could be used to form transparent thin conductive films that could tolerate over 800 bend cycles at a bending angle of 180° while maintaining a constant sheet resistance. Electronic supplementary information (ESI) available: Conductivity test of the SEBS-SWCNTs film, transmission spectra and sheet resistance for the spin-coated SEBS-SWCNTs thin films on PET slides. See DOI: 10

Radiation-induced cleavage of disulfide bonds in proteins. Clivage radiolytique des ponts disulfure des proteines

Energy Technology Data Exchange (ETDEWEB)

Favaudon, V; Tourbez, H; Lhoste, J M [Paris-11 Univ., 91 - Orsay (FR); Houee-Levin, C [Paris-5 Univ., 75 (FR)

1991-06-01

The reduction of the disulfide bonds in apo-Riboflavin-Binding Protein (apoRBP) by the CO{sub 2}{sup -}{center dot} radical occurred under {gamma}-ray irradiation as a chain reaction whose efficiency increased upon acidification of the medium. Pulse-radiolysis analysis showed a rapid one-electron oxidation of the disulfide bonds yielding the anionic or protonated form of the disulfide radical. The main decay path of this radical under acidic conditions consisted of the rapid formation of a thiyl radical intermediate in equilibrium with the closed, cyclic form. At pH 8 the disulfide radical anion decayed via intramolecular and/or intermolecular routes including disproportionation, protein-protein crosslinking, non-dismutative recombination processes, and reaction with sulfhydryl groups in pre-reduced systems.

Fabrication and Characterization of Capacitive Micromachined Ultrasonic Transducers with Low-Temperature Wafer Direct Bonding

Directory of Open Access Journals (Sweden)

Xiaoqing Wang

2016-12-01

Full Text Available This paper presents a fabrication method of capacitive micromachined ultrasonic transducers (CMUTs by wafer direct bonding, which utilizes both the wet chemical and O2plasma activation processes to decrease the bonding temperature to 400 °C. Two key surface properties, the contact angle and surface roughness, are studied in relation to the activation processes, respectively. By optimizing the surface activation parameters, a surface roughness of 0.274 nm and a contact angle of 0° are achieved. The infrared images and static deflection of devices are assessed to prove the good bonding effect. CMUTs having silicon membranes with a radius of 60 μm and a thickness of 2 μm are fabricated. Device properties have been characterized by electrical and acoustic measurements to verify their functionality and thus to validate this low-temperature process. A resonant frequency of 2.06 MHz is obtained by the frequency response measurements. The electrical insertion loss and acoustic signal have been evaluated. This study demonstrates that the CMUT devices can be fabricated by low-temperature wafer direct bonding, which makes it possible to integrate them directly on top of integrated circuit (IC substrates.

Si-O-Si bond-angle distribution in vitreous silica from first-principles 29Si NMR analysis

International Nuclear Information System (INIS)

Mauri, Francesco; Pasquarello, Alfredo; Pfrommer, Bernd G.; Yoon, Young-Gui; Louie, Steven G.

2000-01-01

The correlation between 29 Si chemical shifts and Si-O-Si bond angles in SiO 2 is determined within density-functional theory for the full range of angles present in vitreous silica. This relation closely reproduces measured shifts of crystalline polymorphs. The knowledge of the correlation allows us to reliably extract from the experimental NMR spectrum the mean (151 degree sign ) and the standard deviation (11 degree sign ) of the Si-O-Si angular distribution of vitreous silica. In particular, we show that the Mozzi-Warren Si-O-Si angular distribution is not consistent with the NMR data. This analysis illustrates the potential of our approach for structural determinations of silicate glasses. (c) 2000 The American Physical Society

Method for high resolution magnetic resonance analysis using magic angle technique

Science.gov (United States)

Wind, Robert A.; Hu, Jian Zhi

2003-12-30

A method of performing a magnetic resonance analysis of a biological object that includes placing the object in a main magnetic field (that has a static field direction) and in a radio frequency field; rotating the object at a frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a phase-corrected magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. The object may be reoriented about the magic angle axis between three predetermined positions that are related to each other by 120.degree.. The main magnetic field may be rotated mechanically or electronically. Methods for magnetic resonance imaging of the object are also described.

Increased helix and protein stability through the introduction of a new tertiary hydrogen bond.

Science.gov (United States)

Peterson, R W; Nicholson, E M; Thapar, R; Klevit, R E; Scholtz, J M

1999-03-12

In an effort to quantify the importance of hydrogen bonding and alpha-helix formation to protein stability, a capping box motif was introduced into the small phosphocarrier protein HPr. Previous studies had confirmed that Ser46, at the N-cap position of the short helix-B in HPr, serves as an N-cap in solution. Thus, only a single-site mutation was required to produce a canonical S-X-X-E capping box: Lys49 at the N3 position was substituted with a glutamic acid residue. Thermal and chemical denaturation studies on the resulting K49E HPr show that the designed variant is approximately 2 kcal mol-1 more stable than the wild-type protein. However, NMR studies indicate that the side-chain of Glu49 does not participate in the expected capping H-bond interaction, but instead forms a new tertiary H-bond that links helix-B to the four-stranded beta-sheet of HPr. Here, we demonstrate that a strategy in which new non-native H-bonds are introduced can generate proteins with increased stability. We discuss why the original capping box design failed, and compare the energetic consequences of the new tertiary side-chain to main-chain H-bond with a local (helix-capping) side-chain to main-chain H-bond on the protein's global stability. Copyright 1999 Academic Press.

Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model.

Science.gov (United States)

Ma, Songling; Hwang, Sungbo; Lee, Sehan; Acree, William E; No, Kyoung Tai

2018-04-23

To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined. Although the contribution of HBs to the solvation free energy could be evenly distributed to grid points on the surface of a molecule, the G-SFED model was still inadequate to describe the angle dependency of the HB of a solute with a polarizable continuum solvent. To overcome this shortcoming of the G-SFED model, the contribution of HBs was formulated using the geometric parameters of the grid points described in the HB coordinate system of the solute. We propose an HB angle dependency incorporated into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent acidity and basicity densities are defined and parametrized with experimental data. The G-SFED-HB model was then applied to calculate the solvation free energies of organic molecules in water, various alcohols and ethers, and the log P values of diverse organic molecules, including peptides and a protein. Both the G-SFED model and the G-SFED-HB model reproduced the experimental solvation free energies with similar accuracy, whereas the distributions of the SFED on the molecular surface calculated by the G-SFED and G-SFED-HB models were quite different, especially for molecules having HB donors or acceptors. Since the angle dependency of HBs was included in the G-SFED-HB model, the SFED distribution of the G-SFED-HB model is well described

Bonding pathways of high-pressure chemical transformations

International Nuclear Information System (INIS)

Hu Anguang; Zhang Fan

2013-01-01

A three-stage bonding pathway towards high-pressure chemical transformations from molecular precursors or intermediate states has been identified by first-principles simulations. With the evolution of principal stress tensor components in the response of chemical bonding to compressive loading, the three stages can be defined as the van der Waals bonding destruction, a bond breaking and forming reaction, and equilibrium of new bonds. The three-stage bonding pathway leads to the establishment of a fundamental principle of chemical bonding under compression. It reveals that during high-pressure chemical transformation, electrons moving away from functional groups follow anti-addition, collision-free paths to form new bonds in counteracting the local stress confinement. In applying this principle, a large number of molecular precursors were identified for high-pressure chemical transformations, resulting in new materials. (fast track communication)

High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field

International Nuclear Information System (INIS)

Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Lipton, Andrew S.; Berthold, Deborah A.; Rienstra, Chad M.

2010-01-01

Magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy of uniformly- 13 C, 15 N labeled protein samples provides insight into atomic-resolution chemistry and structure. Data collection efficiency has advanced remarkably in the last decade; however, the study of larger proteins is still challenged by relatively low resolution in comparison to solution NMR. In this study, we present a systematic analysis of SSNMR protein spectra acquired at 11.7, 17.6 and 21.1 Tesla ( 1 H frequencies of 500, 750, and 900 MHz). For two protein systems-GB1, a 6 kDa nanocrystalline protein and DsbA, a 21 kDa nanocrystalline protein-line narrowing is demonstrated in all spectral regions with increasing field. Resolution enhancement is greatest in the aliphatic region, including methine, methylene and methyl sites. The resolution for GB1 increases markedly as a function of field, and for DsbA, resolution in the C-C region increases by 42%, according to the number of peaks that can be uniquely picked and integrated in the 900 MHz spectra when compared to the 500 MHz spectra. Additionally, chemical exchange is uniquely observed in the highest field spectra for at least two isoleucine Cδ1 sites in DsbA. These results further illustrate the benefits of high-field MAS SSNMR spectroscopy for protein structural studies.

Modelling small-angle scattering data from complex protein-lipid systems

DEFF Research Database (Denmark)

Kynde, Søren Andreas Røssell

This thesis consists of two parts. The rst part is divided into five chapters. Chapter 1 gives a general introduction to the bio-molecular systems that have been studied. These are membrane proteins and their lipid environments in the form of phospholipid nanodiscs. Membrane proteins...... the techniques very well suited for the study of the nanodisc system. Chapter 3 explains two different modelling approaches that can be used in the analysis of small-angle scattering data from lipid-protein complexes. These are the continuous approach where the system of interest is modelled as a few regular...... combine the bene ts of each of the methods and give unique structural information about relevant bio-molecular complexes in solution. Chapter 4 describes the work behind a proposal of a small-angle neutron scattering instrument for the European Spallation Source under construction in Lund. The instrument...

Polarized Line Formation in Arbitrary Strength Magnetic Fields Angle-averaged and Angle-dependent Partial Frequency Redistribution

Energy Technology Data Exchange (ETDEWEB)

Sampoorna, M.; Nagendra, K. N. [Indian Institute of Astrophysics, Koramangala, Bengaluru 560 034 (India); Stenflo, J. O., E-mail: sampoorna@iiap.res.in, E-mail: knn@iiap.res.in, E-mail: stenflo@astro.phys.ethz.ch [Institute of Astronomy, ETH Zurich, CH-8093 Zurich (Switzerland)

2017-08-01

Magnetic fields in the solar atmosphere leave their fingerprints in the polarized spectrum of the Sun via the Hanle and Zeeman effects. While the Hanle and Zeeman effects dominate, respectively, in the weak and strong field regimes, both these effects jointly operate in the intermediate field strength regime. Therefore, it is necessary to solve the polarized line transfer equation, including the combined influence of Hanle and Zeeman effects. Furthermore, it is required to take into account the effects of partial frequency redistribution (PRD) in scattering when dealing with strong chromospheric lines with broad damping wings. In this paper, we present a numerical method to solve the problem of polarized PRD line formation in magnetic fields of arbitrary strength and orientation. This numerical method is based on the concept of operator perturbation. For our studies, we consider a two-level atom model without hyperfine structure and lower-level polarization. We compare the PRD idealization of angle-averaged Hanle–Zeeman redistribution matrices with the full treatment of angle-dependent PRD, to indicate when the idealized treatment is inadequate and what kind of polarization effects are specific to angle-dependent PRD. Because the angle-dependent treatment is presently computationally prohibitive when applied to realistic model atmospheres, we present the computed emergent Stokes profiles for a range of magnetic fields, with the assumption of an isothermal one-dimensional medium.

Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure

International Nuclear Information System (INIS)

Wang Lincong; Donald, Bruce Randall

2004-01-01

We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (φ,ψ) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in constant time, the backbone (φ,ψ) angles for a residue from RDCs in two media on any single backbone vector type. Building upon these exact solutions we have designed a novel algorithm for determining a protein backbone substructure consisting of α-helices and β-sheets. Our algorithm employs a systematic search technique to refine the conformation of both α-helices and β-sheets and to determine their orientations using exclusively the angular restraints from RDCs. The algorithm computes the backbone substructure employing very sparse distance restraints between pairs of α-helices and β-sheets refined by the systematic search. The algorithm has been demonstrated on the protein human ubiquitin using only backbone NH RDCs, plus twelve hydrogen bonds and four NOE distance restraints. Further, our results show that both the global orientations and the conformations of α-helices and β-strands can be determined with high accuracy using only two RDCs per residue. The algorithm requires, as its input, backbone resonance assignments, the identification of α-helices and β-sheets as well as sparse NOE distance and hydrogen bond restraints.Abbreviations: NMR - nuclear magnetic resonance; RDC - residual dipolar coupling; NOE - nuclear Overhauser effect; SVD - singular value decomposition; DFS - depth-first search; RMSD - root mean square deviation; POF - principal order frame; PDB - protein data bank; SA - simulated annealing; MD - molecular dynamics

Efficient soluble expression of disulfide bonded proteins in the cytoplasm of Escherichia coli in fed-batch fermentations on chemically defined minimal media.

Science.gov (United States)

Gąciarz, Anna; Khatri, Narendar Kumar; Velez-Suberbie, M Lourdes; Saaranen, Mirva J; Uchida, Yuko; Keshavarz-Moore, Eli; Ruddock, Lloyd W

2017-06-15

The production of recombinant proteins containing disulfide bonds in Escherichia coli is challenging. In most cases the protein of interest needs to be either targeted to the oxidizing periplasm or expressed in the cytoplasm in the form of inclusion bodies, then solubilized and re-folded in vitro. Both of these approaches have limitations. Previously we showed that soluble expression of disulfide bonded proteins in the cytoplasm of E. coli is possible at shake flask scale with a system, known as CyDisCo, which is based on co-expression of a protein of interest along with a sulfhydryl oxidase and a disulfide bond isomerase. With CyDisCo it is possible to produce disulfide bonded proteins in the presence of intact reducing pathways in the cytoplasm. Here we scaled up production of four disulfide bonded proteins to stirred tank bioreactors and achieved high cell densities and protein yields in glucose fed-batch fermentations, using an E. coli strain (BW25113) with the cytoplasmic reducing pathways intact. Even without process optimization production of purified human single chain IgA 1 antibody fragment reached 139 mg/L and hen avidin 71 mg/L, while purified yields of human growth hormone 1 and interleukin 6 were around 1 g/L. Preliminary results show that human growth hormone 1 was also efficiently produced in fermentations of W3110 strain and when glucose was replaced with glycerol as the carbon source. Our results show for the first time that efficient production of high yields of soluble disulfide bonded proteins in the cytoplasm of E. coli with the reducing pathways intact is feasible to scale-up to bioreactor cultivations on chemically defined minimal media.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

Science.gov (United States)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2013-09-01

In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

Ultrafast OH-stretching frequency shifts of hydrogen- bonded 2-naphthol photoacid-base complexes in solution

Directory of Open Access Journals (Sweden)

Batista VictorS.

2013-03-01

Full Text Available We characterize the transient solvent-dependent OH-stretching frequency shifts of photoacid 2-naphthol hydrogen-bonded with CH3CN in the S0- and S1-states using a combined experimental and theoretical approach, and disentangle specific hydrogen-bonding contributions from nonspecific dielectric response.

Design and properties of high-power highly-coherent single-frequency VECSEL emitting in the near- to mid-IR for photonic applications

Science.gov (United States)

Garnache, A.; Laurain, A.; Myara, M.; Sellahi, M.; Cerutti, L.; Perez, J. P.; Michon, A.; Beaudoin, G.; Sagnes, I.; Cermak, P.; Romanini, D.

2017-11-01

We demonstrate high power (multiwatt) low noise single frequency operation of tunable compact verical-external- cavity surface-emitting-lasers exhibiting a low divergence high beam quality, of great interest for photonics applications. The quantum-well based lasers are operating in CW at RT at 1μm and 2.3μm exploiting GaAs and Sb technologies. For heat management purpose the VECSEL membranes were bonded on a SiC substrate. Both high power diode pumping (using GaAs commercial diode) at large incidence angle and electrical pumping are developed. The design and physical properties of the coherent wave are presented. We took advantage of thermal lens-based stability to develop a short (0.5-5mm) external cavity without any intracavity filter. We measured a low divergence circular TEM00 beam (M2 = 1.2) close to diffraction limit, with a linear light polarization (> 30 dB). The side mode suppression ratio is > 45 dB. The free running laser linewidth is 37 kHz limited by pump induced thermal fluctuations. Thanks to this high-Q external cavity approach, the frequency noise is low and the dynamics is in the relaxation-oscillation-free regime, exhibiting low intensity noise (laser power and coherence will be discussed. These design/properties can be extended to other wavelengths.

Identifying Floppy and Rigid Regions in Proteins

Science.gov (United States)

Jacobs, D. J.; Thorpe, M. F.; Kuhn, L. A.

1998-03-01

In proteins it is possible to separate hard covalent forces involving bond lengths and bond angles from other weak forces. We model the microstructure of the protein as a generic bar-joint truss framework, where the hard covalent forces and strong hydrogen bonds are regarded as rigid bar constraints. We study the mechanical stability of proteins using FIRST (Floppy Inclusions and Rigid Substructure Topography) based on a recently developed combinatorial constraint counting algorithm (the 3D Pebble Game), which is a generalization of the 2D pebble game (D. J. Jacobs and M. F. Thorpe, ``Generic Rigidity: The Pebble Game'', Phys. Rev. Lett.) 75, 4051-4054 (1995) for the special class of bond-bending networks (D. J. Jacobs, "Generic Rigidity in Three Dimensional Bond-bending Networks", Preprint Aug (1997)). This approach is useful in identifying rigid motifs and flexible linkages in proteins, and thereby determines the essential degrees of freedom. We will show some preliminary results from the FIRST analysis on the myohemerythrin and lyozyme proteins.

Postprandial changes in cardiometabolic disease risk in young Chinese men following isocaloric high or low protein diets, stratified by either high or low meal frequency - a randomized controlled crossover trial.

Science.gov (United States)

Mok, Alexander; Haldar, Sumanto; Lee, Jetty Chung-Yung; Leow, Melvin Khee-Shing; Henry, Christiani Jeyakumar

2016-03-15

Cardio-Metabolic Disease (CMD) is the leading cause of death globally and particularly in Asia. Postprandial elevation of glycaemia, insulinaemia, triglyceridaemia are associated with an increased risk of CMD. While studies have shown that higher protein intake or increased meal frequency may benefit postprandial metabolism, their combined effect has rarely been investigated using composite mixed meals. We therefore examined the combined effects of increasing meal frequency (2-large vs 6-smaller meals), with high or low-protein (40 % vs 10 % energy from protein respectively) isocaloric mixed meals on a range of postprandial CMD risk markers. In a randomized crossover study, 10 healthy Chinese males (Age: 29 ± 7 years; BMI: 21.9 ± 1.7 kg/m(2)) underwent 4 dietary treatments: CON-2 (2 large Low-Protein meals), CON-6 (6 Small Low-Protein meals), PRO-2 (2 Large High-Protein meals) and PRO-6 (6 Small High-Protein meals). Subjects wore a continuous glucose monitor (CGM) and venous blood samples were obtained at baseline and at regular intervals for 8.5 h to monitor postprandial changes in glucose, insulin, triglycerides and high sensitivity C-reactive protein (hsCRP). Blood pressure was measured at regular intervals pre- and post- meal consumption. Urine was collected to measure excretion of creatinine and F2-isoprostanes and its metabolites over the 8.5 h postprandial period. The high-protein meals, irrespective of meal frequency were beneficial for glycaemic health since glucose incremental area under the curve (iAUC) for PRO-2 (185 ± 166 mmol.min.L(-1)) and PRO-6 (214 ± 188 mmol.min.L(-1)) were 66 and 60 % lower respectively (both p meals with higher protein content, irrespective of meal frequency appears to be beneficial for postprandial glycemic and insulinemic responses in young, healthy Chinese males. Implications of this study may be useful in the Asian context where the consumption of high glycemic index, carbohydrate meals is prevalent. NCT02529228 .

Hydrogen bonds of sodium alginate/Antarctic krill protein composite material.

Science.gov (United States)

Yang, Lijun; Guo, Jing; Yu, Yue; An, Qingda; Wang, Liyan; Li, Shenglin; Huang, Xuelin; Mu, Siyang; Qi, Shanwei

2016-05-20

Sodium alginate/Antarctic krill protein composite material (SA/AKP) was successfully obtained by blending method. The hydrogen bonds of SA/AKP composite material were analyzed by Fourier transform infrared spectroscopy (FT-IR) and Nuclear magnetic resonance hydrogen spectrum (HNMR). Experiment manifested the existence of intermolecular and intramolecular hydrogen bonds in SA/AKP system; strength of intermolecular hydrogen bond enhanced with the increase of AKP in the composite material and the interaction strength of hydrogen bonding followed the order: OH…Ether O>OH…π>OH…N. The percentage of intermolecular hydrogen bond decreased with increase of pH. At the same time, the effect of hydrogen bonds on properties of the composite material was discussed. The increase of intermolecular hydrogen bonding led to the decrease of crystallinity, increase of apparent viscosity and surface tension, as well as obvious decrease of heat resistance of SA/AKP composite material. SA/AKP fiber SEM images and energy spectrum showed that crystallized salt was separated from the fiber, which possibly led to the fibrillation of the composite fibers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Frequency distribution of the reduced unit cells of centred lattices from the Protein Data Bank.

Science.gov (United States)

Swaminathan, Kunchithapadam

2012-03-01

In crystallography, a centred conventional lattice unit cell has its corresponding reduced primitive unit cell. This study presents the frequency distribution of the reduced unit cells of all centred lattice entries of the Protein Data Bank (as of 23 August 2011) in four unit-cell-dimension-based groups and seven interaxial-angle-based subgroups. This frequency distribution is an added layer of support during space-group assignment in new crystals. In addition, some interesting patterns of distribution are discussed as well as how some reduced unit cells could be wrongly accepted as primitive lattices in a different crystal system.

Frequency-dependent squeeze-amplitude attenuation and squeeze-angle rotation by electromagnetically induced transparency for gravitational-wave interferometers

International Nuclear Information System (INIS)

Mikhailov, Eugeniy E.; Goda, Keisuke; Corbitt, Thomas; Mavalvala, Nergis

2006-01-01

We study the effects of frequency-dependent squeeze-amplitude attenuation and squeeze-angle rotation by electromagnetically induced transparency (EIT) on gravitational-wave (GW) interferometers. We propose the use of low-pass, bandpass, and high-pass EIT filters, an S-shaped EIT filter, and an intracavity EIT filter to generate frequency-dependent squeezing for injection into the antisymmetric port of GW interferometers. We find that the EIT filters have several advantages over the previous filter designs with regard to optical losses, compactness, and the tunability of the filter linewidth

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

KAUST Repository

Maadooliat, Mehdi; Gao, Xin; Huang, Jianhua Z.

2012-01-01

Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

KAUST Repository

Maadooliat, Mehdi

2012-08-27

Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

Relation between frequency and H bond length in heavy water: Towards the understanding of the unusual properties of H bond dynamics in nanoporous media

International Nuclear Information System (INIS)

Pommeret, Stanislas; Leicknam, Jean-Claude; Bratos, Savo; Musat, Raluca; Renault, Jean Philippe

2009-01-01

The published work on H bond dynamics mainly refers to diluted solutions HDO/D 2 O rather than to normal water. The reasons for this choice are both theoretical and experimental. Mechanical isolation of the OH vibrator eliminating the resonant energy transfer makes it a better probe of the local H bond network, while the dilution in heavy water reduces the infrared absorption, which permits the use of thicker experimental cells. The isotopic substitution does not alter crucially the nature of the problem. The length r of an OH . . . O group is statistically distributed over a large interval comprised between 2.7 and 3.2 A with a mean value r 0 = 2.86 A. Liquid water may thus be viewed as a mixture of hydrogen bonds of different length. Two important characteristics of hydrogen bonding must be mentioned. (i) The OH stretching vibrations are strongly affected by this interaction. The shorter the length r of the hydrogen bond, the strongest the H bond link and the lower is its frequency ω: the covalent OH bond energy is lent to the OH. . .O bond and reinforces the latter. A number of useful relationships between ω and r were published to express this correlation. The one adopted in our previous work is the relationship due to Mikenda. (ii) Not only the OH vibrations, but also the HDO rotations are influenced noticeably by hydrogen bonding. This is due to steric forces that hinder the HDO rotations. As they are stronger in short than in long hydrogen bonds, rotations are slower in the first case than in the second. This effect was only recently discovered, but its existence is hardly to be contested. In the present contribution, we want to revisit the relationship between the frequency of the OH vibrator and the distance OH. . .O.

Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

DEFF Research Database (Denmark)

Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas

2013-01-01

-protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains...... of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding...... to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1...

Structure-Energy Relationships of Halogen Bonds in Proteins.

Science.gov (United States)

Scholfield, Matthew R; Ford, Melissa Coates; Carlsson, Anna-Carin C; Butta, Hawera; Mehl, Ryan A; Ho, P Shing

2017-06-06

The structures and stabilities of proteins are defined by a series of weak noncovalent electrostatic, van der Waals, and hydrogen bond (HB) interactions. In this study, we have designed and engineered halogen bonds (XBs) site-specifically to study their structure-energy relationship in a model protein, T4 lysozyme. The evidence for XBs is the displacement of the aromatic side chain toward an oxygen acceptor, at distances that are equal to or less than the sums of their respective van der Waals radii, when the hydroxyl substituent of the wild-type tyrosine is replaced by a halogen. In addition, thermal melting studies show that the iodine XB rescues the stabilization energy from an otherwise destabilizing substitution (at an equivalent noninteracting site), indicating that the interaction is also present in solution. Quantum chemical calculations show that the XB complements an HB at this site and that solvent structure must also be considered in trying to design molecular interactions such as XBs into biological systems. A bromine substitution also shows displacement of the side chain, but the distances and geometries do not indicate formation of an XB. Thus, we have dissected the contributions from various noncovalent interactions of halogens introduced into proteins, to drive the application of XBs, particularly in biomolecular design.

Low-Resolution Structure of Detergent-Solubilized Membrane Proteins from Small-Angle Scattering Data.

Science.gov (United States)

Koutsioubas, Alexandros

2017-12-05

Despite the ever-increasing usage of small-angle scattering as a valuable complementary method in the field of structural biology, applications concerning membrane proteins remain elusive mainly due to experimental challenges and the relative lack of theoretical tools for the treatment of scattering data. This fact adds up to general difficulties encountered also by other established methods (crystallography, NMR) for the study of membrane proteins. Following the general paradigm of ab initio methods for low-resolution restoration of soluble protein structure from small-angle scattering data, we construct a general multiphase model with a set of physical constraints, which, together with an appropriate minimization procedure, gives direct structural information concerning the different components (protein, detergent molecules) of detergent-solubilized membrane protein complexes. Assessment of the method's precision and robustness is evaluated by performing shape restorations from simulated data of a tetrameric α-helical membrane channel (Aquaporin-0) solubilized by n-Dodecyl β-D-Maltoside and from previously published small-angle neutron scattering experimental data of the filamentous hemagglutinin adhesin β-barrel protein transporter solubilized by n-Octyl β-D-glucopyranoside. It is shown that the acquisition of small-angle neutron scattering data at two different solvent contrasts, together with an estimation of detergent aggregation number around the protein, permits the reliable reconstruction of the shape of membrane proteins without the need for any prior structural information. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Energetics of hydrogen bonding in proteins: a model compound study.

OpenAIRE

Habermann, S. M.; Murphy, K. P.

1996-01-01

Differences in the energetics of amide-amide and amide-hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide-amide and amide-hydroxyl hydrogen bonds both provide considerable enthalpic stability, but that the amide-...

Iridoschisis: high frequency ultrasound imaging. Evidence for a genetic defect?

Science.gov (United States)

Danias, J; Aslanides, I M; Eichenbaum, J W; Silverman, R H; Reinstein, D Z; Coleman, D J

1996-01-01

AIMS: To elucidate changes in the anatomy of the anterior chamber associated with iridoschisis, a rare form of iris atrophy, and their potential contribution to angle closure glaucoma. METHODS: Both eyes of a 71-year-old woman with bilateral iridoschisis and fibrous dysplasia and her asymptomatic 50-year-old daughter were scanned with a very high frequency (50 MHz) ultrasound system. RESULTS: The symptomatic patient exhibited diffuse changes in the iris stoma with an intact posterior iris pigmented layer in both eyes. These changes were clinically compatible with the lack of iris transillumination defects. Additionally, iris bowing with a resultant narrowing of the angle occurred. The asymptomatic daughter showed discrete, but less severe iris stromal changes. CONCLUSION: This is the first detailed study of high frequency ultrasonic imaging of the iris in iridoschisis. The observed structural changes suggest angle narrowing by forward bowing of the anterior iris stroma may be a mechanism of IOP elevation in this condition. The ultrasonic detection of iris changes in the asymptomatic daughter of the symptomatic patient and the association of iridoschisis with fibrous dysplasia suggest a possible genetic component in the pathogenesis of this condition. Images PMID:9059271

Shedding light on disulfide bond formation: engineering a redox switch in green fluorescent protein

DEFF Research Database (Denmark)

Østergaard, H.; Henriksen, A.; Hansen, Flemming G.

2001-01-01

To visualize the formation of disulfide bonds in living cells, a pair of redox-active cysteines was introduced into the yellow fluorescent variant of green fluorescent protein. Formation of a disulfide bond between the two cysteines was fully reversible and resulted in a >2-fold decrease...... in the intrinsic fluorescence. Inter conversion between the two redox states could thus be followed in vitro as well as in vivoby non- invasive fluorimetric measurements. The 1.5 Angstrom crystal structure of the oxidized protein revealed a disulfide bond- induced distortion of the beta -barrel, as well...... the physiological range for redox-active cysteines. In the cytoplasm of Escherichia coli, the protein was a sensitive probe for the redox changes that occur upon disruption of the thioredoxin reductive pathway....

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil

Science.gov (United States)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2014-06-01

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

Directory of Open Access Journals (Sweden)

Søren W. Pedersen

Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

Energy Technology Data Exchange (ETDEWEB)

Hura, Greg L.; Menon, Angeli L.; Hammel, Michal; Rambo, Robert P.; Poole II, Farris L.; Tsutakawa, Susan E.; Jenney Jr, Francis E.; Classen, Scott; Frankel, Kenneth A.; Hopkins, Robert C.; Yang, Sungjae; Scott, Joseph W.; Dillard, Bret D.; Adams, Michael W. W.; Tainer, John A.

2009-07-20

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

Edge-Oriented Graphene on Carbon Nanofiber for High-Frequency Supercapacitors

Science.gov (United States)

Islam, Nazifah; Warzywoda, Juliusz; Fan, Zhaoyang

2018-03-01

High-frequency supercapacitors are being studied with the aim to replace the bulky electrolytic capacitors for current ripple filtering and other functions used in power systems. Here, 3D edge-oriented graphene (EOG) was grown encircling carbon nanofiber (CNF) framework to form a highly conductive electrode with a large surface area. Such EOG/CNF electrodes were tested in aqueous and organic electrolytes for high-frequency supercapacitor development. For the aqueous and the organic cell, the characteristic frequency at - 45° phase angle was found to be as high as 22 and 8.5 kHz, respectively. At 120 Hz, the electrode capacitance density was 0.37 and 0.16 mF cm-2 for the two cells. In particular, the 3 V high-frequency organic cell was successfully tested as filtering capacitor used in AC/DC converter, suggesting the promising potential of this technology for compact power supply design and other applications. [Figure not available: see fulltext.

Amide proton temperature coefficients as hydrogen bond indicators in proteins

International Nuclear Information System (INIS)

Cierpicki, Tomasz; Otlewski, Jacek

2001-01-01

Correlations between amide proton temperature coefficients (Δσ HN /ΔT) and hydrogen bonds were investigated for a data set of 793 amides derived from 14 proteins. For amide protons showing temperature gradients more positive than -4.6 ppb/K there is a hydrogen bond predictivity value exceeding 85%. It increases to over 93% for amides within the range between -4 and -1 ppb/K. Detailed analysis shows an inverse proportionality between amide proton temperature coefficients and hydrogen bond lengths. Furthermore, for hydrogen bonds of similar bond lengths, values of temperature gradients in α-helices are on average 1 ppb/K more negative than in β-sheets. In consequence, a number of amide protons in α-helices involved in hydrogen bonds shorter than 2 A show Δσ HN /ΔT 10 helices and 98% in β-turns have temperature coefficients more positive than -4.6ppb/K. Ring current effect also significantly influences temperature coefficients of amide protons. In seven out of eight cases non-hydrogen bonded amides strongly deshielded by neighboring aromatic rings show temperature coefficients more positive than -2 ppb/K. In general, amide proton temperature gradients do not change with pH unless they correspond to conformational changes. Three examples of pH dependent equilibrium showing hydrogen bond formation at higher pH were found. In conclusion, amide proton temperature coefficients offer an attractive and simple way to confirm existence of hydrogen bonds in NMR determined structures

Time and frequency structure of causal correlation networks in the China bond market

Science.gov (United States)

Wang, Zhongxing; Yan, Yan; Chen, Xiaosong

2017-07-01

There are more than eight hundred interest rates published in the China bond market every day. Identifying the benchmark interest rates that have broad influences on most other interest rates is a major concern for economists. In this paper, a multi-variable Granger causality test is developed and applied to construct a directed network of interest rates, whose important nodes, regarded as key interest rates, are evaluated with CheiRank scores. The results indicate that repo rates are the benchmark of short-term rates, the central bank bill rates are in the core position of mid-term interest rates network, and treasury bond rates lead the long-term bond rates. The evolution of benchmark interest rates from 2008 to 2014 is also studied, and it is found that SHIBOR has generally become the benchmark interest rate in China. In the frequency domain we identify the properties of information flows between interest rates, and the result confirms the existence of market segmentation in the China bond market.

High-frequency ultrasound-responsive block copolymer micelle.

Science.gov (United States)

Wang, Jie; Pelletier, Maxime; Zhang, Hongji; Xia, Hesheng; Zhao, Yue

2009-11-17

Micelles of a diblock copolymer composed of poly(ethylene oxide) and poly(2-tetrahydropyranyl methacrylate) (PEO-b-PTHPMA) in aqueous solution could be disrupted by high-frequency ultrasound (1.1 MHz). It was found that, upon exposure to a high-intensity focused ultrasound (HIFU) beam at room temperature, the pH value of the micellar solution decreased over irradiation time. The infrared spectroscopic analysis of solid block copolymer samples collected from the ultrasound irradiated micellar solution revealed the formation of carboxylic acid dimers and hydroxyl groups. These characterization results suggest that the high-frequency HIFU beam could induce the hydrolysis reaction of THPMA at room temperature resulting in the cleavage of THP groups. The disruption of PEO-b-PTHPMA micelles by ultrasound was investigated by using dynamic light scattering, atomic force microscopy, and fluorescence spectroscopy. On the basis of the pH change, it was found that the disruption process was determined by a number of factors such as the ultrasound power, the micellar solution volume and the location of the focal spot of the ultrasound beam. This study shows the potential to develop ultrasound-sensitive block copolymer micelles by having labile chemical bonds in the polymer structure, and to use the high-frequency HIFU to trigger a chemical reaction for the disruption of micelles.

Preparation of fluorescence quenched libraries containing interchain disulphide bonds for studies of protein disulphide isomerases

DEFF Research Database (Denmark)

Spetzler, J C; Westphal, V; Winther, Jakob R.

1998-01-01

Protein disulphide isomerase is an enzyme that catalyses disulphide redox reactions in proteins. In this paper, fluorogenic and interchain disulphide bond containing peptide libraries and suitable substrates, useful in the study of protein disulphide isomerase, are described. In order to establish...... the quenching chromophore (Tyr(NO2)) and Cys(pNpys) activated for reaction with a second thiol. The formation and cleavage of the interchain disulphide bonds in the library were monitored under a fluorescence microscope. Substrates to investigate the properties of protein disulphide isomerase in solution were...

Compact structure of ribosomal protein S4 in solution as revealed by small-angle X-ray scattering

International Nuclear Information System (INIS)

Serdyuk, I.N.; Sarkisyan, M.A.; Gogia, Z.V.

1981-01-01

The authors report the results of a small-angle X-ray scattering study of ribosomal protein preparations obtained by neutron scattering method. The theoretical resolution of the diffractometer (Kratky camera, the entrance slit 80 μm, the receiving slit 190 μm, the sample-detector distance 20.4 cm) was the same as the resolution of X-ray diffractometers, on which high rsub(g) values for ribosomal proteins were obtained. They used protein S4 adjusted to 20 mg/ml without any essential loss of solubility. The scattering indicatrix obtained in a wide range of angles has demonstrated that the X-ray rsub(g) obtained here coincides with the earlier obtained neutron rsub(g) and the outer part of the scattering curve is similar to that of slightly elongated compact bodies. They conclude that all discrepancies between their data on the study of ribosomal protein structure in solution and other data are not connected with the characteristics of the instruments used but only with the quality of the protein preparations. (Auth.)

Spectrally- and Time-Resolved Sum Frequency Generation (STiR-SFG): a new tool for ultrafast hydrogen bond dynamics at interfaces.

Science.gov (United States)

Benderskii, Alexander; Bordenyuk, Andrey; Weeraman, Champika

2006-03-01

The recently developed spectrally- and time-resolved Sum Frequency Generation (STiR-SFG) is a surface-selective 3-wave mixing (IR+visible) spectroscopic technique capable of measuring ultrafast spectral evolution of vibrational coherences. A detailed description of this measurement will be presented, and a noniterative method or deconvolving the laser pulses will be introduced to obtain the molecular response function. STiR-SFG, combined with the frequency-domain SFG spectroscopy, was applied to study hydrogen bonding dynamics at aqueous interfaces (D2O/CaF2). Spectral dynamics of the OD-stretch on the 50-150 fs time scale provides real-time observation of ultrafast H-bond rearrangement. Tuning the IR wavelength to the blue or red side of the OD-stretch transition, we selectively monitor the dynamics of different sub-ensembles in the distribution of the H-bond structures. The blue-side excitation (weaker H-bonding) shows monotonic red-shift of the OD-frequency. In contrast, the red-side excitation (stronger H-bonding structures) produces a blue-shift and a recursion, which may indicate the presence of an underdamped intermolecular mode of interfacial water. Effect of electrolyte concentration on the H-bond dynamics will be discussed.

Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry.

Science.gov (United States)

Morrison, Lindsay J; Chai, Wenrui; Rosenberg, Jake A; Henkelman, Graeme; Brodbelt, Jennifer S

2017-08-02

Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.

Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes.

Science.gov (United States)

Raschka, Sebastian; Wolf, Alex J; Bemister-Buffington, Joseph; Kuhn, Leslie A

2018-04-01

Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein-ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.

Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

Science.gov (United States)

Raschka, Sebastian; Wolf, Alex J.; Bemister-Buffington, Joseph; Kuhn, Leslie A.

2018-02-01

Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze data across non-homologous proteins in complex with small biological ligands to address observations made in our inhibitor discovery projects: that proteins favor donating H-bonds to ligands and avoid using groups with both H-bond donor and acceptor capacity. The resulting clear and significant chemical group matching preferences elucidate the code for protein-native ligand binding, similar to the dominant patterns found in nucleic acid base-pairing. On average, 90% of the keto and carboxylate oxygens occurring in the biological ligands formed direct H-bonds to the protein. A two-fold preference was found for protein atoms to act as H-bond donors and ligand atoms to act as acceptors, and 76% of all intermolecular H-bonds involved an amine donor. Together, the tight chemical and geometric constraints associated with satisfying donor groups generate a hydrogen-bonding lock that can be matched only by ligands bearing the right acceptor-rich key. Measuring an index of H-bond preference based on the observed chemical trends proved sufficient to predict other protein-ligand complexes and can be used to guide molecular design. The resulting Hbind and Protein Recognition Index software packages are being made available for rigorously defining intermolecular H-bonds and measuring the extent to which H-bonding patterns in a given complex match the preference key.

Inverter design for high frequency power distribution

Science.gov (United States)

King, R. J.

1985-01-01

A class of simple resonantly commutated inverters are investigated for use in a high power (100 KW - 1000 KW) high frequency (10 KHz - 20 KHz) AC power distribution system. The Mapham inverter is found to provide a unique combination of large thyristor turn-off angle and good utilization factor, much better than an alternate 'current-fed' inverter. The effects of loading the Mapham inverter entirely with rectifier loads are investigated by simulation and with an experimental 3 KW 20 KHz inverter. This inverter is found to be well suited to a power system with heavy rectifier loading.

The chemical bond in inorganic chemistry the bond valence model

CERN Document Server

Brown, I David

2016-01-01

The bond valence model is a version of the ionic model in which the chemical constraints are expressed in terms of localized chemical bonds formed by the valence charge of the atoms. Theorems derived from the properties of the electrostatic flux predict the rules obeyed by both ionic and covalent bonds. They make quantitative predictions of coordination number, crystal structure, bond lengths and bond angles. Bond stability depends on the matching of the bonding strengths of the atoms, while the conflicting requirements of chemistry and space lead to the structural instabilities responsible for the unusual physical properties displayed by some materials. The model has applications in many fields ranging from mineralogy to molecular biology.

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.

Molecular Structure And Vibrational Frequencies of Tetrafluoro isophthalonitrile By Hartree-Fock And Density Functional Theory Calculations

International Nuclear Information System (INIS)

Ayikoglu, A.

2008-01-01

The molecular structure, vibrational frequencies and corresponding vibrational assignments of tetrafluoro isophthalonitrile (TFPN) in the ground state have been calculated using the Hartree-Fock (HF) and density functional methods (B3LYP) with 6-311++G (d, p) basis set. The calculations were utilized in the CS symmetry of TFPN. The obtained vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) were seen to be in good agreement with the experimental data. The comparison of the observed and calculated results showed that the B3LYP method is superior to the HF method for both the vibrational frequencies and geometric parameters

Protein backbone angle restraints from searching a database for chemical shift and sequence homology

Energy Technology Data Exchange (ETDEWEB)

Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

1999-03-15

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

Novel humic acid-bonded magnetite nanoparticles for protein immobilization

Energy Technology Data Exchange (ETDEWEB)

Bayrakci, Mevlut, E-mail: mevlutbayrakci@gmail.com [Ulukisla Vocational School, Nigde University, 51100 Ulukisla, Nigde (Turkey); Gezici, Orhan [Department of Chemistry, Nigde University, 51100 Nigde (Turkey); Bas, Salih Zeki; Ozmen, Mustafa; Maltas, Esra [Department of Chemistry, Selcuk University, 42031 Konya (Turkey)

2014-09-01

The present paper is the first report that introduces (i) a useful methodology for chemical immobilization of humic acid (HA) to aminopropyltriethoxysilane-functionalized magnetite iron oxide nanoparticles (APS-MNPs) and (ii) human serum albumin (HSA) binding to the obtained material (HA-APS-MNPs). The newly prepared magnetite nanoparticle was characterized by using Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and elemental analysis. Results indicated that surface modification of the bare magnetite nanoparticles (MNPs) with aminopropyltriethoxysilane (APS) and HA was successfully performed. The protein binding studies that were evaluated in batch mode exhibited that HA-APS-MNPs could be efficiently used as a substrate for the binding of HSA from aqueous solutions. Usually, recovery values higher than 90% were found to be feasible by HA-APS-MNPs, while that value was around 2% and 70% in the cases of MNPs and APS-MNPs, respectively. Hence, the capacity of MNPs was found to be significantly improved by immobilization of HA. Furthermore, thermal degradation of HA-APS-MNPs and HSA bonded HA-APS-MNPs was evaluated in terms of the Horowitz–Metzger equation in order to determine kinetic parameters for thermal decomposition. Activation energies calculated for HA-APS-MNPs (20.74 kJ mol{sup −1}) and HSA bonded HA-APS-MNPs (33.42 kJ mol{sup −1}) implied chemical immobilization of HA to APS-MNPs, and tight interactions between HA and HA-APS-MNPs. - Highlights: • A new magnetite nanoparticle based humic acid was prepared for the first time. • Protein binding studies of magnetite nanoparticle based humic acid were performed. • Kinetic parameters of protein and/or humic acid bonded nanoparticles were evaluated.

Evaluating the effect of dentin surface pretreatment on the static contact angle of a drop of a bonding agent: an in vitro study

Directory of Open Access Journals (Sweden)

Mehrdad Barekatain

2016-03-01

Full Text Available Introduction: The aim of this study was to investigate the effect of dentinal pretreatment on the static contact angle of a bonding agent as a measure of dentin surface wettability. Materials &Methods: Twenty mid-coronal dentin surfaces were prepared and randomly allocated to four groups (n=5 according to the priming solutions. All segments were etched with 35% phosphoric acid gel for 15 s, rinsed for 30 s and dried. Each group was rehydrated with 10 µL of distilled water, 0.2 % chlorhexidine, 70% ethanol and 5.25% Sodium Hypochlorite respectively and the excess solution was removed after 60 sec using an absorbent paper. Using a micro syringe, a droplet of the Adper Single Bond 2 was placed on each prepared surface. Then the profile and the static contact angle of the droplet were analyzed with a video-based optical contact angle measuring system. The statistical analysis was performed using One-way ANOVA and Dunnett’s t tests (p<0.05. Results: There was a statistically significant difference between the water and sodium hypochlorite groups which indicates the negative effect sodium hypochlorite may have on dentinal surface energy. (p=0.013. The differences between the water and ethanol groups (p=0.168 and between the water and chlorhexidine groups (p=0.665 were not significant. Conclusion: The use of 5.25% sodium hypochlorite as a priming solution in bonding procedure is not recommended. There is no improvement in dentinal surface wettability by using 70% ethanol or 0.2% chlorhexidine instead of water and the recommendation for use of any of the two should be based on other long-term or short-term effects they may have on the bonding procedure.

Can understanding the packing of side chains improve the design of protein-protein interactions?

Science.gov (United States)

Zhou, Alice; O'Hern, Corey; Regan, Lynne

2011-03-01

With the long-term goal to improve the design of protein-protein interactions, we have begun extensive computational studies to understand how side-chains of key residues of binding partners geometrically fit together at protein-peptide interfaces, e.g. the tetratrico-peptide repeat protein and its cognate peptide). We describe simple atomic-scale models of hydrophobic dipeptides, which include hard-core repulsion, bond length and angle constraints, and Van der Waals attraction. By completely enumerating all minimal energy structures in these systems, we are able to reproduce important features of the probability distributions of side chain dihedral angles of hydrophic residues in the protein data bank. These results are the crucial first step in developing computational models that can predict the side chain conformations of residues at protein-peptide interfaces. CSO acknowledges support from NSF grant no. CMMT-1006527.

Angle resolved mass spectrometry of positive ions transmitted through high aspect ratio channels in a radio frequency discharge

NARCIS (Netherlands)

Stoffels - Adamowicz, E.; Stoffels, W.W.; Tachibana, K.; Imai, S.

1997-01-01

The behavior of positive ions in high aspect ratio structures, relevant to the reactive ion etching of deep trenches, has been studied by means of energy resolved mass spectrometry. High aspect ratio trenches are simulated by capillary plates with various aspect ratios. Angle resolved measurements

Molecular dynamics simulation for the influence of incident angles of energetic carbon atoms on the structure and properties of diamond-like carbon films

International Nuclear Information System (INIS)

Li, Xiaowei; Ke, Peiling; Lee, Kwang-Ryeol; Wang, Aiying

2014-01-01

The influence of incident angles of energetic carbon atoms (0–60°) on the structure and properties of diamond-like carbon (DLC) films was investigated by the molecular dynamics simulation using a Tersoff interatomic potential. The present simulation revealed that as the incident angles increased from 0 to 60°, the surface roughness of DLC films increased and the more porous structure was generated. Along the growth direction of DLC films, the whole system could be divided into four regions including substrate region, transition region, stable region and surface region except the case at the incident angle of 60°. When the incident angle was 45°, the residual stress was significantly reduced by 12% with little deterioration of mechanical behavior. The further structure analysis using both the bond angles and bond length distributions indicated that the compressive stress reduction mainly resulted from the relaxation of highly distorted C–C bond length. - Highlights: • The dependence of films properties on different incident angles was investigated. • The change of incident angles reduced the stress without obvious damage of density. • The stress reduction attributed to the relaxation of highly distorted bond length

Change of chemical bond and wettability of polylacticacid implanted with high-flux carbon ion

International Nuclear Information System (INIS)

Zhang Jizhong; Kang Jiachen; Zhang Xiaoji; Zhou Hongyu

2008-01-01

Polylacticacid (PLA) was submitted to high-flux carbon ion implantation with energy of 40 keV. It was investigated to the effect of ion fluence (1 x 10 12 -1 x 10 15 ions/cm 2 ) on the properties of the polymer. X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), wettability, and roughness were employed to study change of structure and properties of the as-implanted PLA samples. Six carbon bonds, that is, C, C-H, C-O-C, C-O, O-C-O, and >C=O, were observed on surfaces of the as-implanted PLA samples. The intensities of various chemical bonds changed with increasing ion fluence. AFM images displayed that there was irradiation damage and that it was related closely with ion fluence. At fluence as high as 1 x 10 15 ions/cm 2 surface-restructuring phenomenum took place on the surface of the PLA. Wettability was also affected by the variation on the fluence. With increasing ion fluence, the water contact angle of the as-implanted PLA samples changed gradually reaching a maximum of 76.5 deg. with 1 x 10 13 ions/cm 2 . The experimental results revealed that carbon ion fluence strongly affected surface chemical bond, morphology, wettability, and roughness of the PLA samples

Long range correlations and folding angle with applications to α-helical proteins

Science.gov (United States)

Krokhotin, Andrey; Nicolis, Stam; Niemi, Antti J.

2014-03-01

The conformational complexity of chain-like macromolecules such as proteins and other linear polymers is much larger than that of point-like atoms and molecules. Unlike particles, chains can bend, twist, and even become knotted. Thus chains might also display a much richer phase structure. Unfortunately, it is not very easy to characterize the phase of a long chain. Essentially, the only known attribute is the radius of gyration. The way how it changes when the degree of polymerization becomes different, and how it evolves when the ambient temperature and solvent properties change, is commonly used to disclose the phase. But in any finite length chain there are corrections to scaling that complicate the detailed analysis of the phase structure. Here we introduce a quantity that we call the folding angle to identify and scrutinize the phase structure, as a complement to the radius of gyration. We argue for a mean-field level relationship between the folding angle and the scaling exponent in the radius of gyration. We then estimate the value of the folding angle in the case of crystallographic α-helical protein structures in the Protein Data Bank. We also show how the experimental value of the folding angle can be obtained computationally, using a semiclassical Born-Oppenheimer description of α-helical chiral chains.

Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry.

Science.gov (United States)

Wongkongkathep, Piriya; Li, Huilin; Zhang, Xing; Loo, Rachel R Ogorzalek; Julian, Ryan R; Loo, Joseph A

2015-11-15

The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in combination with ECD allowed the three disulfide bonds of insulin to be cleaved and the overall sequence coverage to be increased. For the larger sized ribonuclease A with four disulfide bonds, irradiation from an infrared laser (10.6 µm) to disrupt non-covalent interactions was combined with UV-activation to facilitate the cleavage of up to three disulfide bonds. Preferences for disulfide bond cleavage are dependent on protein structure and sequence. Disulfide bonds can reform if the generated radicals remain in close proximity. By varying the time delay between the UV-activation and the ECD events, it was determined that disulfide bonds reform within 10-100 msec after their UV-homolytic cleavage.

Using Order Tracking Analysis Method to Detect the Angle Faults of Blades on Wind Turbine

DEFF Research Database (Denmark)

Li, Pengfei; Hu, Weihao; Liu, Juncheng

2016-01-01

The angle faults of blades on wind turbines are usually included in the set angle fault and the pitch angle fault. They are occupied with a high proportion in all wind turbine faults. Compare with the traditional fault detection methods, using order tracking analysis method to detect angle faults....... By analyzing and reconstructing the fault signals, it is easy to detect the fault characteristic frequency and see the characteristic frequencies of angle faults depend on the shaft rotating frequency, which is known as the 1P frequency and 3P frequency distinctly....

Fixman compensating potential for general branched molecules

Energy Technology Data Exchange (ETDEWEB)

Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States); Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States)

2013-12-28

The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

Comparison of the tensile bond strength of high-noble, noble, and base metal alloys bonded to enamel.

Science.gov (United States)

Sen, D; Nayir, E; Pamuk, S

2000-11-01

Although the bond strengths of various resin composite luting materials have been reported in the literature, the evaluation of these systems with various cast alloys of different compositions has not been completely clarified. To evaluate the tensile bond strength of sandblasted high-noble, noble, and base metal alloys bonded to etched enamel by 2 different bonding agents of different chemical composition: Panavia-Ex (BIS-GMA) and Super-Bond (4-META acrylic). Flat enamel surfaces were prepared on buccal surfaces of 60 extracted noncarious human incisors. Teeth were divided into 3 groups of 20 each. Twenty circular disks of 5 mm diameter were prepared for casting for each group. Group I was cast with a high-noble, group II with a noble, and group III with a base metal alloy. The surfaces of the disks were sandblasted with 250 microm Al(2)O(3). Ten disks of each group were bonded to exposed enamel surfaces with Super-Bond and 10 disks with Panavia-Ex as recommended by the manufacturer. The tensile bond strength was measured with an Instron universal testing machine with a crosshead speed of 0.5 mm/min until failure occurred. Two-way ANOVA was used to evaluate the results. The differences in bond strengths of Super-Bond and Panavia-Ex with different alloys were not significant. The highest bond strengths were obtained in base metal alloys, followed by noble and high-noble alloys. These results were significant. Panavia-Ex and Super-Bond exhibited comparable tensile bond strengths. For both luting agents, the highest bond strengths were achieved with base metal alloys and the lowest with high-noble alloys.

Low-frequency features of the ultrasound echo from an adhesively bonded layer-substrate structure

Institute of Scientific and Technical Information of China (English)

WANG Xiaomin; LI Mingxuan; MAO Jie; LIAN Guoxuan

2005-01-01

The low-frequency features of the ultrasound reflection spectra from the structure of a single layer on a substrate bonded by a thin adhesive layer are theoretically studied; the low-frequency here means the frequency of the interrogating ultrasonic wave is less than the quart-wavelength resonance frequency of the adhesive layer. The possibility of the inversion of the thickness and the evaluation of the cohesion strength of the adhesive layer from the resonance frequency shifts of the layered system is indicated. An analytic solution to the nonlinear equation satisfied by the resonance frequency is presented by Taylor expansion method showing satisfactory agreement with the numerical results by Newton iterative method. The results indicate larger range for application than the traditional spring model for the thin adhesive layer. In a much lower frequency range the thin adhesive layer may be regarded to be a spring.

Effect of fat content and homogenization under conventional or ultra-high-pressure conditions on interactions between proteins in rennet curds.

Science.gov (United States)

Zamora, A; Trujillo, A J; Armaforte, E; Waldron, D S; Kelly, A L

2012-09-01

The objective of this study was to investigate the influence of conventional and ultra-high-pressure homogenization on interactions between proteins within drained rennet curds. The effect of fat content of milk (0.0, 1.8, or 3.6%) and homogenization treatment on dissociation of proteins by different chemical agents was thus studied. Increasing the fat content of raw milk increased levels of unbound whey proteins and calcium-bonded caseins in curds; in contrast, hydrophobic interactions and hydrogen bonds were inhibited. Both homogenization treatments triggered the incorporation of unbound whey proteins in the curd, and of caseins through ionic bonds involving calcium salts. Conventional homogenization-pasteurization enhanced interactions between caseins through hydrogen bonds and hydrophobic interactions. In contrast, ultra-high-pressure homogenization impaired hydrogen bonding, led to the incorporation of both whey proteins and caseins through hydrophobic interactions and increased the amount of unbound caseins. Thus, both homogenization treatments provoked changes in the protein interactions within rennet curds; however, the nature of the changes depended on the homogenization conditions. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Formation of the market of high-bond (junk bonds in the United States in 1970–1980 years

Directory of Open Access Journals (Sweden)

Moshenskyi S.Z.

2017-03-01

Full Text Available Market of high-yield bonds (also known as «junk bonds» began to emerge in the US in the mid-1970s and was associated with the activities of «junk bond king» Michael Milken from Drexel investment company. Junk bonds emitents are small and newly established companies which cannot get a high credit rating. Emission of high-yield (8–10 % bond was their only chance to find its place in the financial market. Michael Milken realized the potential of these bonds, which, in fact, were often quite reliable securities, and started organizing their emissions by selling junk bonds to Savings and Loan Associations and other investors. In the 1980 issue of such bonds used for aggressive corporate takeovers, which supplied the capital from junk bonds market. Some of takeovers carried out in violation of laws that led to the arrest of Michael Milken, Drexel bankruptcy and the collapse of the entire junk bonds market.

HIGH FREQUENCY ELECTROSTATIC INSTABILITIES IN A PLASMA

Energy Technology Data Exchange (ETDEWEB)

Klein, M W; Auer, P L

1963-06-15

The dispersion relation is examined for a collisionless infinite plasma in the presence of an anisotropic Maxwellian velocity distribution and a uniform external magnetic field. Unstable solutions exist below the muitiples of the electron cyclotron frequency provided the temperature anisotropy is sufficiently large. The dependence of the growth rate upon harmonic number, density, angle of propagation with respect to the magnetic field, and frequency is discussed for zero as well as non-zero parallel temperatures. In the latter case, the waves are strongly damped as their frequency approaches a multiple of the gyro- frequency. (auth)

Application of the O-lattice theory for the reconstruction of the high-angle near 90° tilt Si(1 1 0)/(0 0 1) boundary created by wafer bonding

International Nuclear Information System (INIS)

Cherkashin, N.; Kononchuk, O.; Reboh, S.; Hÿtch, M.

2012-01-01

This work presents an experimental and theoretical identification of defects and morphologies of a high-angle near-90° tilt Si (1 ¯ 10)//(001) boundary created by direct wafer bonding. Two samples with different twist misorientations, between the (1 ¯ 10) layer and the (0 0 1) substrate, were studied using conventional transmission electron microscopy (TEM) and geometric phase analysis of high-resolution TEM images. The O-lattice theory was used for atom reconstruction of the interface along the [11 ¯ 0] sub //[001] lay direction. It is demonstrated that to preserve covalent bonding across the interface, it should consist of {11 ¯ 1} sub,lay //{1 ¯ 12} lay,sub facets intersected by maximum of six {11 ¯ 1} lay,sub planes with three 90° Shockley dislocations per facet. It is shown that a particular atom reconstruction is needed at transition points from one facet to another. The presence or absence of deviation from exact 90° tilt of the layer with respect to the substrate is shown to be related directly to the undulations of the interface. It is demonstrated that the latter has an influence on the Burgers vector of the dislocations adjusting in-plane twist misorientation. A general model for cubic face-centered materials for an arbitrary 〈1 1 0〉 sub,lay tilt interface is proposed, which predicts the net Burgers vector and the spacing between dislocations necessary to realize transition from the lattice of the substrate (layer) to the layer (substrate).

Invisible detergents for structure determination of membrane proteins by small-angle neutron scattering

DEFF Research Database (Denmark)

Midtgaard, Søren Roi; Darwish, Tamim A.; Pedersen, Martin Cramer

2018-01-01

A novel and generally applicable method for determining structures of membrane proteins in solution via small-angle neutron scattering (SANS) is presented. Common detergents for solubilizing membrane proteins were synthesized in isotope-substituted versions for utilizing the intrinsic neutron sca...... solution structure determination of membrane proteins by SANS and subsequent data analysis available to non-specialists. This article is protected by copyright. All rights reserved....

Planck 2013 results. VI. High Frequency Instrument data processing

CERN Document Server

Ade, P.A.R.; Armitage-Caplan, C.; Arnaud, M.; Ashdown, M.; Atrio-Barandela, F.; Aumont, J.; Baccigalupi, C.; Banday, A.J.; Barreiro, R.B.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J. -P.; Bersanelli, M.; Bielewicz, P.; Bobin, J.; Bock, J.J.; Bond, J.R.; Borrill, J.; Bouchet, F.R.; Boulanger, F.; Bowyer, J.W.; Bridges, M.; Bucher, M.; Burigana, C.; Cardoso, J. -F.; Catalano, A.; Chamballu, A.; Chary, R. -R.; Chen, X.; Chiang, L. -Y; Chiang, H.C.; Christensen, P.R.; Church, S.; Clements, D.L.; Colombi, S.; Colombo, L.P.L.; Combet, C.; Couchot, F.; Coulais, A.; Crill, B.P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R.D.; Davis, R.J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Delouis, J. -M.; Désert, F. -X.; Dickinson, C.; Diego, J.M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Dunkley, J.; Dupac, X.; Efstathiou, G.; Enßlin, T.A.; Eriksen, H.K.; Finelli, F.; Forni, O.; Frailis, M.; Fraisse, A.A.; Franceschi, E.; Galeotta, S.; Ganga, K.; Giard, M.; Giardino, G.; Girard, D.; Giraud-Héraud, Y.; González-Nuevo, J.; Górski, K.M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Gudmundsson, J.E.; Hansen, F.K.; Hanson, D.; Harrison, D.; Helou, G.; Henrot-Versillé, S.; Herent, O.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S.R.; Hivon, E.; Hobson, M.; Holmes, W.A.; Hornstrup, A.; Hou, Z.; Hovest, W.; Huffenberger, K.M.; Hurier, G.; Jaffe, T.R.; Jaffe, A.H.; Jones, W.C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T.S.; Kneissl, R.; Knoche, J.; Knox, L.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lamarre, J. -M.; Lasenby, A.; Laureijs, R.J.; Lawrence, C.R.; Jeune, M. Le; Leonardi, R.; Leroy, C.; Lesgourgues, J.; Liguori, M.; Lilje, P.B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P.M.; Macías-Pérez, J.F.; MacTavish, C.J.; Maffei, B.; Mandolesi, N.; Maris, M.; Marshall, D.J.; Martin, P.G.; Martínez-González, E.; Masi, S.; Matarrese, S.; Matthai, F.; Mazzotta, P.; McGehee, P.; Meinhold, P.R.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M. -A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Mottet, S.; Munshi, D.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C.B.; Nørgaard-Nielsen, H.U.; North, C.; Noviello, F.; Novikov, D.; Novikov, I.; Orieux, F.; Osborne, S.; Oxborrow, C.A.; Paci, F.; Pagano, L.; Pajot, F.; Paladini, R.; Paoletti, D.; Pasian, F.; Patanchon, G.; Perdereau, O.; Perotto, L.; Perrotta, F.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pointecouteau, E.; Polenta, G.; Ponthieu, N.; Popa, L.; Poutanen, T.; Pratt, G.W.; Prézeau, G.; Prunet, S.; Puget, J. -L.; Rachen, J.P.; Racine, B.; Reach, W.T.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Ricciardi, S.; Riller, T.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Roudier, G.; Rowan-Robinson, M.; Rusholme, B.; Sanselme, L.; Santos, D.; Sauvé, A.; Savini, G.; Shellard, E.P.S.; Spencer, L.D.; Starck, J. -L.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sureau, F.; Sutton, D.; Suur-Uski, A. -S.; Sygnet, J. -F.; Tauber, J.A.; Tavagnacco, D.; Techene, S.; Terenzi, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Umana, G.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Vibert, L.; Vielva, P.; Villa, F.; Vittorio, N.; Wade, L.A.; Wandelt, B.D.; White, S.D.M.; Yvon, D.; Zacchei, A.; Zonca, A.

2014-01-01

We describe the processing of the 531 billion raw data samples from the High Frequency Instrument (hereafter HFI), which we performed to produce six temperature maps from the first 473 days of Planck-HFI survey data. These maps provide an accurate rendition of the sky emission at 100, 143, 217, 353, 545, and 857 GHz with an angular resolution ranging from 9.7 to 4.6 arcmin. The detector noise per (effective) beam solid angle is respectively, 10, 6, 12 and 39 microKelvin in HFI four lowest frequency channel (100--353 GHz) and 13 and 14 kJy/sr for the 545 and 857 GHz channels. Using the 143 GHz channel as a reference, these two high frequency channels are intercalibrated within 5% and the 353 GHz relative calibration is at the percent level. The 100 and 217 GHz channels, which together with the 143 GHz channel determine the high-multipole part of the CMB power spectrum (50 < l <2500), are intercalibrated at better than 0.2 %.

Development and characterization of high-frequency resonance-enhanced microjet actuators for control of high-speed jets

Science.gov (United States)

Upadhyay, Puja; Gustavsson, Jonas P. R.; Alvi, Farrukh S.

2016-05-01

For flow control applications requiring high-frequency excitation, very few actuators have sufficient dynamic response and/or control authority to be useful in high-speed flows. Due to this reason, experiments involving high-frequency excitation, attempted in the past, have been limited to either low-frequency actuation with reasonable control authority or moderate-frequency actuation with limited control authority. The current work expands on the previous development of the resonance-enhanced microactuators to design actuators that are capable of producing high-amplitude pulses at much higher frequencies [{O} (10 kHz)]. Using lumped element modeling, two actuators have been designed with nominal frequencies of 20 and 50 kHz. Extensive benchtop characterization using acoustic measurements as well as optical diagnostics using a high-resolution micro-schlieren setup is employed to characterize the dynamic response of these actuators. The actuators performed at a range of frequencies, 20.3-27.8 and 54.8-78.2 kHz, respectively. In addition to providing information on the actuator flow physics and performance at various operating conditions, this study serves to develop easy-to-integrate high-frequency actuators for active control of high-speed jets. Preliminary testing of these actuators is performed by implementing the 20-kHz actuator on a Mach 0.9 free jet flow field for noise reduction. Acoustic measurements in the jet near field demonstrate attenuation of radiated noise at all observation angles.

Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family

Directory of Open Access Journals (Sweden)

Dallakyan Sargis

2008-08-01

Full Text Available Abstract Background Gram-negative bacteria use periplasmic-binding proteins (bPBP to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo and closed (ligated conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding. Results We use a distance constraint model (DCM to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network. Conclusion Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect

Hydrogen bonds in the vicinity of the special pair of the bacterial reaction center probed by hydrostatic high-pressure absorption spectroscopy.

Science.gov (United States)

Kangur, Liina; Jones, Michael R; Freiberg, Arvi

2017-12-01

Using the native bacteriochlorophyll a pigment cofactors as local probes, we investigated the response to external hydrostatic high pressure of reaction center membrane protein complexes from the photosynthetic bacterium Rhodobacter sphaeroides. Wild-type and engineered complexes were used with a varied number (0, 1 or 2) of hydrogen bonds that bind the reaction center primary donor bacteriochlorophyll cofactors to the surrounding protein scaffold. A pressure-induced breakage of hydrogen bonds was established for both detergent-purified and membrane-embedded reaction centers, but at rather different pressures: between 0.2 and 0.3GPa and at about 0.55GPa, respectively. The free energy change associated with the rupture of the single hydrogen bond present in wild-type reaction centers was estimated to be equal to 13-14kJ/mol. In the mutant with two symmetrical hydrogen bonds (FM197H) a single cooperative rupture of the two bonds was observed corresponding to an about twice stronger bond, rather than a sequential rupture of two individual bonds. Copyright © 2017 Elsevier B.V. All rights reserved.

Covalent Bonding of Chlorogenic Acid Induces Structural Modifications on Sunflower Proteins

NARCIS (Netherlands)

Karefyllakis, D.; Salakou, Stavroula; Bitter, J.H.; Goot, van der A.J.; Nikiforidis, K.

2018-01-01

Proteins and phenols coexist in the confined space of plant cells leading to reactions between them, which result in new covalently bonded complex molecules. This kind of reactions has been widely observed during storage and processing of plant materials. However, the nature of the new complex

Reflectivity quenching of ESR multilayer polymer film reflector in optically bonded scintillator arrays

Science.gov (United States)

Loignon-Houle, Francis; Pepin, Catherine M.; Charlebois, Serge A.; Lecomte, Roger

2017-04-01

The 3M-ESR multilayer polymer film is a widely used reflector in scintillation detector arrays. As specified in the datasheet and confirmed experimentally by measurements in air, it is highly reflective (> 98 %) over the entire visible spectrum (400-1000 nm) for all angles of incidence. Despite these outstanding characteristics, it was previously found that light crosstalk between pixels in a bonded LYSO scintillator array with ESR reflector can be as high as ∼30-35%. This unexplained light crosstalk motivated further investigation of ESR optical performance. Analytical simulation of a multilayer structure emulating the ESR reflector showed that the film becomes highly transparent to incident light at large angles when surrounded on both sides by materials of refractive index higher than air. Monte Carlo simulations indicate that a considerable fraction (∼25-35%) of scintillation photons are incident at these leaking angles in high aspect ratio LYSO scintillation crystals. The film transparency was investigated experimentally by measuring the scintillation light transmission through the ESR film sandwiched between a scintillation crystal and a photodetector with or without layers of silicone grease. Strong light leakage, up to nearly 30%, was measured through the reflector when coated on both sides with silicone, thus elucidating the major cause of light crosstalk in bonded arrays. The reflector transparency was confirmed experimentally for angles of incidence larger than 60 ° using a custom designed setup allowing illumination of the bonded ESR film at selected grazing angles. The unsuspected ESR film transparency can be beneficial for detector arrays exploiting light sharing schemes, but it is highly detrimental for scintillator arrays designed for individual pixel readout.

Single Frequency Impedance Analysis on Reduced Graphene Oxide Screen-Printed Electrode for Biomolecular Detection.

Science.gov (United States)

Rajesh; Singal, Shobhita; Kotnala, Ravinder K

2017-10-01

A biofunctionalized reduced graphene oxide (rGO)-modified screen-printed carbon electrode (SPCE) was constructed as an immunosensor for C-reactive protein (CRP) detection, a biomarker released in early stage acute myocardial infarction. A different approach of single frequency analysis (SFA) study was utilized for the biomolecular sensing, by monitoring the response in phase angle changes obtained at an optimized frequency resulting from antigen-antibody interactions. A set of measurements were carried out to optimize a frequency where a maximum change in phase angle was observed, and in this case, we found it at around 10 Hz. The bioelectrode was characterized by contact angle measurements, scanning electron microscopy, and electrochemical techniques. A concentration-dependent response of immunosensor to CRP with the change in phase angle, at a fixed frequency of 10 Hz, was found to be in the range of 10 ng mL -1 to 10 μg mL -1 in PBS and was fit quantitative well with the Hill-Langmuir equation. Based on the concentration-response data, the dissociation constant (K d ) was found to be 3.5 nM (with a Hill coefficient n = 0.57), which indicated a negative cooperativity with high anti-CRP (antibody)-CRP (antigen) binding at the electrode surface. A low-frequency analysis of sensing with an ease of measurement on a disposable electroactive rGO-modified electrode with high selectivity and sensitivity makes it a potential tool for biological sensors.

Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.

Science.gov (United States)

Fritch, Benjamin; Kosolapov, Andrey; Hudson, Phillip; Nissley, Daniel A; Woodcock, H Lee; Deutsch, Carol; O'Brien, Edward P

2018-04-18

Mechanical forces acting on the ribosome can alter the speed of protein synthesis, indicating that mechanochemistry can contribute to translation control of gene expression. The naturally occurring sources of these mechanical forces, the mechanism by which they are transmitted 10 nm to the ribosome's catalytic core, and how they influence peptide bond formation rates are largely unknown. Here, we identify a new source of mechanical force acting on the ribosome by using in situ experimental measurements of changes in nascent-chain extension in the exit tunnel in conjunction with all-atom and coarse-grained computer simulations. We demonstrate that when the number of residues composing a nascent chain increases, its unstructured segments outside the ribosome exit tunnel generate piconewtons of force that are fully transmitted to the ribosome's P-site. The route of force transmission is shown to be through the nascent polypetide's backbone, not through the wall of the ribosome's exit tunnel. Utilizing quantum mechanical calculations we find that a consequence of such a pulling force is to decrease the transition state free energy barrier to peptide bond formation, indicating that the elongation of a nascent chain can accelerate translation. Since nascent protein segments can start out as largely unfolded structural ensembles, these results suggest a pulling force is present during protein synthesis that can modulate translation speed. The mechanism of force transmission we have identified and its consequences for peptide bond formation should be relevant regardless of the source of the pulling force.

Angle-of-arrival-based gesture recognition using ultrasonic multi-frequency signals

KAUST Repository

Chen, Hui

2017-11-02

Hand gestures are tools for conveying information, expressing emotion, interacting with electronic devices or even serving disabled people as a second language. A gesture can be recognized by capturing the movement of the hand, in real time, and classifying the collected data. Several commercial products such as Microsoft Kinect, Leap Motion Sensor, Synertial Gloves and HTC Vive have been released and new solutions have been proposed by researchers to handle this task. These systems are mainly based on optical measurements, inertial measurements, ultrasound signals and radio signals. This paper proposes an ultrasonic-based gesture recognition system using AOA (Angle of Arrival) information of ultrasonic signals emitted from a wearable ultrasound transducer. The 2-D angles of the moving hand are estimated using multi-frequency signals captured by a fixed receiver array. A simple redundant dictionary matching classifier is designed to recognize gestures representing the numbers from `0\\' to `9\\' and compared with a neural network classifier. Average classification accuracies of 95.5% and 94.4% are obtained, respectively, using the two classification methods.

High frequency of tumor cells with nuclear Egr-1 protein expression in human bladder cancer is associated with disease progression

International Nuclear Information System (INIS)

Egerod, Frederikke Lihme; Bartels, Annette; Fristrup, Niels; Borre, Michael; Ørntoft, Torben F; Oleksiewicz, Martin B; Brünner, Nils; Dyrskjøt, Lars

2009-01-01

Egr-1 (early growth response-1 transcription factor) has been proposed to be involved in invasion and metastasis processes of human bladder cancer, but Egr-1 protein expression levels in human bladder cancer have not been investigated. In the present study we investigated the expression levels of Egr-1 protein in early stages of human bladder cancer and correlated it to later progression. Expression of Egr-1 protein in human bladder cancer was examined by immunohistochemistry, on a tissue microarray constructed from tumors from 289 patients with non-muscle invasive urothelial bladder cancer. The frequency of tumor cells with nuclear Egr-1 immunolabelling correlated to bladder cancer stage, grade and to later progression to muscle-invasive bladder cancer (T2-4). Stage T1 tumors exhibited significantly higher frequencies of tumor cells with nuclear Egr-1 immunolabelling than Ta tumors (P = 0.001). Furthermore, Kaplan-Meier survival analysis showed that a high frequency of tumor cells with nuclear Egr-1 immunolabelling was significantly associated with a higher risk of progression to stage T2-4 (log-rank test, P = 0.035). Tumor cells with nuclear Egr-1 immunolabelling were found to localize at the tumor front in some of the tumor biopsies. The results from this study support a potential involvement of Egr-1 in the progression from non-muscle invasive bladder cancers to muscle invasive bladder cancer

Vibrational frequency analysis, FT-IR, DFT and M06-2X studies on tert-Butyl N-(thiophen-2yl)carbamate

Science.gov (United States)

Sert, Yusuf; Singer, L. M.; Findlater, M.; Doğan, Hatice; Çırak, Ç.

2014-07-01

In this study, the experimental and theoretical vibrational frequencies of a newly synthesized tert-Butyl N-(thiophen-2yl)carbamate have been investigated. The experimental FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with the 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The vibrational frequencies have been assigned using potential energy distribution (PED) analysis by using VEDA 4 software. The computational optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with related literature results. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and are depicted.

Molecular Structure And Vibrational Frequencies of 2,3,4 Nitro anilines By Hartree-Fock And Density Functional Theory Calculations

International Nuclear Information System (INIS)

Sert, Y.

2008-01-01

The optimised molecular structure, vibrational frequencies and corresponding vibrational assignments of 2-, 3- and 4- nitro anilines have been calculated using the Hartree-Fock (HF) and density functional methods (B3LYP) with 6-311++G (d, p) basis set. The calculations were adapted to the C S symmetries of all the molecules. The calculated vibrational frequencies and geometric parameters (bond lengths and bond angles) were seen to be in good agreement with the experimental data. The comparison of the experimental and theoretical results showed that the HF method is superior to the B3LYP method for both the vibrational frequencies and geometric parameters

Effects of multi-frequency ultrasound pretreatment under low power density on the enzymolysis and the structure characterization of defatted wheat germ protein.

Science.gov (United States)

Yang, Xue; Li, Yunliang; Li, Suyun; Oladejo, Ayobami Olayemi; Wang, Yucheng; Huang, Shanfen; Zhou, Cunshan; Wang, Yang; Mao, Li; Zhang, Yanyan; Ma, Haile; Ye, Xiaofei

2017-09-01

The effects of ultrasonic frequency mode, power density, pretreatment time and other parameters under low power density on the degree of hydrolysis (DH) of defatted wheat germ protein (DWGP) and angiotensin-I-converting enzyme (ACE) inhibitory activity of DWGP hydrolysate were studied in this research. Ultraviolet-visible (UV-Vis) spectra, free sulfhydryl (SH), disulfide bond (SS), surface hydrophobicity and hydrophobic protein content of ultrasound-pretreated protein and hydrophobic amino acid (HAA) content of alcalase-hydrolysate of DWGP were measured under optimized ultrasonic condition. The ultrasonic frequency mode with dual-fixed frequency combination of 28/40kHz showed higher ACE inhibitory activity of DWGP hydrolysate compared with that of other ultrasound frequency modes and all the ultrasonic frequency combinations involving in 28kHz showed higher ACE inhibitory activity. Under the dual-fixed frequency ultrasound mode of 28/40kHz, ultrasonic power density of 60W/L, pretreatment time of 70min, temperature of 60°C and substrate concentration of 60g/L, the ACE inhibitory activity of DWGP hydrolysate was the highest with its value of 74.75% (increased by 62.30% compared to control). However, all the ultrasonic pretreatment did not increase the DH of DWGP significantly (p>0.05). The changes in UV-Vis spectra, SH and SS groups, surface hydrophobicity and hydrophobic protein content indicated that the structure of DWGP unfolded after ultrasound pretreatment. The HAA content of hydrolysate from the pretreated DWGP increased significantly (p<0.05). The results proved that ultrasound pretreatment loosed the protein structure and exposed more HAA residues of protein to be attacked easily by alcalase. This resulted in the increase in the HAA content which related to the ACE inhibitory activity. Copyright © 2017 Elsevier B.V. All rights reserved.

Modulating nanoparticle superlattice structure using proteins with tunable bond distributions

International Nuclear Information System (INIS)

McMillan, Janet R.; Brodin, Jeffrey D.; Millan, Jaime A.; Lee, Byeongdu; Olvera de la Cruz, Monica; Mirkin, Chad A.

2017-01-01

Here, we investigate the use of proteins with tunable DNA modification distributions to modulate nanoparticle superlattice structure. Using Beta-galactosidase (βgal) as a model system, we have employed the orthogonal chemical reactivities of surface amines and thiols to synthesize protein-DNA conjugates with 36 evenly distributed or 8 specifically positioned oligonucleotides. When assembled into crystalline superlattices with AuNPs, we find that the distribution of DNA modifications modulates the favored structure: βgal with uniformly distributed DNA bonding elements results in body-centered cubic crystals, whereas DNA functionalization of cysteines results in AB 2 packing. We probe the role of protein oligonucleotide number and conjugate size on this observation, which revealed the importance of oligonucleotide distribution and number in this observed assembly behavior. These results indicate that proteins with defined DNA-modification patterns are powerful tools to control the nanoparticle superlattices architecture, and establish the importance of oligonucleotide distribution in the assembly behavior of protein-DNA conjugates.

Spondylolysis and the sacro-horizontal angle in athletes

International Nuclear Information System (INIS)

Swaerd, L.; Hellstroem, M.; Jacobsson, B.; Peterson, L.; Sahlgrenska Sjukhuset, Goeteborg; King Faisal Specialist Hospital and Research Centre, Riyadh

1989-01-01

The frequency of spondylolysis and the relationship between spondylolysis and the sacro-horizontal angle in 143 athletes and 30 non-athletes is reported. Athletes had a larger sacro-horizontal angle than non-athletes. The sacro-horizontal angle was larger in athletes with spondylolysis as compared with those without. An increased incidence of spondylolysis with an increased angle was demonstrated. It is suggested that an increased sacro-horizontal angle may predispose to spondylolysis, especially in combination with the high mechanical loads sustained in certain sports. (orig.)

Spondylolysis and the sacro-horizontal angle in athletes

Energy Technology Data Exchange (ETDEWEB)

Swaerd, L.; Hellstroem, M.; Jacobsson, B.; Peterson, L. (Oestra Sjukhuset, Goeteborg (Sweden). Dept. of Orthopaedics; Sahlgrenska Sjukhuset, Goeteborg (Sweden). Dept. of Diagnostic Radiology; King Faisal Specialist Hospital and Research Centre, Riyadh (Saudi Arabia). Dept. of Radiology)

The frequency of spondylolysis and the relationship between spondylolysis and the sacro-horizontal angle in 143 athletes and 30 non-athletes is reported. Athletes had a larger sacro-horizontal angle than non-athletes. The sacro-horizontal angle was larger in athletes with spondylolysis as compared with those without. An increased incidence of spondylolysis with an increased angle was demonstrated. It is suggested that an increased sacro-horizontal angle may predispose to spondylolysis, especially in combination with the high mechanical loads sustained in certain sports. (orig.).

The Information Content of Treasury Bond Options Concerning Future Volatility and Price Jumps

DEFF Research Database (Denmark)

Busch, Thomas; Christensen, Bent Jesper; Nielsen, Morten Ørregaard

We study the relation between realized and implied volatility in the bond market. Realizedvolatility is constructed from high-frequency (5-minute) returns on 30 year Treasury bond futures.Implied volatility is backed out from prices of associated bond options. Recent nonparametric statisticaltech......We study the relation between realized and implied volatility in the bond market. Realizedvolatility is constructed from high-frequency (5-minute) returns on 30 year Treasury bond futures.Implied volatility is backed out from prices of associated bond options. Recent nonparametric...... components. We also introduce a new vector HAR (VecHAR) modelfor the resulting simultaneous system, controlling for possible endogeneity of implied volatility inthe forecasting equations. We show that implied volatility is a biased and inefficient forecast in thebond market. However, implied volatility does...

Raman spectroscopy of supported chromium oxide catalysts : determination of chromium-oxygen bond distances and bond orders

NARCIS (Netherlands)

Weckhuysen, B.M.; Wachs, I.E.

1996-01-01

An empirical correlation is described for relating Raman stretching frequencies of chromium—oxygen (Cr—O) bonds to their bond lengths in chromium oxide reference compounds. An exponential fit of crystallographically determined Cr—O bond lengths to Cr—O Raman symmetric stretching frequencies

Automated microfluidic sample-preparation platform for high-throughput structural investigation of proteins by small-angle X-ray scattering

DEFF Research Database (Denmark)

Lafleur, Josiane P.; Snakenborg, Detlef; Nielsen, Søren Skou

2011-01-01

A new microfluidic sample-preparation system is presented for the structural investigation of proteins using small-angle X-ray scattering (SAXS) at synchrotrons. The system includes hardware and software features for precise fluidic control, sample mixing by diffusion, automated X-ray exposure...... control, UV absorbance measurements and automated data analysis. As little as 15 l of sample is required to perform a complete analysis cycle, including sample mixing, SAXS measurement, continuous UV absorbance measurements, and cleaning of the channels and X-ray cell with buffer. The complete analysis...

Active Control of High-Speed Free Jets Using High-Frequency Excitation

Science.gov (United States)

Upadhyay, Puja

Control of aerodynamic noise generated by high-performance jet engines continues to remain a serious problem for the aviation community. Intense low frequency noise produced by large-scale coherent structures is known to dominate acoustic radiation in the aft angles. A tremendous amount of research effort has been dedicated towards the investigation of many passive and active flow control strategies to attenuate jet noise, while keeping performance penalties to a minimum. Unsteady excitation, an active control technique, seeks to modify acoustic sources in the jet by leveraging the naturally-occurring flow instabilities in the shear layer. While excitation at a lower range of frequencies that scale with the dynamics of large-scale structures, has been attempted by a number of studies, effects at higher excitation frequencies remain severely unexplored. One of the major limitations stems from the lack of appropriate flow control devices that have sufficient dynamic response and/or control authority to be useful in turbulent flows, especially at higher speeds. To this end, the current study seeks to fulfill two main objectives. First, the design and characterization of two high-frequency fluidic actuators (25 and 60 kHz) are undertaken, where the target frequencies are guided by the dynamics of high-speed free jets. Second, the influence of high-frequency forcing on the aeroacoustics of high-speed jets is explored in some detail by implementing the nominally 25 kHz actuator on a Mach 0.9 (Re D = 5 x 105) free jet flow field. Subsequently, these findings are directly compared to the results of steady microjet injection experiments performed in the same rig and to prior jet noise control studies, where available. Finally, limited acoustic measurements were also performed by implementing the nominally 25 kHz actuators on jets at higher Mach numbers, including shock containing jets, and elevated temperatures. Using lumped element modeling as an initial guide, the current

Mussel byssus-inspired engineering of synergistic nanointerfacial interactions as sacrificial bonds into carbon nanotube-reinforced soy protein/nanofibrillated cellulose nanocomposites: Versatile mechanical enhancement

Science.gov (United States)

Wang, Zhong; Zhao, Shujun; Kang, Haijiao; Zhang, Wei; Zhang, Shifeng; Li, Jianzhang

2018-03-01

Achieving flexible and stretchable biobased nanocomposites combining high strength and toughness is still a very challenging endeavor. Herein, we described a novel and versatile biomimetic design for tough and high-performance TEMPO-oxidized nanofibrillated cellulose (TONFC)/soy protein isolate (SPI) nanocomposites, which are triggered by catechol-mimetic carbon nanotubes (PCT) and iron ions (Fe(III)) to yield a strong yet sacrificial metal-ligand motifs into a chemically cross-linked architecture network. Taking advantage of self-polymerization of catechol-inspired natural tannic acid, PCT nanohybrid was prepared through adhering reactive poly-(tannic acid) (PTA) layer onto surfaces of carbon nanotubes via a simple dip-coating process. The high-functionality PCT induced the formation of the metal-ligand bonds through the ionic coordinates between the catechol groups in PCT and -COOH groups of TONFC skeleton with Fe(III) mediation that mimicked mussel byssus. Upon stretching, this tailored TONFC-Fe(III)-catechol coordination bonds served as sacrificial bonds that preferentially detach prior to the covalent network, which gave rise to efficient energy dissipation that the nanocomposites integrity was survived. As a result of these kind of synergistic interfacial interactions (sacrificial and covalent bonding), the optimal nanocomposite films processed high tensile strength (ca. 11.5 MPa), large elongation (ca. 79.3%), remarkable toughness (ca. 6.9 MJ m-3), and favorable water resistance as well as electrical conductivity. The proposed bioinspired strategy for designing plant protein-based materials enables control over their mechanical performance through the synergistic engineering of sacrificial bonds into the composite interface.

High frequency of labral pathology in dysplastic hips with a CE angle between 20-25

DEFF Research Database (Denmark)

Jakobsen, Stig Storgaard; Hartig-Andreasen, Charlotte; Mikkelsen, Lone Rømer

Background: Hip dysplasia becomes symptomatic due to labral pathology and secondary muscular pain. A CE angle dysplasia in PAO centres in Denmark. However, it is debated whether a CE angle between 20 and 25 is borderline. Purpose / Aim of Study: We aimed...... to investigate the degree of labral pathology in symptomatic patients with CE between 20 and 25 compared with patients with CE hips) with a mean age 34.1 years (range 14.5- 58.9 years) consecutively scheduled for PAO due to symptomatic DDH were enrolled...... in the study. Five patients were excluded from the study and four patients failed to show up at follow- up, hence 90 patients were evaluated. Indication for PAO were persisting hip pain, a center-edge angle of Wiberg 15, hip flexion

Hydrogen bond based smart polymer for highly selective and tunable capture of multiply phosphorylated peptides.

Science.gov (United States)

Qing, Guangyan; Lu, Qi; Li, Xiuling; Liu, Jing; Ye, Mingliang; Liang, Xinmiao; Sun, Taolei

2017-09-06

Multisite phosphorylation is an important and common mechanism for finely regulating protein functions and subsequent cellular responses. However, this study is largely restricted by the difficulty to capture low-abundance multiply phosphorylated peptides (MPPs) from complex biosamples owing to the limitation of enrichment materials and their interactions with phosphates. Here we show that smart polymer can serve as an ideal platform to resolve this challenge. Driven by specific but tunable hydrogen bonding interactions, the smart polymer displays differential complexation with MPPs, singly phosphorylated and non-modified peptides. Importantly, MPP binding can be modulated conveniently and precisely by solution conditions, resulting in highly controllable MPP adsorption on material surface. This facilitates excellent performance in MPP enrichment and separation from model proteins and real biosamples. High enrichment selectivity and coverage, extraordinary adsorption capacities and recovery towards MPPs, as well as high discovery rates of unique phosphorylation sites, suggest its great potential in phosphoproteomics studies.Capture of low-abundance multiply phosphorylated peptides (MPPs) is difficult due to limitation of enrichment materials and their interactions with phosphates. Here the authors show, a smart polymer driven by specific but tunable hydrogen bonding interactions can differentially complex with MPPs, singly phosphorylated and non-modified peptides.

Strength and Character of Halogen Bonds in Protein-Ligand Complexes

Czech Academy of Sciences Publication Activity Database

Riley, Kevin Eugene; Hobza, Pavel

2011-01-01

Roč. 11, č. 10 (2011), s. 4272-4278 ISSN 1528-7483 R&D Projects: GA MŠk LC512 Grant - others:Research and Development for Innovations of European Social Fund(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : halogen bond * protein-ligand complexes * calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.720, year: 2011

Role of the Disulfide Bond in Prion Protein Amyloid Formation: A Thermodynamic and Kinetic Analysis.

Science.gov (United States)

Honda, Ryo

2018-02-27

Prion diseases are associated with the structural conversion of prion protein (PrP) to a β-sheet-rich aggregate, PrP Sc . Previous studies have indicated that a reduction of the disulfide bond linking C179 and C214 of PrP yields an amyloidlike β-rich aggregate in vitro. To gain mechanistic insights into the reduction-induced aggregation, here I characterized how disulfide bond reduction modulates the protein folding/misfolding landscape of PrP, by examining 1) the equilibrium stabilities of the native (N) and aggregated states relative to the unfolded (U) state, 2) the transition barrier separating the U and aggregated states, and 3) the final structure of amyloidlike misfolded aggregates. Kinetic and thermodynamic experiments revealed that disulfide bond reduction decreases the equilibrium stabilities of both the N and aggregated states by ∼3 kcal/mol, without changing either the amyloidlike aggregate structure, at least at the secondary structural level, or the transition barrier of aggregation. Therefore, disulfide bond reduction modulates the protein folding/misfolding landscape by entropically stabilizing disordered states, including the U and transition state of aggregation. This also indicates that the equilibrium stability of the N state, but not the transition barrier of aggregation, is the dominant factor determining the reduction-induced aggregation of PrP. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.

Science.gov (United States)

Saito, Minoru; Okazaki, Isao

2009-12-01

The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field. (c) 2009 Wiley Periodicals, Inc.

Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress

Directory of Open Access Journals (Sweden)

Tyo Keith EJ

2012-03-01

Full Text Available Abstract Background The protein secretory pathway must process a wide assortment of native proteins for eukaryotic cells to function. As well, recombinant protein secretion is used extensively to produce many biologics and industrial enzymes. Therefore, secretory pathway dysfunction can be highly detrimental to the cell and can drastically inhibit product titers in biochemical production. Because the secretory pathway is a highly-integrated, multi-organelle system, dysfunction can happen at many levels and dissecting the root cause can be challenging. In this study, we apply a systems biology approach to analyze secretory pathway dysfunctions resulting from heterologous production of a small protein (insulin precursor or a larger protein (α-amylase. Results HAC1-dependent and independent dysfunctions and cellular responses were apparent across multiple datasets. In particular, processes involving (a degradation of protein/recycling amino acids, (b overall transcription/translation repression, and (c oxidative stress were broadly associated with secretory stress. Conclusions Apparent runaway oxidative stress due to radical production observed here and elsewhere can be explained by a futile cycle of disulfide formation and breaking that consumes reduced glutathione and produces reactive oxygen species. The futile cycle is dominating when protein folding rates are low relative to disulfide bond formation rates. While not strictly conclusive with the present data, this insight does provide a molecular interpretation to an, until now, largely empirical understanding of optimizing heterologous protein secretion. This molecular insight has direct implications on engineering a broad range of recombinant proteins for secretion and provides potential hypotheses for the root causes of several secretory-associated diseases.

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

2013-07-15

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

KAUST Repository

Li, Jianping

2013-06-05

Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

KAUST Repository

Li, Jianping; Pilla, Kala Bharath; Li, Qingfeng; Zhang, Zhengfeng; Su, Xuncheng; Huber, Thomas; Yang, Jun

2013-01-01

Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

Cement bond evaluation method in horizontal wells using segmented bond tool

Science.gov (United States)

Song, Ruolong; He, Li

2018-06-01

Most of the existing cement evaluation technologies suffer from tool eccentralization due to gravity in highly deviated wells and horizontal wells. This paper proposes a correction method to lessen the effects of tool eccentralization on evaluation results of cement bond using segmented bond tool, which has an omnidirectional sonic transmitter and eight segmented receivers evenly arranged around the tool 2 ft from the transmitter. Using 3-D finite difference parallel numerical simulation method, we investigate the logging responses of centred and eccentred segmented bond tool in a variety of bond conditions. From the numerical results, we find that the tool eccentricity and channel azimuth can be estimated from measured sector amplitude. The average of the sector amplitude when the tool is eccentred can be corrected to the one when the tool is centred. Then the corrected amplitude will be used to calculate the channel size. The proposed method is applied to both synthetic and field data. For synthetic data, it turns out that this method can estimate the tool eccentricity with small error and the bond map is improved after correction. For field data, the tool eccentricity has a good agreement with the measured well deviation angle. Though this method still suffers from the low accuracy of calculating channel azimuth, the credibility of corrected bond map is improved especially in horizontal wells. It gives us a choice to evaluate the bond condition for horizontal wells using existing logging tool. The numerical results in this paper can provide aids for understanding measurements of segmented tool in both vertical and horizontal wells.

Pressure evolution of the high-frequency sound velocity in liquid water

International Nuclear Information System (INIS)

Krisch, M.; Sette, F.; D'Astuto, M.; Lorenzen, M.; Mermet, A.; Monaco, G.; Verbeni, R.; Loubeyre, P.; Le Toullec, R.; Ruocco, G.; Cunsolo, A.

2002-01-01

The high-frequency sound velocity v ∞ of liquid water has been determined to densities of 1.37 g/cm 3 by inelastic x-ray scattering. In comparison to the hydrodynamic sound velocity v 0 , the increase of v ∞ with density is substantially less pronounced, indicating that, at high density, the hydrogen-bond network is decreasingly relevant to the physical properties of liquid water. Furthermore, we observe an anomaly in v ∞ at densities around 1.12 g/cm 3 , contrasting the smooth density evolution of v 0

Room temperature direct bonding of LiNbO3 crystal layers and its application to high-voltage optical sensing

International Nuclear Information System (INIS)

Tulli, D; Janner, D; Pruneri, V

2011-01-01

LiNbO 3 is a crystal widely used in photonics and acoustics, for example in electro-optic modulation, nonlinear optical frequency conversion, electric field sensing and surface acoustic wave filtering. It often needs to be combined with other materials and used in thin layers to achieve the adequate device performance. In this paper, we investigate direct bonding of LiNbO 3 crystals with other dielectric materials, such as Si and fused silica (SiO 2 ), and we show that specific surface chemical cleaning, together with Ar or O 2 plasma activation, can be used to increase the surface free energy and achieve effective bonding at room temperature. The resulting hybrid material bonding is very strong, making the dicing and grinding of LiNbO 3 layers as thin as 15 µm possible. To demonstrate the application potentials of the proposed bonding technique, we have fabricated and characterized a high-voltage field sensor with high sensitivity in a domain inverted and bonded LiNbO 3 waveguide substrate

Solid-state diffusion bonding of high-Cr ODS ferritic steel

Energy Technology Data Exchange (ETDEWEB)

Noh, Sanghoon, E-mail: sh-noh@iae.kyoto-u.ac.jp [Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto (Japan); Kasada, Ryuta; Kimura, Akihiko [Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto (Japan)

2011-05-15

Research highlights: > Oxide dispersion strengthened ferritic steel joined by solid-state diffusion bonding. > Free of precipitates and micro-voids at the bonding interface was existed. > Joints had the same tensile properties with anisotropy of the base material. > USE of joints was fully reserved in L-R bonding orientation. > Cracks did not propagate on the bonding interface at the Charpy impact test. - Abstract: Solid-state diffusion bonding (SSDB) was employed to join high-Cr oxide dispersion strengthened (ODS) ferritic steel (Fe-15Cr-2W-0.2Ti-0.35Y{sub 2}O{sub 3}) blocks under uniaxial hydrostatic pressure using a high-vacuum hot press, and the microstructure and mechanical properties of the joints were investigated. High-Cr ODS ferritic steels were successfully diffusion bonded at 1200 deg. C for 1 h, without precipitates and microvoids at the bonding interface or degradation in the base materials. Transmission electron microscopic observation revealed that the nano-oxide particles near the bonding interface were uniformly distributed in the matrix and that the chemical composition across the bonding interface was virtually constant. At room temperature, the joint had nearly the same tensile properties and exhibited anisotropic behavior similar to that of the base material. The tensile strength of the joint region at elevated temperatures is nearly the same as that of the base material, with necking behavior at several micrometers from the bonding interface. The total elongation of the joint region decreased slightly at 700 {sup o}C, with an exfoliation fracture surface at the bonding interface. Although a small ductile-brittle transition temperature shift was observed in the joints, the upper shelf energy was fully reserved in the case of joints with L-R bonding orientation, for which cracks did not propagate on the bonding interface. Therefore, it is concluded that SSDB can be potentially employed as a joining method for high-Cr ODS ferritic steel owing to

Development of bonded semiconductor device for high counting rate high efficiency photon detectors

International Nuclear Information System (INIS)

Kanno, Ikuo

2008-01-01

We are trying to decrease dose exposure in medical diagnosis by way of measuring the energy of X-rays. For this purpose, radiation detectors for X-ray energy measurement with high counting rate should be developed. Direct bonding of Si wafers was carried out to make a radiation detector, which had separated X-ray absorber and detector. The resistivity of bonding interface was estimated with the results of four-probe measurements and model calculations. Direct bonding of high resistivity p and n-Si wafers was also performed. The resistance of the pn bonded diode was 0.7 MΩ. The resistance should be increased in the future. (author)

Angle-dependent XPS study of the mechanisms of 'high-low temperature' activation of GaAs photocathode

International Nuclear Information System (INIS)

Du Xiaoqing; Chang Benkang

2005-01-01

The surface chemical compositions, atomic concentration percentage and layer thickness after 'high-temperature' single-step activation and 'high-low temperature' two-step activation were obtained using quantitative analysis of angle-dependent X-ray photoelectron spectroscopy (XPS). It was found that compared to single-step activation, the thickness of GaAs-O interface barrier had a remarkable decrease, the degree of As-O bond became much smaller and the Ga-O bond became dominating, and at the same time the thickness of (Cs, O) layer also had a deduction while the ratio of Cs to O had no change after two-step activation. The measured spectral response curves showed that a increase of 29% of sensitivity had been obtained after two-step activation. To explore the inherent mechanisms of influences of the evolution of GaAs(Cs, O) surface layers on photoemission, surface electric barrier models based on the experimental results were built. By calculation of electron escape probability it was found that the decrease of thickness of GaAs-O interface barrier and (Cs, O) layer is the main reasons, which explained why higher sensitivity is achieved after two-step activation than single-step activation

Inactivation of Enterobacter aerogenes in reconstituted skim milk by high- and low-frequency ultrasound.

Science.gov (United States)

Gao, Shengpu; Hemar, Yacine; Lewis, Gillian D; Ashokkumar, Muthupandian

2014-11-01

The inactivation of Enterobacter aerogenes in skim milk using low-frequency (20kHz) and high-frequency (850kHz) ultrasonication was investigated. It was found that low-frequency acoustic cavitation resulted in lethal damage to E. aerogenes. The bacteria were more sensitive to ultrasound in water than in reconstituted skim milk having different protein concentrations. However, high-frequency ultrasound was not able to inactivate E. aerogenes in milk even when powers as high as 50W for 60min were used. This study also showed that high-frequency ultrasonication had no influence on the viscosity and particle size of skim milk, whereas low-frequency ultrasonication resulted in the decrease in viscosity and particle size of milk. The decrease in particle size is believed to be due to the breakup of the fat globules, and possibly to the cleavage of the κ-casein present at the surface of the casein micelles. Whey proteins were also found to be slightly affected by low-frequency ultrasound, with the amounts of α-lactalbumin and β-lactoglobulin slightly decreasing. Copyright © 2013. Published by Elsevier B.V.

Pricing index-based catastrophe bonds: Part 2: Object-oriented design issues and sensitivity analysis

Science.gov (United States)

Unger, André J. A.

2010-02-01

This work is the second installment in a two-part series, and focuses on object-oriented programming methods to implement an augmented-state variable approach to aggregate the PCS index and introduce the Bermudan-style call feature into the proposed CAT bond model. The PCS index is aggregated quarterly using a discrete Asian running-sum formulation. The resulting aggregate PCS index augmented-state variable is used to specify the payoff (principle) on the CAT bond based on reinsurance layers. The purpose of the Bermudan-style call option is to allow the reinsurer to minimize their interest rate risk exposure on making fixed coupon payments under prevailing interest rates. A sensitivity analysis is performed to determine the impact of uncertainty in the frequency and magnitude of hurricanes on the price of the CAT bond. Results indicate that while the CAT bond is highly sensitive to the natural variability in the frequency of landfalling hurricanes between El Ninõ and non-El Ninõ years, it remains relatively insensitive to uncertainty in the magnitude of damages. In addition, results indicate that the maximum price of the CAT bond is insensitive to whether it is engineered to cover low frequency high magnitude events in a 'high' reinsurance layer relative to high frequency low magnitude events in a 'low' reinsurance layer. Also, while it is possible for the reinsurer to minimize their interest rate risk exposure on the fixed coupon payments, the impact of this risk on the price of the CAT bond appears small relative to the natural variability in the CAT bond price, and consequently catastrophic risk, due to uncertainty in the frequency and magnitude of landfalling hurricanes.

Building alternate protein structures using the elastic network model.

Science.gov (United States)

Yang, Qingyi; Sharp, Kim A

2009-02-15

We describe a method for efficiently generating ensembles of alternate, all-atom protein structures that (a) differ significantly from the starting structure, (b) have good stereochemistry (bonded geometry), and (c) have good steric properties (absence of atomic overlap). The method uses reconstruction from a series of backbone framework structures that are obtained from a modified elastic network model (ENM) by perturbation along low-frequency normal modes. To ensure good quality backbone frameworks, the single force parameter ENM is modified by introducing two more force parameters to characterize the interaction between the consecutive carbon alphas and those within the same secondary structure domain. The relative stiffness of the three parameters is parameterized to reproduce B-factors, while maintaining good bonded geometry. After parameterization, violations of experimental Calpha-Calpha distances and Calpha-Calpha-Calpha pseudo angles along the backbone are reduced to less than 1%. Simultaneously, the average B-factor correlation coefficient improves to R = 0.77. Two applications illustrate the potential of the approach. (1) 102,051 protein backbones spanning a conformational space of 15 A root mean square deviation were generated from 148 nonredundant proteins in the PDB database, and all-atom models with minimal bonded and nonbonded violations were produced from this ensemble of backbone structures using the SCWRL side chain building program. (2) Improved backbone templates for homology modeling. Fifteen query sequences were each modeled on two targets. For each of the 30 target frameworks, dozens of improved templates could be produced In all cases, improved full atom homology models resulted, of which 50% could be identified blind using the D-Fire statistical potential. (c) 2008 Wiley-Liss, Inc.

Studies of protein structure in solution and protein folding using synchrotron small-angle x-ray scattering

Energy Technology Data Exchange (ETDEWEB)

Chen, Lingling [Stanford Univ., CA (United States)

1996-04-01

Synchrotron small angle x-ray scattering (SAXS) has been applied to the structural study of several biological systems, including the nitrogenase complex, the heat shock cognate protein (hsc70), and lysozyme folding. The structural information revealed from the SAXS experiments is complementary to information obtained by other physical and biochemical methods, and adds to our knowledge and understanding of these systems.

Three-dimensionally porous graphene: A high-performance adsorbent for removal of albumin-bonded bilirubin.

Science.gov (United States)

Ma, Chun Fang; Gao, Qiang; Xia, Kai Sheng; Huang, Zhi Yuan; Han, Bo; Zhou, Cheng Gang

2017-01-01

The development of bilirubin adsorbents with high adsorption efficiencies towards albumin-bonded bilirubin is still a considerable challenge. In this work, a three-dimensionally porous graphene (3D-pGR) has been fabricated through a simple carbon dioxide (CO 2 ) activation of thermally exfoliated graphite oxide (EGO). Intriguingly, the resultant 3D-pGR material showed hierarchically micro-meso-macroporous structure, high specific surface area of up to 843m 2 g -1 , and large pore volume as high as 2.71cm 3 g -1 . Besides, the large planar π-configuration structure of 3D-pGR made it possible to compete effectively with albumin for bilirubin binding. Taking advantages of these fantastic characteristics, the 3D-pGR was demonstrated to be extraordinarily efficient for bilirubin removal from a bovine serum albumin (BSA)-rich solution. Under optimized conditions, the maximum adsorption capacity of 3D-pGR for BSA-bonded bilirubin was up to 126.1mgg -1 , which is not only significantly higher than the adsorption capacities of currently available adsorbents towards albumin-bonded bilirubin, but also superior to those of many reported adsorbents towards free bilirubin. In addition, the hemolysis assay of 3D-pGR indicated that this material had negligible hemolysis effect. Findings from this study may open up important new possibilities for removal of protein-bonded toxins. Copyright © 2016 Elsevier B.V. All rights reserved.

High Pressure Angle Gears: Comparison to Typical Gear Designs

Science.gov (United States)

Handschuh, Robert F.; Zabrajsek, Andrew J.

2010-01-01

A preliminary study has been completed to determine the feasibility of using high-pressure angle gears in aeronautic and space applications. Tests were conducted in the NASA Glenn Research Center (GRC) Spur Gear Test Facility at speeds up to 10,000 rpm and 73 N*m (648 in.*lb) for 3.18, 2.12, and 1.59 module gears (8, 12, and 16 diametral pitch gears), all designed to operate in the same test facility. The 3.18 module (8-diametral pitch), 28 tooth, 20deg pressure angle gears are the GRC baseline test specimen. Also, 2.12 module (12-diametral pitch), 42 tooth, 25deg pressure angle gears were tested. Finally 1.59 module (16-diametral pitch), 56 tooth, 35deg pressure angle gears were tested. The high-pressure angle gears were the most efficient when operated in the high-speed aerospace mode (10,000 rpm, lubricated with a synthetic turbine engine oil), and produced the lowest wear rates when tested with a perfluoroether-based grease. The grease tests were conducted at 150 rpm and 71 N*m (630 in.*lb).

Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory

Directory of Open Access Journals (Sweden)

Igor V. Uporov

2015-09-01

Full Text Available The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.

Silicate bonding properties: Investigation through thermal conductivity measurements

Energy Technology Data Exchange (ETDEWEB)

Lorenzini, M; Cesarini, E; Cagnoli, G; Campagna, E; Losurdo, G; Martelli, F; Piergiovanni, F; Vetrano, F [INFN, Istituto Nazionale di Fisica Nucleare, Sez. di Firenze, via G. Sansone 1, 50019 Sesto Fiorentino (Italy); Haughian, K; Hough, J; Martin, I; Reid, S; Rowan, S; Veggel, A A van, E-mail: lorenzini@fi.infn.i [SUPA, University of Glasgow, Department of Physics and Astronomy, Kelvin Building G12 8QQ Glasgow, Scotland (United Kingdom)

2010-05-01

A direct approach to reduce the thermal noise contribution to the sensitivity limit of a GW interferometric detector is the cryogenic cooling of the mirrors and mirrors suspensions. Future generations of detectors are foreseen to implement this solution. Silicon has been proposed as a candidate material, thanks to its very low intrinsic loss angle at low temperatures and due to its very high thermal conductivity, allowing the heat deposited in the mirrors by high power lasers to be efficiently extracted. To accomplish such a scheme, both mirror masses and suspension elements must be made of silicon, then bonded together forming a quasi-monolithic stage. Elements can be assembled using hydroxide-catalysis silicate bonding, as for silica monolithic joints. The effect of Si to Si bonding on suspension thermal conductance has therefore to be experimentally studied. A measurement of the effect of silicate bonding on thermal conductance carried out on 1 inch thick silicon bonded samples, from room temperature down to 77 K, is reported. In the explored temperature range, the silicate bonding does not seem to affect in a relevant way the sample conductance.

Directionality of Cation/Molecule Bonding in Lewis Bases Containing the Carbonyl Group.

Science.gov (United States)

Valadbeigi, Younes; Gal, Jean-François

2017-09-14

Relationship between the C═O-X + (X = H, Li, Na, K, Al, Cu) angle and covalent characteristic of the X + -M (M = CH 2 O, CH 3 CHO, acetone, imidazol-2-one (C 2 H 2 N 2 O), cytosine, γ-butyrolactone) was investigated, theoretically. The calculated electron densities ρ at the bond critical points revealed that the covalency of the M-X + interaction depended on the nature of the cation and varied as H + > Cu + > Al + > Li + > Na + > K + . The alkali cations tended to participate in electrostatic interactions and aligned with the direction of the molecule dipole or local dipole of C═O group to form linear C═O-X geometries. Because of overlapping with lone-pair electrons of the sp 2 carbonyl oxygen, the H + and Cu + formed a bent C═O-X angle. Al + displayed an intermediate behavior; the C═O-Al angle was 180° in [CH 2 O/Al] + (mainly electrostatic), but when the angle was bent (146°) under the effect of local dipole of an adjacent imine group in cytosine, the covalency of the CO-Al + interaction increased. The C═O-X angles in M/X + adduct ions were scanned in different O-X bond lengths. It was found that the most favorable C═O-X angle depended on the O-X bond length. This dependency was attributed to variation of covalent and electrostatic contributions with O-X distance. In addition, the structures of [CH 2 S/X] + and [CH 2 Se/X] + were studied, and only bent C═S-X and C═Se-X angles were obtained for all cations, although the dipole vectors of CH 2 S and CH 2 Se coincide with the C═S and C═Se bonds. The bending of the C═S-X and C═Se-X angles was attributed to the covalent characteristic of S-X and Se-X interactions due to high polarizability of S and Se atoms.

Multi-angle compound imaging

DEFF Research Database (Denmark)

Jespersen, Søren Kragh; Wilhjelm, Jens Erik; Sillesen, Henrik

1998-01-01

This paper reports on a scanning technique, denoted multi-angle compound imaging (MACI), using spatial compounding. The MACI method also contains elements of frequency compounding, as the transmit frequency is lowered for the highest beam angles in order to reduce grating lobes. Compared to conve......This paper reports on a scanning technique, denoted multi-angle compound imaging (MACI), using spatial compounding. The MACI method also contains elements of frequency compounding, as the transmit frequency is lowered for the highest beam angles in order to reduce grating lobes. Compared...... to conventional B-mode imaging MACI offers better defined tissue boundaries and lower variance of the speckle pattern, resulting in an image with reduced random variations. Design and implementation of a compound imaging system is described, images of rubber tubes and porcine aorta are shown and effects...... on visualization are discussed. The speckle reduction is analyzed numerically and the results are found to be in excellent agreement with existing theory. An investigation of detectability of low-contrast lesions shows significant improvements compared to conventional imaging. Finally, possibilities for improving...

On the involvement of single-bond rotation in the primary photochemistry of photoactive yellow protein

NARCIS (Netherlands)

Stahl, A.D.; Hospes, M.; Singhal, K.; van Stokkum, I.; van Grondelle, R.; Groot, M.L.; Hellingwerf, K.J.

2011-01-01

Prior experimental observations, as well as theoretical considerations, have led to the proposal that C4-C7 single-bond rotation may play an important role in the primary photochemistry of photoactive yellow protein (PYP). We therefore synthesized an analog of this protein's 4-hydroxy-cinnamic acid

Anomalous H/D isotope effect on 35Cl NQR frequencies in piperidinium p-chlorobenzoate

International Nuclear Information System (INIS)

Nakano, Ryo; Honda, Hisashi; Kimura, Taiki; Nakata, Eiichi; Takamizawa, Satoshi; Noro, Sumiko; Ishimaru, Shin'ichi

2008-01-01

Anomalous isotope effects were detected in the 35 Cl nuclear quadrupole resonance (NQR) frequency of piperidinium p-chlrobenzoate (C 5 H 10 NH. ClC 6 H 4 COOH) by deuteration of hydrogen atoms. The atoms were determined to form two kinds of N-H...O type H-bonds in the crystal structure. Large frequency shifts of the 35 Cl resonance lines reaching 288 kHz at 77 K and 278 kHz at room temperature were caused upon deuteration, in spite of the fact that the Cl atoms in the molecule do not form hydrogen bonds in the crystal. Results of single crystal X-ray diffraction measurements and density-functional-theorem calculations suggest that a dihedral-angle change of 1.8 o between benzene and the piperidine ring contributes to 35 Cl NQR anomalous frequency shifts.

High-temperature, high-pressure bonding of nested tubular metallic components

International Nuclear Information System (INIS)

Quinby, T.C.

1980-01-01

This invention is a tool for effecting high-temperature, high compression bonding between the confronting faces of nested, tubular, metallic components. In a typical application, the tool is used to produce tubular target assemblies for irradiation in nuclear reactors or particle accelerators, the target assembly comprising a uranium foil and an aluminum-alloy substrate. The tool preferably is composed throughout of graphite. It comprises a tubular restraining member in which a mechanically expandable tubular core is mounted to form an annulus with the member. The components to be bonded are mounted in nested relation in the annulus. The expandable core is formed of individually movable, axially elongated segments whose outer faces cooperatively define a cylindrical pressing surface and whose inner faces cooperatively define two opposed, inwardly tapered, axial bores. Tapered rams extend respectively into the bores. The loaded tool is mounted in a conventional hot-press provided with evacuation means, heaters for maintaining its interior at bonding temperature, and hydraulic cylinders for maintaining a selected inwardly directed pressure on the tapered rams. With the hotpress evacuated and the loaded tool at the desired temperature, the cylinders are actuated to apply the selected pressure to the rams. The rams in turn expand the segmented core to maintain the nested components in compression against the restraining member. These conditions are maintained until the confronting faces of the nested components are joined in a continuous, uniform bond characterized by high thermal conductivity

High-temperature, high-pressure bonding of nested tubular metallic components

Science.gov (United States)

Quinby, T.C.

A tool is described for effecting high-temperature, high-compression bonding between the confronting faces of nested, tubular, metallic components. In a typical application, the tool is used to produce tubular target assemblies for irradiation in nuclear reactors or particle accelerators. The target assembly comprising a uranum foil and an aluninum-alloy substrate. The tool is composed of graphite. It comprises a tubular restraining member in which a mechanically expandable tubular core is mounted to form an annulus. The components to be bonded are mounted in nested relation in the annulus. The expandable core is formed of individually movable, axially elongated segments whose outer faces cooperatively define a cylindrical pressing surface and whose inner faces cooperatively define two opposed, inwardly tapered, axial bores. Tapered rams extend into the bores. The loaded tool is mounted in a conventional hot-press provided with evacuation means, heaters for maintaining its interior at bonding temperature, and hydraulic cylinders for maintaining a selected inwardly directed pressure on the tapered rams. With the hot-press evacuated and the loaded tool at the desired temperature, the cylinders are actuated to apply the selected pressure to the rams. The rams in turn expand the segmented core to maintain the nested components in compression against the restraining member. These conditions are maintained until the confronting faces of the nested components are joined in a continuous, uniform bond characterized by high thermal conductivity.

A Solvatochromic Model Calibrates Nitriles’ Vibrational Frequencies to Electrostatic Fields

Science.gov (United States)

Bagchi, Sayan; Fried, Stephen D.; Boxer, Steven G.

2012-01-01

Electrostatic interactions provide a primary connection between a protein’s three-dimensional structure and its function. Infrared (IR) probes are useful because vibrational frequencies of certain chemical groups, such as nitriles, are linearly sensitive to local electrostatic field, and can serve as a molecular electric field meter. IR spectroscopy has been used to study electrostatic changes or fluctuations in proteins, but measured peak frequencies have not been previously mapped to total electric fields, because of the absence of a field-frequency calibration and the complication of local chemical effects such as H-bonds. We report a solvatochromic model that provides a means to assess the H-bonding status of aromatic nitrile vibrational probes, and calibrates their vibrational frequencies to electrostatic field. The analysis involves correlations between the nitrile’s IR frequency and its 13C chemical shift, whose observation is facilitated by a robust method for introducing isotopes into aromatic nitriles. The method is tested on the model protein Ribonuclease S (RNase S) containing a labeled p-CN-Phe near the active site. Comparison of the measurements in RNase S against solvatochromic data gives an estimate of the average total electrostatic field at this location. The value determined agrees quantitatively with MD simulations, suggesting broader potential for the use of IR probes in the study of protein electrostatics. PMID:22694663

Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry

OpenAIRE

Wongkongkathep, Piriya; Li, Huilin; Zhang, Xing; Loo, Rachel R. Ogorzalek; Julian, Ryan R.; Loo, Joseph A.

2015-01-01

The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in comb...

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Shen Yang; Delaglio, Frank [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Cornilescu, Gabriel [National Magnetic Resonance Facility (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

2009-08-15

NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between {sup 13}C, {sup 15}N and {sup 1}H chemical shifts and backbone torsion angles {phi} and {psi} (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted {phi} and {psi} angles, equals {+-}13{sup o}. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

Methods and system for controlled laser-driven explosive bonding

Science.gov (United States)

Rubenchik, Alexander M.; Farmer, Joseph C.; Hackel, Lloyd; Rankin, Jon

2015-11-19

A technique for bonding two dissimilar materials includes positioning a second material over a first material at an oblique angle and applying a tamping layer over the second martial. A laser beam is directed at the second material that generates a plasma at the location of impact on the second material. The plasma generates pressure that accelerates a portion of the second material to a very high velocity and towards the first material. The second material impacts the first material causing bonding of the two materials.

Quantitative Surface Chirality Detection with Sum Frequency Generation Vibrational Spectroscopy: Twin Polarization Angle Approach

International Nuclear Information System (INIS)

Wei, Feng; Xu, Yanyan; Guo, Yuan; Liu, Shi-lin; Wang, Hongfei

2009-01-01

Here we report a novel twin polarization angle (TPA) approach in the quantitative chirality detection with the surface sum-frequency generation vibrational spectroscopy (SFG-VS). Generally, the achiral contribution dominates the surface SFG-VS signal, and the pure chiral signal is usually two or three orders of magnitude smaller. Therefore, it has been difficult to make quantitative detection and analysis of the chiral contributions to the surface SFG-VS signal. In the TPA method, by varying together the polarization angles of the incoming visible light and the sum frequency signal at fixed s or p polarization of the incoming infrared beam, the polarization dependent SFG signal can give not only direct signature of the chiral contribution in the total SFG-VS signal, but also the accurate measurement of the chiral and achiral components in the surface SFG signal. The general description of the TPA method is presented and the experiment test of the TPA approach is also presented for the SFG-VS from the S- and R-limonene chiral liquid surfaces. The most accurate degree of chiral excess values thus obtained for the 2878 cm -1 spectral peak of the S- and R-limonene liquid surfaces are (23.7±0.4)% and (25.4±1.3)%, respectively.

Hydrogen bond dynamics and water structure in glucose-water solutions by depolarized Rayleigh scattering and low-frequency Raman spectroscopy

Science.gov (United States)

Paolantoni, Marco; Sassi, Paola; Morresi, Assunta; Santini, Sergio

2007-07-01

The effect of glucose on the relaxation process of water at picosecond time scales has been investigated by depolarized Rayleigh scattering (DRS) experiments. The process is assigned to the fast hydrogen bonding dynamics of the water network. In DRS spectra this contribution can be safely separated from the slower relaxation process due to the sugar. The detected relaxation time is studied at different glucose concentrations and modeled considering bulk and hydrating water contributions. As a result, it is found that in diluted conditions the hydrogen bond lifetime of proximal water molecules becomes about three times slower than that of the bulk. The effect of the sugar on the hydrogen bond water structure is investigated by analyzing the low-frequency Raman (LFR) spectrum sensitive to intermolecular modes. The addition of glucose strongly reduces the intensity of the band at 170cm-1 assigned to a collective stretching mode of water molecules arranged in cooperative tetrahedral domains. These findings indicate that proximal water molecules partially lose the tetrahedral ordering typical of the bulk leading to the formation of high density environments around the sugar. Thus the glucose imposes a new local order among water molecules localized in its hydration shell in which the hydrogen bond breaking dynamics is sensitively retarded. This work provides new experimental evidences that support recent molecular dynamics simulation and thermodynamics results.

DC biased low-frequency insulating constriction dielectrophoresis for protein biomolecules concentration.

Science.gov (United States)

Zhang, Peng; Liu, Yuxin

2017-09-01

Sample enrichment or molecules concentration is considered an essential step in sample processing of miniaturized devices aimed at biosensing and bioanalysis. Among all the means involved to achieve this aim, dielectrophoresis (DEP) is increasingly employed in molecules manipulation and concentration because it is non-destructive and high efficiency. This paper presents a methodology to achieve protein concentration utilizing the combination effects of electrokinetics and low frequency insulating dielectrophoresis (iDEP) generated within a microfluidic device, in which a submicron constricted channel was fabricated using DNA molecular combing and replica molding. This fabrication technique avoids using e-beam lithography or other complicated nanochannel fabrication methods, and provides an easy and low cost approach with the flexibility of controlling channel dimensions to create highly constricted channels embedded in a microfluidic device. With theoretical analysis and experiments, we demonstrated that fluorescein isothiocyanate conjugated bovine serum albumin (FITC-BSA) protein molecules can be significantly concentrated to form an arc-shaped band near the constricted channel under the effects of a negative dielectrophoretic force and DC electrokinetic forces within a short period of time. It was also observed that the amplitudes of the applied DC and AC electric fields, the AC frequencies as well as the suspending medium conductivities had strong effects on the concentration responses of the FITC-BSA molecules, including the concentrated area and position, intensities of the focused molecules, and concentration speed. Our method provides a simple and flexible approach for quickly concentrating protein molecules by controlling the applied electric field parameters. The iDEP device reported in this paper can be used as a stand-alone sensor or worked as a pre-concentration module integrated with biosensors for protein biomarker detection. Furthermore, low

Pressure-dependent {sup 13}C chemical shifts in proteins: origins and applications

Energy Technology Data Exchange (ETDEWEB)

Wilton, David J. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom); Kitahara, Ryo [Ritsumeikan University, College of Pharmaceutical Sciences (Japan); Akasaka, Kazuyuki [Kinki University, Department of Biotechnological Science, School of Biology-Oriented Science and Technology (Japan); Williamson, Mike P. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom)], E-mail: m.williamson@sheffield.ac.uk

2009-05-15

Pressure-dependent {sup 13}C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH{sub 3}, CH{sub 2} and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the {gamma}-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual {sup 13}C{alpha} shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas {sup 13}C{beta} shifts retain significant dependence on local compression, making them less useful as structural restraints.

Modulation of Thiol-Disulfide Oxidoreductases for Increased Production of Disulfide-Bond-Containing Proteins in Bacillus subtilis

NARCIS (Netherlands)

Kouwen, Thijs R. H. M.; Dubois, Jean-Yves F.; Freudl, Roland; Quax, Wim J.; van Dijl, Jan Maarten

2008-01-01

Disulfide bonds are important for the correct folding, structural integrity, and activity of many biotechnologically relevant proteins. For synthesis and subsequent secretion of these proteins in bacteria, such as the well-known "cell factory" Bacillus subtilis, it is often the correct formation of

Recoupling and decoupling of nuclear spin interactions at high MAS frequencies: numerical design of CNnν symmetry-based RF pulse schemes

International Nuclear Information System (INIS)

Herbst, Christian; Herbst, Jirada; Kirschstein, Anika; Leppert, Joerg; Ohlenschlaeger, Oliver; Goerlach, Matthias; Ramachandran, Ramadurai

2009-01-01

The CN n ν class of RF pulse schemes, commonly employed for recoupling and decoupling of nuclear spin interactions in magic angle spinning solid state NMR studies of biological systems, involves the application of a basic 'C' element corresponding to an RF cycle with unity propagator. In this study, the design of CN n ν symmetry-based RF pulse sequences for achieving 13 C- 13 C double-quantum dipolar recoupling and through bond scalar coupling mediated 13 C- 13 C chemical shift correlation has been examined at high MAS frequencies employing broadband, constant-amplitude, phase-modulated basic 'C' elements. The basic elements were implemented as a sandwich of a small number of short pulses of equal duration with each pulse characterised by an RF phase value. The phase-modulation profile of the 'C' element was optimised numerically so as to generate efficient RF pulse sequences. The performances of the sequences were evaluated via numerical simulations and experimental measurements and are presented here

Numerical design of RNnν symmetry-based RF pulse schemes for recoupling and decoupling of nuclear spin interactions at high MAS frequencies

International Nuclear Information System (INIS)

Herbst, Christian; Herbst, Jirada; Leppert, Joerg; Ohlenschlaeger, Oliver; Goerlach, Matthias; Ramachandran, Ramadurai

2009-01-01

An approach for the efficient implementation of RN n ν symmetry-based pulse schemes that are often employed for recoupling and decoupling of nuclear spin interactions in biological solid state NMR investigations is demonstrated at high magic-angle spinning frequencies. RF pulse sequences belonging to the RN n ν symmetry involve the repeated application of the pulse sandwich {R φ R -φ }, corresponding to a propagator U RF = exp(-i4φI z ), where φ = πν/N and R is typically a pulse that rotates the nuclear spins through 180 o about the x-axis. In this study, broadband, phase-modulated 180 o pulses of constant amplitude were employed as the initial 'R' element and the phase-modulation profile of this 'R' element was numerically optimised for generating RN n ν symmetry-based pulse schemes with satisfactory magnetisation transfer characteristics. At representative MAS frequencies, RF pulse sequences were implemented for achieving 13 C- 13 C double-quantum dipolar recoupling and through bond scalar coupling mediated chemical shift correlation and evaluated via numerical simulations and experimental measurements. The results from these investigations are presented here

Modeling on-column reduction of trisulfide bonds in monoclonal antibodies during protein A chromatography.

Science.gov (United States)

Ghose, Sanchayita; Rajshekaran, Rupshika; Labanca, Marisa; Conley, Lynn

2017-01-06

Trisulfides can be a common post-translational modification in many recombinant monoclonal antibodies. These are a source of product heterogeneity that add to the complexity of product characterization and hence, need to be reduced for consistent product quality. Trisulfide bonds can be converted to the regular disulfide bonds by incorporating a novel cysteine wash step during Protein A affinity chromatography. An empirical model is developed for this on-column reduction reaction to compare the reaction rates as a function of typical operating parameters such as temperature, cysteine concentration, reaction time and starting level of trisulfides. The model presented here is anticipated to assist in the development of optimal wash conditions for the Protein A step to effectively reduce trisulfides to desired levels. Copyright © 2016 Elsevier B.V. All rights reserved.

Deuteriation of an asymmetric short hydrogen bond. X-ray crystal structure of KF.(CH2CO2D)2

International Nuclear Information System (INIS)

Emsley, J.; Jones, D.J.; Kuroda, R.

1981-01-01

Deuteriation of the strong hydrogen bonds of KF.(CH 2 CO 2 H) 2 shows no isotope effect on the bond lengths. The only significant change is in the bond angle at the fluoride ion which widens to 128.5 from 116 0 . The i.r. spectrum shows very little change. Since the O-H ... F - hydrogen bonds are highly asymmetric, these observations challenge previous predictions about the effects of deuteriation on such bonds. (author)

Analysis of a flip-chip bonded tunable high-temperature superconducting coplanar waveguide resonator using the conformal mapping technique

CERN Document Server

Misra, M; Murakami, H; Tonouchi, M

2003-01-01

We have studied the tuning properties of a high-temperature superconducting (HTS) half-wavelength coplanar waveguide (CPW) resonator operating at 5 GHz. The tuning schemes are based on flip-chip bonding of an electrically tunable ferroelectric (FE) thin film and a mechanically movable low-loss single crystal on top of the resonator. Using the conformal mapping method, closed-form analytical expressions have been derived for a flip-chip bonded conductor-backed and top-shielded CPW transmission line. The obtained expressions are used to analyse the volume effect of the FE thin film and the gap between the flip-chip and the CPW resonator on the tuning properties of the device. It has been found that large frequency modulation of the resonator produces impedance mismatch, which can considerably enhance the insertion loss of high-performance HTS microwave devices. Analysis also suggests that, for electrically tunable devices, flip-chip bonded FE thin films on HTS CPW devices provide a relatively higher performance...

Low frequency phase signal measurement with high frequency squeezing

OpenAIRE

Zhai, Zehui; Gao, Jiangrui

2011-01-01

We calculate the utility of high-frequency squeezed-state enhanced two-frequency interferometry for low-frequency phase measurement. To use the high-frequency sidebands of the squeezed light, a two-frequency intense laser is used in the interferometry instead of a single-frequency laser as usual. We find that the readout signal can be contaminated by the high-frequency phase vibration, but this is easy to check and avoid. A proof-of-principle experiment is in the reach of modern quantum optic...

Effect of incidence angle on the wake turbulence of a turbine rotor blade

International Nuclear Information System (INIS)

Chang, Sung Il; Lee, Sang Woo

2005-01-01

This paper describes effects of incidence angle on the wake turbulent flow of a high-turning turbine rotor blade. For three incidence angles of -5, 0 and 5 degrees, energy spectra as well as profiles of mean velocity magnitude and turbulence intensity at mid-span are reported in the wake. Vortex shedding frequencies are obtained from the energy spectra. The result shows that as the incidence angle changes from -5 to 5 degrees, the suction-side wake tends to be widened and the deviation angle is increased. Strouhal numbers based on the shedding frequencies have a nearly constant value, regardless of the tested incidence angles

Detection of small conformational changes of proteins by small-angle scattering

International Nuclear Information System (INIS)

Durchschlag, H.; Purr, G.; Zipper, P.; Wilfing, R.

1991-01-01

In the past the technique of small-angle scattering has been a powerful tool for studying conformational changes of protein which occur, for example, upon binding with ligands. Results obtained by different authors from X-ray and neutron experiments on a variety of proteins and under various conditions have been compiled. This offers the possibility of comparing the extent of changes in the molecular parameters investigated (e.g. change of the radius of gyration). Problems encountered with the detection of small changes are discussed. As an example, conformational changes of the enzyme citrate synthase upon substrate binding (oxaloacetate) are presented. X-ray crystallography had already found distinct changes between open and closed forms of the enzyme. Small-angle X-ray scattering studies registered slight changes of some parameters in solution. These changes could be paralleled with the results of other solution techniques (UV absorption, fluorescence and circular dichroism spectroscopy, analytical ultracentrifugation). The results found for citrate synthase are also compared with previous findings for malate synthase, an enzyme of similar enzymatic function. Above all, this study shows that care has to be taken when studying small conformational changes. It is absolutely necessary to use different methods and conditions and to study the problem from different points of view to avoid pitfalls. (orig.)

In-situ identification of marine organisms using high frequency, wideband ultrasound

DEFF Research Database (Denmark)

Pham, An Hoai

methods. Conventional acoustical methods use frequencies in the range of 10 to 500 kHz and give reasonable estimations of size distribution, if the species is known, but can only significantly support the determination of the actual species, if there are only a few known species available. It is expected...... that higher frequencies and broader bandwidths than used until now will give more information useful for fish species identification. The objective of this Ph.D. study has been to develop a method to investigate the possibility of in-situ identification of fish with high-frequency, wideband ultrasound...... and the fish bodies. The frequencies are 2, 3.5, and 6 MHz. The angles are -30°, -15°, 0°, 15°, and 30°. The results show that even though there are variations, a scan of the ultrasound backscatter along a fish of a specific species contains patterns that are characteristic for that species. This is true...

Structural analysis of protein complexes with sodium alkyl sulfates by small-angle scattering and polyacrylamide gel electrophoresis.

Science.gov (United States)

Ospinal-Jiménez, Mónica; Pozzo, Danilo C

2011-02-01

Small-angle X-ray (SAXS) and neutron (SANS) scattering is used to probe the structure of protein-surfactant complexes in solution and to correlate this information with their performance in gel electrophoresis. Proteins with sizes between 6.5 to 116 kDa are denatured with sodium alkyl sulfates (SC(x)S) of variable tail lengths. Several combinations of proteins and surfactants are analyzed to measure micelle radii, the distance between micelles, the extension of the complex, the radius of gyration, and the electrophoretic mobility. The structural characterization shows that most protein-surfactant complexes can be accurately described as pearl-necklace structures with spherical micelles. However, protein complexes with short surfactants (SC(8)S) bind with micelles that deviate significantly from spherical shape. Sodium decyl (SC(10)S) and dodecyl (SC(12)S, more commonly abbreviated as SDS) sulfates result in the best protein separations in standard gel electrophoresis. Particularly, SC(10)S shows higher resolutions for complexes of low molecular weight. The systematic characterization of alkyl sulfate surfactants demonstrates that changes in the chain architecture can significantly affect electrophoretic migration so that protein-surfactant structures could be optimized for high resolution protein separations.

Small angle scattering study of the structure and organization of RNA and protein in Brome Mosaic Virus (BMV)

Science.gov (United States)

Das, Narayan C.; Warren, Garfield T.; Cheng, Si; Kao, C. Cheng; Ni, Peng; Dragnea, Bogdan; Sokol, Paul E.

2012-02-01

Brome mosaic virus (BMV) is a small icosahedral of the alpha virus-like superfamily of RNA with a segmented positive-strand RNA genome and a mean diameter ˜ 268å that offers high levels of RNA synthesis and virus production in plants. BMV also tightly regulates the packaging of its four RNAs (RNA1 through RNA4) into three separate particles; RNA1 and RNA2 are encapsidated separately while one copy each of RNA3 and RNA4 are normally packaged together. Small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) were applied to study the size, shape and protein-RNA organization of BMV. D2O/H2O mixture was used to enhance contrast in SANS measurement. The radial distribution of BMV from the Fourier transform of scattering spectrum gives a clear indication of RNA packing, and distribution and their structure in the BMV. The result reveals that the virus is about 266 å in diameter and is composed of RNA inside the virion coated with a protein shell.

Early diagnosis and research of high myopia with primary open angle glaucoma

Directory of Open Access Journals (Sweden)

Yan Guo

2014-04-01

Full Text Available People with high myopia are high risk populations to have primary open angle glaucoma. Clinically, we found that patients with primary open angle glaucoma and high myopia is closely related. So to understand the clinical features of high myopia with primary open angle glaucoma and the importance of early diagnosis, to avoiding missed diagnosis or lower misdiagnosed rate, can help to improve the vigilance and level of early diagnosis of the clinicians. In this paper, high myopia with clinical features of primary open angle glaucoma, and the research progress on the main points of early diagnosis were reviewed.

Method and device for secure, high-density tritium bonded with carbon

Science.gov (United States)

Wertsching, Alan Kevin; Trantor, Troy Joseph; Ebner, Matthias Anthony; Norby, Brad Curtis

2016-04-05

A method and device for producing secure, high-density tritium bonded with carbon. A substrate comprising carbon is provided. A precursor is intercalated between carbon in the substrate. The precursor intercalated in the substrate is irradiated until at least a portion of the precursor, preferably a majority of the precursor, is transmutated into tritium and bonds with carbon of the substrate forming bonded tritium. The resulting bonded tritium, tritium bonded with carbon, produces electrons via beta decay. The substrate is preferably a substrate from the list of substrates consisting of highly-ordered pyrolytic graphite, carbon fibers, carbon nanotunes, buckministerfullerenes, and combinations thereof. The precursor is preferably boron-10, more preferably lithium-6. Preferably, thermal neutrons are used to irradiate the precursor. The resulting bonded tritium is preferably used to generate electricity either directly or indirectly.

A novel bonding method for fabrication of PET planar nanofluidic chip with low dimension loss and high bonding strength

International Nuclear Information System (INIS)

Yin, Zhifu; Zou, Helin; Sun, Lei; Xu, Shenbo; Qi, Liping

2015-01-01

Plastic planar nanofluidic chips are becoming increasingly important for biological and chemical applications. However, the majority of the present bonding methods for planar nanofluidic chips suffer from high dimension loss and low bonding strength. In this work, a novel thermal bonding technique based on O 2 plasma and ethanol treatment was proposed. With the assistance of O 2 plasma and ethanol, the PET (polyethylene terephthalate) planar nanofluidic chip can be bonded at a low bonding temperature of 50 °C. To increase the bonding rate and bonding strength, the O 2 plasma parameters and thermal bonding parameters were optimized during the bonding process. The tensile test indicates that the bonding strength of the PET planar nanofluidic chip can reach 0.954 MPa, while the auto-fluorescence test demonstrates that there is no leakage or blockage in any of the bonded micro- or nanochannels. (paper)

Thermally robust and biomolecule-friendly room-temperature bonding for the fabrication of elastomer-plastic hybrid microdevices.

Science.gov (United States)

Nguyen, T P O; Tran, B M; Lee, N Y

2016-08-16

Here, we introduce a simple and fast method for bonding a poly(dimethylsiloxane) (PDMS) silicone elastomer to different plastics. In this technique, surface modification and subsequent bonding processes are performed at room temperature. Furthermore, only one chemical is needed, and no surface oxidation step is necessary prior to bonding. This bonding method is particularly suitable for encapsulating biomolecules that are sensitive to external stimuli, such as heat or plasma treatment, and for embedding fracturable materials prior to the bonding step. Microchannel-fabricated PDMS was first oxidized by plasma treatment and reacted with aminosilane by forming strong siloxane bonds (Si-O-Si) at room temperature. Without the surface oxidation of the amine-terminated PDMS and plastic, the two heterogeneous substrates were brought into intimate physical contact and left at room temperature. Subsequently, aminolysis occurred, leading to the generation of a permanent seal via the formation of robust urethane bonds after only 5 min of assembling. Using this method, large-area (10 × 10 cm) bonding was successfully realized. The surface was characterized by contact angle measurements and X-ray photoelectron spectroscopy (XPS) analyses, and the bonding strength was analyzed by performing peel, delamination, leak, and burst tests. The bond strength of the PDMS-polycarbonate (PC) assembly was approximately 409 ± 6.6 kPa, and the assembly withstood the injection of a tremendous amount of liquid with the per-minute injection volume exceeding 2000 times its total internal volume. The thermal stability of the bonded microdevice was confirmed by performing a chamber-type multiplex polymerase chain reaction (PCR) of two major foodborne pathogens - Escherichia coli O157:H7 and Salmonella typhimurium - and assessing the possibility for on-site direct detection of PCR amplicons. This bonding method demonstrated high potential for the stable construction of closed microfluidic systems

Real-Time Price Discovery in Global Stock, Bond and Foreign Exchange Markets

DEFF Research Database (Denmark)

Andersen, Torben G.; Bollerslev, Tim; Diebold, Francis X.

Using a unique high-frequency futures dataset, we characterize the response of U.S., German and British stock, bond and foreign exchange markets to real-time U.S. macroeconomic news. We find that news produces conditional mean jumps; hence high-frequency stock, bond and exchange rate dynamics...... are linked to fundamentals. Equity markets, moreover, react differently to news depending on the stage of the business cycle, which explains the low correlation between stock and bond returns when averaged over the cycle. Hence our results qualify earlier work suggesting that bond markets react most strongly...... to macroeconomic news; in particular, when conditioning on the state of the economy, the equity and foreign exchange markets appear equally responsive. Finally, we also document important contemporaneous links across all markets and countries, even after controlling for the effects of macroeconomic news....

Different redox sensitivity of endoplasmic reticulum associated degradation clients suggests a novel role for disulphide bonds in secretory proteins.

Science.gov (United States)

Medraño-Fernandez, Iria; Fagioli, Claudio; Mezghrani, Alexandre; Otsu, Mieko; Sitia, Roberto

2014-04-01

To maintain proteostasis in the endoplasmic reticulum (ER), terminally misfolded secretory proteins must be recognized, partially unfolded, and dislocated to the cytosol for proteasomal destruction, in a complex process called ER-associated degradation (ERAD). Dislocation implies reduction of inter-chain disulphide bonds. When in its reduced form, protein disulphide isomerase (PDI) can act not only as a reductase but also as an unfoldase, preparing substrates for dislocation. PDI oxidation by Ero1 favours substrate release and transport across the ER membrane. Here we addressed the redox dependency of ERAD and found that DTT stimulates the dislocation of proteins with DTT-resistant disulphide bonds (i.e., orphan Ig-μ chains) but stabilizes a ribophorin mutant (Ri332) devoid of them. DTT promotes the association of Ri332, but not of Ig-µ, with PDI. This discrepancy may suggest that disulphide bonds in cargo proteins can be utilized to oxidize PDI, hence facilitating substrate detachment and degradation also in the absence of Ero1. Accordingly, Ero1 silencing retards Ri332 degradation, but has little if any effect on Ig-µ. Thus, some disulphides can increase the stability and simultaneously favour quality control of secretory proteins.

High-frequency, high-intensity photoionization

Science.gov (United States)

Reiss, H. R.

1996-02-01

Two analytical methods for computing ionization by high-frequency fields are compared. Predicted ionization rates compare well, but energy predictions for the onset of ionization differ radically. The difference is shown to arise from the use of a transformation in one of the methods that alters the zero from which energy is measured. This alteration leads to an apparent energy threshold for ionization that can, especially in the stabilization regime, differ strongly from the laboratory measurement. It is concluded that channel closings in intense-field ionization can occur at high as well as low frequencies. It is also found that the stabilization phenomenon at high frequencies, very prominent for hydrogen, is absent in a short-range potential.

Anomalous H/D isotope effect on {sup 35}Cl NQR frequencies in piperidinium p-chlorobenzoate

Energy Technology Data Exchange (ETDEWEB)

Nakano, Ryo; Honda, Hisashi, E-mail: hhonda@yokohama-cu.ac.jp [Yokohama City University, Graduate School of Integrated Science (Japan); Kimura, Taiki [Yokohama City University, Faculty of Science (Japan); Nakata, Eiichi; Takamizawa, Satoshi; Noro, Sumiko [Yokohama City University, Graduate School of Integrated Science (Japan); Ishimaru, Shin' ichi [Tokyo Denki University, Department of Green and Sustainable Chemistry (Japan)

2008-01-15

Anomalous isotope effects were detected in the {sup 35}Cl nuclear quadrupole resonance (NQR) frequency of piperidinium p-chlrobenzoate (C{sub 5}H{sub 10}NH. ClC{sub 6}H{sub 4}COOH) by deuteration of hydrogen atoms. The atoms were determined to form two kinds of N-H...O type H-bonds in the crystal structure. Large frequency shifts of the {sup 35}Cl resonance lines reaching 288 kHz at 77 K and 278 kHz at room temperature were caused upon deuteration, in spite of the fact that the Cl atoms in the molecule do not form hydrogen bonds in the crystal. Results of single crystal X-ray diffraction measurements and density-functional-theorem calculations suggest that a dihedral-angle change of 1.8{sup o} between benzene and the piperidine ring contributes to {sup 35}Cl NQR anomalous frequency shifts.

The effects of pressure sensor acoustics on airdata derived from a High-angle-of-attack Flush Airdata Sensing (HI-FADS) system

Science.gov (United States)

Whitmore, Stephen A.; Moes, Timothy R.

1991-01-01

The accuracy of a nonintrusive high angle-of-attack flush airdata sensing (HI-FADS) system was verified for quasi-steady flight conditions up to 55 deg angle of attack during the F-18 High Alpha Research Vehicle (HARV) Program. The system is a matrix of nine pressure ports arranged in annular rings on the aircraft nose. The complete airdata set is estimated using nonlinear regression. Satisfactory frequency response was verified to the system Nyquist frequency (12.5 Hz). The effects of acoustical distortions within the individual pressure sensors of the nonintrusive pressure matrix on overall system performance are addressed. To quantify these effects, a frequency-response model describing the dynamics of acoustical distortion is developed and simple design criteria are derived. The model adjusts measured HI-FADS pressure data for the acoustical distortion and quantifies the effects of internal sensor geometries on system performance. Analysis results indicate that sensor frequency response characteristics very greatly with altitude, thus it is difficult to select satisfactory sensor geometry for all altitudes. The solution used presample filtering to eliminate resonance effects, and short pneumatic tubing sections to reduce lag effects. Without presample signal conditioning the system designer must use the pneumatic transmission line to attenuate the resonances and accept the resulting altitude variability.

Phenylacetylene and H bond

Indian Academy of Sciences (India)

... all resembling H bonds. Non-linear H bonds due to secondary interactions. C-H stretching frequency shows blue shift. Heavy atom distances are longer than the sum of van der Waals radii. Formed a task group through IUPAC to come up with a modern definition of H bond. 15 international experts including Desiraju.

Fabrication of surfaces with extremely high contact angle hysteresis from polyelectrolyte multilayer.

Science.gov (United States)

Wang, Liming; Wei, Jingjing; Su, Zhaohui

2011-12-20

High contact angle hysteresis on polyelectrolyte multilayers (PEMs) ion-paired with hydrophobic perfluorooctanoate anions is reported. Both the bilayer number of PEMs and the ionic strength of deposition solutions have significant influence on contact angle hysteresis: higher ionic strength and greater bilayer number cause increased contact angle hysteresis values. The hysteresis values of ~100° were observed on smooth PEMs and pinning of the receding contact line on hydrophilic defects is implicated as the cause of hysteresis. Surface roughness can be used to further tune the contact angle hysteresis on the PEMs. A surface with extremely high contact angle hysteresis of 156° was fabricated when a PEM was deposited on a rough substrate coated with submicrometer scale silica spheres. It was demonstrated that this extremely high value of contact angle hysteresis resulted from the penetration of water into the rough asperities on the substrate. The same substrate hydrophobized by chemical vapor deposition of 1H,1H,2H,2H-perfluorooctyltriethoxysilane exhibits high advancing contact angle and low hysteresis. © 2011 American Chemical Society

Effects of density functionals and dispersion interactions on geometries, bond energies and harmonic frequencies of Etbnd UX3 (E = N, P, CH; X = H, F, Cl)

Science.gov (United States)

Pandey, Krishna Kumar; Patidar, Pankaj; Patidar, Sunil Kumar; Vishwakarma, Ravi

2014-12-01

Quantum-chemical calculations have been performed to evaluate the geometries, bonding nature and harmonic frequencies of the compounds [Etbnd UX3] at DFT, DFT-D3, DFT-D3(BJ) and DFT-dDSc levels using different density functionals BP86, BLYP, PBE, revPBE, PW91, TPSS and M06-L. The stretching frequency of Utbnd N bond in [Ntbnd UF3] calculated with DFT/BLYP closely resembles with the experimental value. The performance of different density functionals for accurate Utbnd N vibrational frequencies follows the order BLYP > revPBE > BP86 > PW91 > TPSS > PBE > M06-L. The BLYP functional gives accurate value of the Utbnd E bond distances. The uranium atom in the studied compounds [Etbnd UX3] is positively charged. Upon going from [Etbnd UF3] to [Etbnd UCl3], the partial Hirshfeld charge on uranium atom decreases because of the lower electronegativity of chlorine compared to flourine. The Gopinathan-Jug bond order for Utbnd E bonds ranges from 2.90 to 3.29. The Utbnd E bond dissociation energies vary with different density functionals as M06-L < TPSS < BLYP < revPBE < BP86 < PBE ≈ PW91. The orbital interactions ΔEorb, in all studied compounds [Etbnd UX3] are larger than the electrostatic interaction ΔEelstat, which means the Utbnd N bonds in these compound have greater degree of covalent character (in the range 63.8-77.2%). The Usbnd E σ-bonding interaction is the dominant bonding interaction in the nitride and methylidyne complexes while it is weaker in [Ptbnd UX3]. The dispersion energy contributions to the total bond dissociation energies are rather small. Compared to the Grimme's D3(BJ) corrections, the Corminboeuf's dispersion corrections are larger with metaGGA functionals (TPSS, M06-L) while smaller with GGA functionals.

Quantiles of the Realized Stock-Bond Correlation and Links to the Macroeconomy

DEFF Research Database (Denmark)

Aslanidis, Nektarios; Christiansen, Charlotte

2014-01-01

This paper adopts quantile regressions to scrutinize the realized stock–bond correlation based upon high frequency returns. The paper provides in-sample and out-of-sample analysis and considers factors constructed from a large number of macro-finance predictors well-known from the return predicta......This paper adopts quantile regressions to scrutinize the realized stock–bond correlation based upon high frequency returns. The paper provides in-sample and out-of-sample analysis and considers factors constructed from a large number of macro-finance predictors well-known from the return...

Use of high flip angle in T1-prepared FAST sequences for myocardial perfusion quantification

International Nuclear Information System (INIS)

Vallee, Jean-Paul; Ivancevic, Marko; Lazeyras, Francois; Didier, Dominique; Kasuboski, Larry; Chatelain, Pascal; Righetti, Alberto

2003-01-01

This study reports on the first use of high flip angle and radio-frequency (RF) spoiling in T1-prepared fast acquisition in steady state (FAST) sequence for myocardial perfusion in patients. T1 dynamic range was measured in vitro with a FAST, an RF FAST and a snapshot fast low-angle shot (FLASH) sequences with a 90 flip angle. Myocardial perfusion was then measured twice in 6 patients during the same MR session. The RF FAST and FLASH, but not the FAST sequence, demonstrated an extended T1 dynamic range; however, the FLASH images were degraded by artifacts not present on the RF FAST images. The myocardial perfusion indices K1 (first-order transfer constant from the blood to the myocardium for the Gd-DTPA) and Vd (distribution volume of Gd-DTPA in myocardium) did not differ significantly between the two injections. K1 was 0.48±0.12 ml/min g -1 and Vd was 12.5±2.9%. With an extended T1 dynamic range and the sensitivity required for myocardial perfusion quantification, the RF FAST sequence with a 90 flip angle outperformed the snapshot FLASH sequence in terms of image quality and the FAST sequence in terms of contrast dynamic range. (orig.)

The structure of formate on TiO{sub 2}(110) by scanned-energy and scanned-angle photoelectron diffraction

Energy Technology Data Exchange (ETDEWEB)

Thevuthasan, S.; Kim, Y.J.; Herman, G.S. [Pacific Northwest National Laboratory, Richland, WA (United States)] [and others

1997-04-01

There is a considerable interest in understanding the interaction of small organic molecules with oxide surfaces. The chemistry of formate interactions with TiO{sub 2}(110) has been investigated by several groups, but there is little information on the structure of the adsorbate/surface complex. Recently the authors combined high-energy x-ray photoelectron diffraction (XPD) measurements at PNNL with low-energy scanned-angle and scanned-energy photoelectron diffraction measurements at the ALS to investigate the structure of the formate ion on TiO{sub 2}(110) in detail. The high-energy XPD results reveal that formate binds through the oxygens in a bidentate fashion to Ti cation rows along the [001] direction with an O-C-O bond angle of about 126{degrees}. Low-energy photoelectron diffraction data, which is briefly described below, was used to identify the specific bonding geometry, including the bond length between the Ti cation and the oxygen in the formate.

Frequency tripling of convergent beam employing crystals tiling in large-aperture high-energy laser facilities

Science.gov (United States)

Wang, Junhua; Li, Dazhen; Wang, Bo; Yang, Jing; Yang, Houwen; Wang, Xiaoqian; Cheng, Wenyong

2017-11-01

In inertial confinement fusion, ultraviolet laser damage of the fused silica lens is an important limiting factor for load capability of the laser driver. To solve this problem, a new configuration of frequency tripling is proposed in this paper. The frequency tripling crystal is placed on downstream of the focusing lens, thus sum frequency generation of fundamental frequency light and doubling frequency light occurs in the beam convergence path. The focusing lens is only irradiated by fundamental light and doubling frequency lights. Thus, its damage threshold will increase. LiB3O5 (LBO) crystals are employed as frequency tripling crystals for its larger acceptance angle and higher damage threshold than KDP/DKDP crystals'. With the limitation of acceptance angle and crystal growth size are taken into account, the tiling scheme of LBO crystals is proposed and designed optimally to adopt to the total convergence angle of 36.0 mrad. Theoretical results indicate that 3 LBO crystals titling with different cutting angles in θ direction can meet the phase matching condition. Compared with frequency tripling of parallel beam using one LBO crystal, 83.8% (93.1% with 5 LBO crystals tiling) of the frequency tripling conversion efficiency can be obtained employing this new configuration. The results of a principle experiment also support this scheme. By employing this new design, not only the load capacity of a laser driver will be significantly improved, but also the fused silica lens can be changed to K9 glass lens which has the mature technology and low cost.

Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models

Directory of Open Access Journals (Sweden)

Stovgaard Kasper

2010-08-01

Full Text Available Abstract Background Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that this gap will disappear in the near future. Small angle X-ray scattering (SAXS is an established low resolution method for routinely determining the structure of proteins in solution. The purpose of this study is to develop a method for the efficient calculation of accurate SAXS curves from coarse-grained protein models. Such a method can for example be used to construct a likelihood function, which is paramount for structure determination based on statistical inference. Results We present a method for the efficient calculation of accurate SAXS curves based on the Debye formula and a set of scattering form factors for dummy atom representations of amino acids. Such a method avoids the computationally costly iteration over all atoms. We estimated the form factors using generated data from a set of high quality protein structures. No ad hoc scaling or correction factors are applied in the calculation of the curves. Two coarse-grained representations of protein structure were investigated; two scattering bodies per amino acid led to significantly better results than a single scattering body. Conclusion We show that the obtained point estimates allow the calculation of accurate SAXS curves from coarse-grained protein models. The resulting curves are on par with the current state-of-the-art program CRYSOL, which requires full atomic detail. Our method was also comparable to CRYSOL in recognizing native structures among native-like decoys. As a proof-of-concept, we combined the coarse-grained Debye calculation with a previously described probabilistic model of protein structure, TorusDBN. This resulted in a significant improvement in the decoy recognition performance. In conclusion, the presented method shows great promise for

CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

Directory of Open Access Journals (Sweden)

Hamed Bostan

2012-01-01

Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

Large angle tracking and high discriminating tracking in nuclear emulsion

International Nuclear Information System (INIS)

Matsuo, Tomokazu; Shibuya, Hiroshi; Ogawa, Satoru; Fukuda, Tsutomu; Mikado, Shoji

2015-01-01

Nuclear emulsion is a high resolution and re-analyzable detector. Conventional “Track Selector” which have angle acceptance |tan θ|<0.6 are widely used to find tracks in emulsion. We made a new track selector “Fine Track Selector” (FTS) which has large angle acceptance and high discriminating ability. The FTS reduces fake tracks using new algorithms, navigation etc. FTS also keeps finding efficiency of tracks around 90% in an angle range of |tan θ| < 3.5. FTS was applied to the τ candidate in OPERA and no additional tracks found. FTS will be useful to our new J-PARC emulsion experiment.

In vitro marginal adaptation of high-viscosity resin composite restorations bonded to dentin cavities.

Science.gov (United States)

Rahiotis, Christos; Tzoutzas, John; Kakaboura, Afrodite

2004-01-01

The aim of this study was to evaluate the marginal adaptation of high-viscosity resin composite restoratives bonded to dentin in a cylindrical cavity model. The buccal enamel of 64 human premolars was removed and cylindrical cavities 3 mm in diameter and 1.3 mm in depth were prepared on each dentin surface. The cavities were divided into 8 groups of 8 cavities each and restored according to the manufacturers' instructions with the following adhesive/composite systems: Bond 1/Alert, Stae/Glacier, OptiBond Solo/Prodigy Condensable, One-Step/Pyramid, Solidbond/Solitaire, Prime&Bond NT/Surefil, One Coat Bond/Synergy, and Scotchbond 1/Z250. The composite surfaces were pressed against mylar strips, covered with cover slips, and photopolymerized in a single increment for 40 s. The restorations were polished with wet SiC papers of 320 to 1000 grit size to expose dentin margins. The marginal adaptation was evaluated immediately after photopolymerization and again after 1 week of storage in water at 37 +/- 1 degrees C. Evaluation was performed under a metallographic microscope at 200X magnification by recording the frequency of gap-free restorations (GF), the percentage length of the debonded margins relative to the cavity periphery (DM), the width of the maximum marginal gap (MG), and the marginal index (MI = MG x DM / 100). The results were statistically analyzed with one-way ANOVA and the Mann-Whitney U-test at alpha = 0.05. No incidence of gaps was found in 62.5% of One Coat Bond/Synergy and 37.5% of OptiBond Solo/Prodigy Condensable restorations. All the other restorative systems exhibited restorations with gaps. One Coat Bond/Synergy, Scotchbond 1/Z250, and OptiBond Solo/Prodigy Condensable were the groups with the lowest DM values, while Stae/Glacier showed the highest DM values. One Coat Bond/Synergy and OptiBond Solo/Prodigy Condensable revealed the lowest MI values and Stae/Glacier the highest. No statistically significant differences were recorded between

Design of a self-calibration high precision micro-angle deformation optical monitoring scheme

Science.gov (United States)

Gu, Yingying; Wang, Li; Guo, Shaogang; Wu, Yun; Liu, Da

2018-03-01

In order to meet the requirement of high precision and micro-angle measurement on orbit, a self-calibrated optical non-contact real-time monitoring device is designed. Within three meters, the micro-angle variable of target relative to measuring basis can be measured in real-time. The range of angle measurement is +/-50'', the angle measurement accuracy is less than 2''. The equipment can realize high precision real-time monitoring the micro-angle deformation, which caused by high strength vibration and shock of rock launching, sun radiation and heat conduction on orbit and so on.

Selenoglutathione Diselenide: Unique Redox Reactions in the GPx-Like Catalytic Cycle and Repairing of Disulfide Bonds in Scrambled Protein.

Science.gov (United States)

Shimodaira, Shingo; Asano, Yuki; Arai, Kenta; Iwaoka, Michio

2017-10-24

Selenoglutathione (GSeH) is a selenium analogue of naturally abundant glutathione (GSH). In this study, this water-soluble small tripeptide was synthesized in a high yield (up to 98%) as an oxidized diselenide form, i.e., GSeSeG (1), by liquid-phase peptide synthesis (LPPS). Obtained 1 was applied to the investigation of the glutathione peroxidase (GPx)-like catalytic cycle. The important intermediates, i.e., GSe - and GSeSG, besides GSeO 2 H were characterized by 77 Se NMR spectroscopy. Thiol exchange of GSeSG with various thiols, such as cysteine and dithiothreitol, was found to promote the conversion to GSe - significantly. In addition, disproportionation of GSeSR to 1 and RSSR, which would be initiated by heterolytic cleavage of the Se-S bond and catalyzed by the generated selenolate, was observed. On the basis of these redox behaviors, it was proposed that the heterolytic cleavage of the Se-S bond can be facilitated by the interaction between the Se atom and an amino or aromatic group, which is present at the GPx active site. On the other hand, when a catalytic amount of 1 was reacted with scrambled 4S species of RNase A in the presence of NADPH and glutathione reductase, native protein was efficiently regenerated, suggesting a potential use of 1 to repair misfolded proteins through reduction of the non-native SS bonds.

Physical mechanisms of copper-copper wafer bonding

International Nuclear Information System (INIS)

Rebhan, B.; Hingerl, K.

2015-01-01

The study of the physical mechanisms driving Cu-Cu wafer bonding allowed for reducing the bonding temperatures below 200 °C. Metal thermo-compression Cu-Cu wafer bonding results obtained at such low temperatures are very encouraging and suggest that the process is possible even at room temperature if some boundary conditions are fulfilled. Sputtered (PVD) and electroplated Cu thin layers were investigated, and the analysis of both metallization techniques demonstrated the importance of decreasing Cu surface roughness. For an equal surface roughness, the bonding temperature of PVD Cu wafers could be even further reduced due to the favorable microstructure. Their smaller grain size enhances the length of the grain boundaries (observed on the surface prior bonding), acting as efficient mass transfer channels across the interface, and hence the grains are able to grow over the initial bonding interface. Due to the higher concentration of random high-angle grain boundaries, this effect is intensified. The model presented is explaining the microstructural changes based on atomic migration, taking into account that the reduction of the grain boundary area is the major driving force to reduce the Gibbs free energy, and predicts the subsequent microstructure evolution (grain growth) during thermal annealing

The electronic donation and frequency shifts on the YCCH⋯BH₄⁻ boron-bonded complexes (Y=H, CH₃, CF₃ and CCl₃).

Science.gov (United States)

Pordeus, Renato Q; Rego, Danilo G; Oliveira, Boaz G

2015-06-15

In this theoretical work, the tetrahydroborate ion (BH4(-)) was used as proton acceptor in the formation of the YCC-H⋯BH4(-) complexes (Y=H, CH3, CCl3 and CF3). Using B3LYP/6-311++G(d,p) level of theory, the results of structure corroborate with the analyses of infrared spectra showing that the changes in the bond lengths are in good agreement with the frequency shifts of the HCC-H, H3CCC-H, Cl3CCC-H and F3CCC-H proton donors. Based on the calculations carried out by the Quantum Theory of Atoms in Molecules (QTAIM), the reductions of electronic density corroborate with the red shifts in the frequencies of the C-H bonds. In addition to that, the C-H bonds are polarized because the contributions of s orbital diminish whereas of p increase. In line with this, the variations on the atomic radii computed via QTAIM calculations show that carbon outweigh hydrogen as follows (ΔrC>ΔrH). This scenario is indirectly supported by the Bent's rule of the chemical bonding. Although the interaction energies (corrected with BSSE and ZPE) vary between -19 and -67 kJ mol(-1), these complexes interact without covalent character. Copyright © 2015 Elsevier B.V. All rights reserved.

Time- and angle-resolved photoemission spectroscopy with optimized high-harmonic pulses using frequency-doubled Ti:Sapphire lasers

International Nuclear Information System (INIS)

Eich, S.; Stange, A.; Carr, A.V.; Urbancic, J.; Popmintchev, T.; Wiesenmayer, M.; Jansen, K.; Ruffing, A.; Jakobs, S.; Rohwer, T.; Hellmann, S.; Chen, C.; Matyba, P.; Kipp, L.; Rossnagel, K.; Bauer, M.; Murnane, M.M.; Kapteyn, H.C.; Mathias, S.; Aeschlimann, M.

2014-01-01

Highlights: • We present a scheme to generate high intensity XUV pulses from HHG with variable time-bandwidth product. • Shorter-wavelength driven high-harmonic XUV trARPES provides higher photon flux and increased energy resolution. • High-quality high-harmonic XUV trARPES data with sub 150 meV energy and sub 30 fs time resolution is presented. - Abstract: Time- and angle-resolved photoemission spectroscopy (trARPES) using femtosecond extreme ultraviolet high harmonics has recently emerged as a powerful tool for investigating ultrafast quasiparticle dynamics in correlated-electron materials. However, the full potential of this approach has not yet been achieved because, to date, high harmonics generated by 800 nm wavelength Ti:Sapphire lasers required a trade-off between photon flux, energy and time resolution. Photoemission spectroscopy requires a quasi-monochromatic output, but dispersive optical elements that select a single harmonic can significantly reduce the photon flux and time resolution. Here we show that 400 nm driven high harmonic extreme-ultraviolet trARPES is superior to using 800 nm laser drivers since it eliminates the need for any spectral selection, thereby increasing photon flux and energy resolution to <150 meV while preserving excellent time resolution of about 30 fs

Expression, Purification and Characterization of GMZ2'.10C, a Complex Disulphide-Bonded Fusion Protein Vaccine Candidate against the Asexual and Sexual Life-Stages of the Malaria-Causing Plasmodium falciparum Parasite

NARCIS (Netherlands)

Mistarz, U.H.; Singh, S.K; Nguyen, T.; Roeffen, W.; Lissau, C.; Madsen, S.M.; Vrang, A.; Tiendrebeogo, R.W.; Kana, I.H.; Sauerwein, R.W.; Theisen, M.; Rand, K.D.

2017-01-01

PURPOSE: Production and characterization of a chimeric fusion protein (GMZ2'.10C) which combines epitopes of key malaria parasite antigens: glutamate-rich protein (GLURP), merozoite surface protein 3 (MSP3), and the highly disulphide bonded Pfs48/45 (10C). GMZ2'.10C is a potential candidate for a

Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling

International Nuclear Information System (INIS)

Knight, Jennifer L.; Zhou, Zhiyong; Gallicchio, Emilio; Himmel, Daniel M.; Friesner, Richard A.; Arnold, Eddy; Levy, Ronald M.

2008-01-01

Torsion-angle sampling, as implemented in the Protein Local Optimization Program (PLOP), is used to generate multiple structurally variable single-conformer models which are in good agreement with X-ray data. An ensemble-refinement approach to differentiate between positional uncertainty and conformational heterogeneity is proposed. Modeling structural variability is critical for understanding protein function and for modeling reliable targets for in silico docking experiments. Because of the time-intensive nature of manual X-ray crystallographic refinement, automated refinement methods that thoroughly explore conformational space are essential for the systematic construction of structurally variable models. Using five proteins spanning resolutions of 1.0–2.8 Å, it is demonstrated how torsion-angle sampling of backbone and side-chain libraries with filtering against both the chemical energy, using a modern effective potential, and the electron density, coupled with minimization of a reciprocal-space X-ray target function, can generate multiple structurally variable models which fit the X-ray data well. Torsion-angle sampling as implemented in the Protein Local Optimization Program (PLOP) has been used in this work. Models with the lowest R free values are obtained when electrostatic and implicit solvation terms are included in the effective potential. HIV-1 protease, calmodulin and SUMO-conjugating enzyme illustrate how variability in the ensemble of structures captures structural variability that is observed across multiple crystal structures and is linked to functional flexibility at hinge regions and binding interfaces. An ensemble-refinement procedure is proposed to differentiate between variability that is a consequence of physical conformational heterogeneity and that which reflects uncertainty in the atomic coordinates

Reliable and repeatable bonding technology for high temperature automotive power modules for electrified vehicles

International Nuclear Information System (INIS)

Yoon, Sang Won; Shiozaki, Koji; Glover, Michael D; Mantooth, H Alan

2013-01-01

This paper presents the feasibility of highly reliable and repeatable copper–tin transient liquid phase (Cu–Sn TLP) bonding as applied to die attachment in high temperature operational power modules. Electrified vehicles are attracting particular interest as eco-friendly vehicles, but their power modules are challenged because of increasing power densities which lead to high temperatures. Such high temperature operation addresses the importance of advanced bonding technology that is highly reliable (for high temperature operation) and repeatable (for fabrication of advanced structures). Cu–Sn TLP bonding is employed herein because of its high remelting temperature and desirable thermal and electrical conductivities. The bonding starts with a stack of Cu–Sn–Cu metal layers that eventually transforms to Cu–Sn alloys. As the alloys have melting temperatures (Cu 3 Sn: > 600 °C, Cu 6 Sn 5 : > 400 °C) significantly higher than the process temperature, the process can be repeated without damaging previously bonded layers. A Cu–Sn TLP bonding process was developed using thin Sn metal sheets inserted between copper layers on silicon die and direct bonded copper substrates, emulating the process used to construct automotive power modules. Bond quality is characterized using (1) proof-of-concept fabrication, (2) material identification using scanning electron microscopy and energy-dispersive x-ray spectroscopy analysis, and (3) optical analysis using optical microscopy and scanning acoustic microscope. The feasibility of multiple-sided Cu–Sn TLP bonding is demonstrated by the absence of bondline damage in multiple test samples fabricated with double- or four-sided bonding using the TLP bonding process. (paper)

Low-Cost High-Efficiency Solar Cells with Wafer Bonding and Plasmonic Technologies

Science.gov (United States)

Tanake, Katsuaki

InP/Si substrates for bulk InP in the fabrication of such a four-junction solar cell could significantly reduce the substrate cost since the current prices for commercial InP substrates are much higher than those for Si substrates by two orders of magnitude. Direct heteroepitaxial growth of InP thin films on Si substrates has not produced the low dislocation-density high quality layers required for active InGaAs/InP in optoelectronic devices due to the ˜8% lattice mismatch between InP and Si. We successfully fabricated InP/Si substrates by He implantation of InP prior to bonding to a thermally oxidized Si substrate and annealing to exfoliate an InP thin film. The thickness of the exfoliated InP films was only 900 nm, which means hundreds of the InP/Si substrates could be prepared from a single InP wafer in principle. The photovoltaic current-voltage characteristics of the In0.53Ga0.47As cells fabricated on the wafer-bonded InP/Si substrates were comparable to those synthesized on commercially available epi-ready InP substrates, and had a ˜20% higher short-circuit current which we attribute to the high reflectivity of the InP/SiO2/Si bonding interface. This work provides an initial demonstration of wafer-bonded InP/Si substrates as an alternative to bulk InP substrates for solar cell applications. We have observed photocurrent enhancements up to 260% at 900 nm for a GaAs cell with a dense array of Ag nanoparticles with 150 nm diameter and 20 nm height deposited through porous alumina membranes by thermal evaporation on top of the cell, relative to reference GaAs cells with no metal nanoparticle array. This dramatic photocurrent enhancement is attributed to the effect of metal nanoparticles to scatter the incident light into photovoltaic layers with a wide range of angles to increase the optical path length in the absorber layer. GaAs solar cells with metallic structures at the bottom of the photovoltaic active layers, not only at the top, using semiconductor

High-Frequency Neuromuscular Electrical Stimulation Increases Anabolic Signaling.

Science.gov (United States)

Mettler, Joni A; Magee, Dillon M; Doucet, Barbara M

2018-03-16

Neuromuscular electrical stimulation (NMES) is commonly used in rehabilitation settings to increase muscle mass and strength. However, the effects of NMES on muscle growth are not clear and no human studies have compared anabolic signaling between low-frequency (LF-) and high-frequency (HF-) NMES. The purpose of this study was to determine the skeletal muscle anabolic signaling response to an acute bout of LF- and HF-NMES. Eleven young healthy volunteers (6 men; 5 women) received an acute bout of LF- (20 Hz) and HF- (60 Hz) NMES. Muscle biopsies were obtained from the vastus lateralis muscle prior to the first NMES treatment and 30-mins following each NMES treatment. Phosphorylation of the following key anabolic signaling proteins was measured by Western blot and proteins are expressed as a ratio of phosphorylated to total: mammalian target of rapamycin (mTOR), p70-S6 kinase 1 (S6K1), and eukaryotic initiation factor 4E binding protein 1 (4E-BP1). Compared to Pre-NMES, phosphorylation of mTOR was upregulated 40.2% for LF-NMES (P = 0.018) and 68.4% for HF-NMES (P 0.05). There were no differences between treatment conditions for 4E-BP1 phosphorylation (P > 0.05). An acute bout of LF- and HF-NMES upregulated anabolic signaling with HF-NMES producing a greater anabolic response compared to LF-NMES, suggesting that HF-stimulation may provide a stronger stimulus for processes that initiate muscle hypertrophy. Additionally, the stimulation frequency parameter should be considered by clinicians in the design of optimal NMES treatment protocols.

The small angle x-ray scattering of globular proteins in solution during heat denaturation

Science.gov (United States)

Banuelos, Jose; Urquidi, Jacob

2008-10-01

The ability of proteins to change their conformation in response to changes in their environment has consequences in biological processes like metabolism, chemical regulation in cells, and is believed to play a role in the onset of several neurodegenerative diseases. Factors such as a change in temperature, pressure, and the introduction of ions into the aqueous environment of a protein can give rise to the folding/unfolding of a protein. As a protein unfolds, the ratio of nonpolar to polar groups exposed to water changes, affecting a protein's thermodynamic properties. Using small angle x-ray scattering (SAXS), we are currently studying the intermediate protein conformations that arise during the folding/unfolding process as a function of temperature for five globular proteins. Trends in the observed intermediate structures of these globular proteins, along with correlations with data on protein thermodynamics may help elucidate shared characteristics between all proteins in the folding/unfolding process. Experimental design considerations will be discussed and preliminary results for some of these systems will be presented.

Finding high-temperature superconductors by metallizing the σ-bonding electrons

International Nuclear Information System (INIS)

Gao Miao; Lu Zhongyi; Xiang Tao

2015-01-01

Raising superconducting transition temperature (T_c) is an important task of fundamental research on superconductivity. It is also a prerequisite for the large scale application of superconductors. Since the microscopic mechanism of high-T_c superconductivity is unknown, the conventional approach for increasing T_c is either to apply high pressure to a material which has the potential to become superconducting, or to push it close to an antiferromagnetic or some other quantum instability point by chemical doping. In this article, the authors point out that another general approach for raising T_c is to lift the σ-bonding bands to the Fermi level, or to metallize the σ-bonding elections. This approach can increase the probability of finding a novel high-T_c superconductor because the coupling of σ-bonding electrons with phonons is generally strong and the superconducting transition induced by this interaction can occur at relatively high temperatures. After elucidating the underlying mechanism, the authors discuss a number of schemes to metallize σ-bonding electrons, and present their recent prediction for the crystalline and electronic structures of two potential high-T_c superconductors, Li_2B_3C and Li_3B_4C_2, with T_c higher than 50 K. (authors)

PMN-PT single crystal, high-frequency ultrasonic needle transducers for pulsed-wave Doppler application.

Science.gov (United States)

Zhou, Qifa; Xu, Xiaochen; Gottlieb, Emanuel J; Sun, Lei; Cannata, Jonathan M; Ameri, Hossein; Humayun, Mark S; Han, Pengdi; Shung, K Kirk

2007-03-01

High-frequency needle ultrasound transducers with an aperture size of 0.4 mm were fabricated using lead magnesium niobate-lead titanate (PMN-33% PT) as the active piezoelectric material. The active element was bonded to a conductive silver particle matching layer and a conductive epoxy backing through direct contact curing. An outer matching layer of parylene was formed by vapor deposition. The active element was housed within a polyimide tube and a 20-gauge needle housing. The magnitude and phase of the electrical impedance of the transducer were 47 omega and -38 degrees, respectively. The measured center frequency and -6 dB fractional bandwidth of the PMN-PT needle transducer were 44 MHz and 45%, respectively. The two-way insertion loss was approximately 15 dB. In vivo high-frequency, pulsed-wave Doppler patterns of blood flow in the posterior portion and in vitro ultrasonic backscatter microscope (UBM) images of the rabbit eye were obtained with the 44-MHz needle transducer.

The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations

Science.gov (United States)

Li, Yin; Lukács, András; Bordács, Sándor; Móczár, János; Nyitrai, Miklós; Hebling, János

2018-02-01

Low-frequency modes of L-Asp and L-Asn were studied in the range from 0.1 to 3.0 THz using time-domain Terahertz spectroscopy and density functional theory calculation. The results show that PBE-D2 shows more success than BLYP-D2 in prediction of THz absorption spectra. To compare their low-frequency modes, we adopted ;vibrational character ID strips; proposed by Schmuttenmaer and coworkers [Journal of Physical Chemistry B, 117, 10444(2013)]. We found that the most intense THz absorption peaks of two compounds both involve severe distortion of their hydrogen bonding networks. Due to less rigid hydrogen bonding network in L-Asp, the side chain (carboxyl group) of L-Asp exhibits larger motions than that (carboxamide group) of L-Asn in low-frequency modes.

High prevalence of narrow angles among Filipino-American patients.

Science.gov (United States)

Seider, Michael I; Sáles, Christopher S; Lee, Roland Y; Agadzi, Anthony K; Porco, Travis C; Weinreb, Robert N; Lin, Shan C

2011-03-01

To determine the prevalence of gonioscopically narrow anterior chamber angles in a Filipino-American clinic population. The records of 122 consecutive, new, self-declared Filipino-American patients examined in a comprehensive ophthalmology clinic in Vallejo, California were reviewed retrospectively. After exclusion, 222 eyes from 112 patients remained for analysis. Data were collected for anterior chamber angle grade as determined by gonioscopy (Shaffer system), age, sex, manifest refraction (spherical equivalent), intraocular pressure, and cup-to-disk ratio. Data from both eyes of patients were included and modeled using standard linear mixed-effects regression. As a comparison, data were also collected from a group of 30 consecutive White patients from the same clinic. After exclusion, 50 eyes from 25 White patients remained for comparison. At least 1 eye of 24% of Filipino-American patients had a narrow anterior chamber angle (Shaffer grade ≤ 2). Filipino-American angle grade significantly decreased with increasingly hyperopic refraction (P=0.007) and larger cup-to-disk ratio (P=0.038). Filipino-American women had significantly decreased angle grades compared with men (P=0.028), but angle grade did not vary by intraocular pressure or age (all, P≥ 0.059). Narrow anterior chamber angles are highly prevalent in Filipino-American patients in our clinic population.

Interface bonding of SA508-3 steel under deformation and high temperature diffusion

Science.gov (United States)

Xu, Bin; Shao, Chunjuan; Sun, Mingyue

2018-05-01

There are mainly two parameters affecting high temperature interface bonding: deformation and diffusion. To study these two parameters, interface bonding of SA508-3 bainitic steel at 1100°C are simulated by gleeble3500 thermal simulator. The results show that interface of SA508-3 steel can be bonded under deformation and high temperature. For a specimen pressed at 1100°C without further high temperature diffusion, a reduction ratio of 30% can make the interface begun to bond, but the interface is still part of the grain boundary and small grains exist near the interface. When reduction ratio reaches 50%, the interface can be completely bonded and the microstructure near the interface is the same as that of the base material. When deformation is small, long time diffusion can also help the interface bonding. The results show that when the diffusion time is long enough, the interface under small deformation can also be bonded. For a specimen holding for 24h at 1100°C, only 13% reduction ratio is enough for interface bonding.

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

International Nuclear Information System (INIS)

Bellstedt, Peter; Herbst, Christian; Häfner, Sabine; Leppert, Jörg; Görlach, Matthias; Ramachandran, Ramadurai

2012-01-01

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC′C and 3D C′NCA with sequential 13 C acquisitions, 3D NHH and 3D NC′H with sequential 1 H acquisitions and 3D CANH and 3D C’NH with broadband 13 C– 15 N mixing are demonstrated using microcrystalline samples of the β1 immunoglobulin binding domain of protein G (GB1) and the chicken α-spectrin SH3 domain.

Molecular structures and vibrational frequencies of xanthine and its methyl derivatives (caffeine and theobromine) by ab initio Hartree-Fock and density functional theory calculations

Science.gov (United States)

Ucun, Fatih; Sağlam, Adnan; Güçlü, Vesile

2007-06-01

The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.

Scalable bonding of nanofibrous polytetrafluoroethylene (PTFE) membranes on microstructures

Science.gov (United States)

Mortazavi, Mehdi; Fazeli, Abdolreza; Moghaddam, Saeed

2018-01-01

Expanded polytetrafluoroethylene (ePTFE) nanofibrous membranes exhibit high porosity (80%-90%), high gas permeability, chemical inertness, and superhydrophobicity, which makes them a suitable choice in many demanding fields including industrial filtration, medical implants, bio-/nano- sensors/actuators and microanalysis (i.e. lab-on-a-chip). However, one of the major challenges that inhibit implementation of such membranes is their inability to bond to other materials due to their intrinsic low surface energy and chemical inertness. Prior attempts to improve adhesion of ePTFE membranes to other surfaces involved surface chemical treatments which have not been successful due to degradation of the mechanical integrity and the breakthrough pressure of the membrane. Here, we report a simple and scalable method of bonding ePTFE membranes to different surfaces via the introduction of an intermediate adhesive layer. While a variety of adhesives can be used with this technique, the highest bonding performance is obtained for adhesives that have moderate contact angles with the substrate and low contact angles with the membrane. A thin layer of an adhesive can be uniformly applied onto micro-patterned substrates with feature sizes down to 5 µm using a roll-coating process. Membrane-based microchannel and micropillar devices with burst pressures of up to 200 kPa have been successfully fabricated and tested. A thin layer of the membrane remains attached to the substrate after debonding, suggesting that mechanical interlocking through nanofiber engagement is the main mechanism of adhesion.

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

Directory of Open Access Journals (Sweden)

Li Karen

2008-12-01

Full Text Available Abstract Background Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT or Whelan and Goldman (WAG models, are based on empirical amino acid interchange matrices estimated from databases of protein alignments that incorporate the average amino acid frequencies of the data set under examination (e.g JTT + F. Variation in the evolutionary process between sites is typically modelled by a rates-across-sites distribution such as the gamma (Γ distribution. However, sites in proteins also vary in the kinds of amino acid interchanges that are favoured, a feature that is ignored by standard empirical substitution matrices. Here we examine the degree to which the pattern of evolution at sites differs from that expected based on empirical amino acid substitution models and evaluate the impact of these deviations on phylogenetic estimation. Results We analyzed 21 large protein alignments with two statistical tests designed to detect deviation of site-specific amino acid distributions from data simulated under the standard empirical substitution model: JTT+ F + Γ. We found that the number of states at a given site is, on average, smaller and the frequencies of these states are less uniform than expected based on a JTT + F + Γ substitution model. With a four-taxon example, we show that phylogenetic estimation under the JTT + F + Γ model is seriously biased by a long-branch attraction artefact if the data are simulated under a model utilizing the observed site-specific amino acid frequencies from an alignment. Principal components analyses indicate the existence of at least four major site-specific frequency classes in these 21 protein alignments. Using a mixture model with these four separate classes of site-specific state frequencies plus a fifth class of global frequencies (the JTT + cF + Γ model, significant improvements in model fit for real data sets can be achieved. This simple mixture model also reduces the long

Ring magnet firing angle control

International Nuclear Information System (INIS)

Knott, M.J.; Lewis, L.G.; Rabe, H.H.

1975-01-01

A device is provided for controlling the firing angles of thyratrons (rectifiers) in a ring magnet power supply. A phase lock loop develops a smooth ac signal of frequency equal to and in phase with the frequency of the voltage wave developed by the main generator of the power supply. A counter that counts from zero to a particular number each cycle of the main generator voltage wave is synchronized with the smooth AC signal of the phase lock loop. Gates compare the number in the counter with predetermined desired firing angles for each thyratron and with coincidence the proper thyratron is fired at the predetermined firing angle

Probing nanoparticle-macromolecule interaction and resultant structure by small-angle neutron scattering

International Nuclear Information System (INIS)

Aswal, V.K.

2013-01-01

Nanoparticles display unique and distinct characteristics from those of their constituent atoms and bulk materials which are being employed in numerous applications in the fields of medicine, electronics, optics, communications, energy, environment etc. Many of these applications require adjoining of nanoparticles with macromolecules such as proteins, polymers and surfactants to obtain functional objects. For example, nanoparticle-protein complexes are of great importance in controlling enzymatic behavior, targeted drug delivery and developing biocompatible materials. The nanoparticles interfaced with polymers are shown to be useful in developing protein sensor arrays. Interaction of surfactants with nanoparticles is utilized extensively for technical and industrial applications associated with colloidal stability, detergency and design of nanostructured functional interfaces. The interaction of two components, nanoparticles and macromolecule, strongly depends on the characteristics of both the nanoparticles (size, shape, surface roughness, charge density etc.) and macromolecules (type, charge, shape and solution conditions etc.) used. The interaction of macromolecule on nanoparticle surface is a cumulative effect of a number of forces such as electrostatic force, covalent bonding, hydrogen bonding, non-polar interaction, hydrophobic interactions etc. These interactions depending on the system conditions can lead to various structures. Small-angle neutron scattering (SANS) with the possibility to vary contrast is an ideal technique to study such multi-component systems. In this talk, some of our results of SANS from the complexes of nanoparticle-protein and nanoparticle surfactant systems will be discussed. (author)

Influence of multiple well defined conformations on small-angle scattering of proteins in solution.

Science.gov (United States)

Heller, William T

2005-01-01

A common structural motif for many proteins comprises rigid domains connected by a flexible hinge or linker. The flexibility afforded by these domains is important for proper function and such proteins may be able to adopt more than one conformation in solution under equilibrium conditions. Small-angle scattering of proteins in solution samples all conformations that exist in the sampled volume during the time of the measurement, providing an ensemble-averaged intensity. In this paper, the influence of sampling an ensemble of well defined protein structures on the small-angle solution scattering intensity profile is examined through common analysis methods. Two tests were performed using simulated data: one with the extended and collapsed states of the bilobal calcium-binding protein calmodulin and the second with the catalytic subunit of protein kinase A, which has two globular domains connected by a glycine hinge. In addition to analyzing the simulated data for the radii of gyration Rg, distance distribution function P(r) and particle volume, shape restoration was applied to the simulated data. Rg and P(r) of the ensemble profiles could be easily mistaken for a single intermediate state. The particle volumes and models of the ensemble intensity profiles show that some indication of multiple conformations exists in the case of calmodulin, which manifests an enlarged volume and shapes that are clear superpositions of the conformations used. The effect on the structural parameters and models is much more subtle in the case of the catalytic subunit of protein kinase A. Examples of how noise influences the data and analyses are also presented. These examples demonstrate the loss of the indications of multiple conformations in cases where even broad distributions of structures exist. While the tests using calmodulin show that the ensemble states remain discernible from the other ensembles tested or a single partially collapsed state, the tests performed using the

Reduction of disulfide bonds in peptides and proteins. Reduction des groupes disulfure dans les peptides et proteines

Energy Technology Data Exchange (ETDEWEB)

Conte, D [Institut Curie, 75 - Paris (France); Houee-Levin, C [Paris-5 Univ., 75 (France)

1993-04-01

We have re-examined the mechanism of disulfide bond reduction in oxidized glutathione by C0[sub 2][sup .-] free radicals. The process appears to be a chain reaction whose initial yield depends on pH and on both peptide and formate ion concentrations, but remains independent on the radiation dose rate. Kinetic schemes drawn from studies on dithiothreitol are unable to account for the results obtained with glutathione and proteins, although the disulfide radical anion is the primary intermediate found with all compounds. The rate constant for its formation from C0[sub 2][sup .-] and glutathione is in the same range as those found using proteins, while decay pathways are somewhat different. Hypotheses are proposed to account for these differences. 6 figs., 2 tabs.

Interphase effects in dental nanocomposites investigated by small-angle neutron scattering.

Science.gov (United States)

Wilson, Kristen S; Allen, Andrew J; Washburn, Newell R; Antonucci, Joseph M

2007-04-01

Small-angle and ultrasmall-angle neutron scattering (SANS and USANS) were used to characterize silica nanoparticle dispersion morphologies and the interphase in thermoset dimethacrylate polymer nanocomposites. Silica nanoparticle fillers were silanized with varying mass ratios of 3-methacryloxypropyltrimethoxysilane (MPTMS), a silane that interacts with the matrix through covalent and H-bonding, and n-octyltrimethoxysilane (OTMS), a silane that interacts through weak dispersion forces. Interphases with high OTMS mass fractions were found to be fractally rough with fractal dimensions, D(s), between 2.19 and 2.49. This roughness was associated with poor interfacial adhesion and inferior mechanical properties. Mean interparticle distances calculated for composites containing 10 mass % and 25 mass % silica suggest that the nanoparticles treated with more MPTMS than OTMS may be better dispersed than OTMS-rich nanoparticles. The results indicate that the covalent bonding and H-bonding of MPTMS-rich nanoparticles with the matrix are necessary for preparing well-dispersed nanocomposites. In addition, interphases containing equal masses of MPTMS and OTMS may yield composites with overall optimal properties. Finally, the combined SANS/USANS data could distinguish the differences, as a function of silane chemistry, in the nanoparticle/silane and silane/matrix interfaces that affect the overall mechanical properties of the composites. (c) 2006 Wiley Periodicals, Inc.

Achieving highly efficient and broad-angle polarization beam filtering using epsilon-near-zero metamaterials mimicked by metal-dielectric multilayers

Science.gov (United States)

Wu, Feng

2018-03-01

We report a highly efficient and broad-angle polarization beam filter at visible wavelengths using an anisotropic epsilon-near-zero metamaterial mimicked by a multilayer composed of alternative subwavelength magnesium fluoride and silver layers. The underlying physics can be explained by the dramatic difference between two orthogonal polarizations' iso-frequency curves of anisotropic epsilon-near-zero metamaterials. Transmittance for two orthogonal polarization waves and the polarization extinction ratio are calculated via the transfer matrix method to assess the comprehensive performance of the proposed polarization beam filter. From the simulation results, the proposed polarization beam filter is highly efficient (the polarization extinction ratio is far larger than two orders of magnitude) and has a broad operating angle range (ranging from 30° to 75°). Finally, we show that the proper tailoring of the periodic number enables us to obtain high comprehensive performance of the proposed polarization beam filter.

High angle of attack aerodynamics subsonic, transonic, and supersonic flows

CERN Document Server

Rom, Josef

1992-01-01

The aerodynamics of aircraft at high angles of attack is a subject which is being pursued diligently, because the modern agile fighter aircraft and many of the current generation of missiles must perform well at very high incidence, near and beyond stall. However, a comprehensive presentation of the methods and results applicable to the studies of the complex aerodynamics at high angle of attack has not been covered in monographs or textbooks. This book is not the usual textbook in that it goes beyond just presenting the basic theoretical and experimental know-how, since it contains reference material to practical calculation methods and technical and experimental results which can be useful to the practicing aerospace engineers and scientists. It can certainly be used as a text and reference book for graduate courses on subjects related to high angles of attack aerodynamics and for topics related to three-dimensional separation in viscous flow courses. In addition, the book is addressed to the aerodynamicist...

Solder bond requirement for large, built-up, high-performance conductors

International Nuclear Information System (INIS)

Willig, R.L.

1981-01-01

Some large built-up conductors fabricated for large superconducting magnets are designed to operate above the maximum recovery current. Because the stability of these conductors is sensitive to the quality of the solder bond joining the composite superconductor to the high-conductivity substrate, a minimum bond requirement is necessary. The present analysis finds that the superconductor is unstable and becomes abruptly resistive when there are temperature excursions into the current sharing region of a poorly bonded conductor. This abrupt transition, produces eddy current heating in the vicinity of the superconducting filaments and causes a sharp reduction in the minimum propagating zone (MPZ) energy. This sensitivity of the MPZ energy to the solder bond contact area is used to specify a minimum bond requirement. For the superconducting MHD magnet built for the Component Development Integration Facility (CDIF), the minimum bonded surface area is .68 cm/sup 2//cm which is 44% of the composite perimeter. 5 refs

Global low-frequency motions in protein allostery: CAP as a model system.

Science.gov (United States)

Townsend, Philip D; Rodgers, Thomas L; Pohl, Ehmke; Wilson, Mark R; McLeish, Tom C B; Cann, Martin J

2015-06-01

Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distant site. There is considerable evidence that allosteric cooperativity can be communicated by the modulation of protein dynamics without conformational change. The Catabolite Activator Protein (CAP) of Escherichia coli is an important experimental exemplar for entropically driven allostery. Here we discuss recent experimentally supported theoretical analysis that highlights the role of global low-frequency dynamics in allostery in CAP and identify how allostery arises as a natural consequence of changes in global low-frequency protein fluctuations on ligand binding.

The influence of erupting lateral teeth on maxillary anterior crowding in two Angle Class I maloclussion cases with high and low angles

Directory of Open Access Journals (Sweden)

Hiroshi Ueda

2016-01-01

Full Text Available Two cases of anterior crowding, both Skeletal Class I and Angle Class I maloclussion, one being low angle and the other high angle respectively, respectively, were treated and evaluated to ascertain whether or not there is a relationship among disproportionate mesial axial angulation of the maxillary lateral teeth and the Frankfurt Horizontal-Functional Occlusal plane, therefore generating maxillary anterior crowding. Both cases were Japanese boys, the first one aged 9 years 10 months with chief complaint being anterior crowding and the second case aged 7 years and 8 months complaining of inadequate space for satisfying canine eruption. During and after the second stage of orthodontic treatment on both cases, several radiographic analysis were performed to assess treatment progress and retention; from these radiographs, it was noticed among other findings that in the high-angle case, the axial angulations of the maxillary lateral incisors were markedly smaller than in the low-angle case, thus indicating mesial tipping in the upper dental arch. This decreased mesial axial angulation of the lateral teeth observed at high angles may potentially cause maxillary space deficiency.

Disulfide bond effects on protein stability: designed variants of Cucurbita maxima trypsin inhibitor-V.

Science.gov (United States)

Zavodszky, M; Chen, C W; Huang, J K; Zolkiewski, M; Wen, L; Krishnamoorthi, R

2001-01-01

Attempts to increase protein stability by insertion of novel disulfide bonds have not always been successful. According to the two current models, cross-links enhance stability mainly through denatured state effects. We have investigated the effects of removal and addition of disulfide cross-links, protein flexibility in the vicinity of a cross-link, and disulfide loop size on the stability of Cucurbita maxima trypsin inhibitor-V (CMTI-V; 7 kD) by differential scanning calorimetry. CMTI-V offers the advantage of a large, flexible, and solvent-exposed loop not involved in extensive intra-molecular interactions. We have uncovered a negative correlation between retention time in hydrophobic column chromatography, a measure of protein hydrophobicity, and melting temperature (T(m)), an indicator of native state stabilization, for CMTI-V and its variants. In conjunction with the complete set of thermodynamic parameters of denaturation, this has led to the following deductions: (1) In the less stable, disulfide-removed C3S/C48S (Delta Delta G(d)(50 degrees C) = -4 kcal/mole; Delta T(m) = -22 degrees C), the native state is destabilized more than the denatured state; this also applies to the less-stable CMTI-V* (Delta Delta G(d)(50 degrees C) = -3 kcal/mole; Delta T(m) = -11 degrees C), in which the disulfide-containing loop is opened by specific hydrolysis of the Lys(44)-Asp(45) peptide bond; (2) In the less stable, disulfide-inserted E38C/W54C (Delta Delta G(d)(50 degrees C) = -1 kcal/mole; Delta T(m) = +2 degrees C), the denatured state is more stabilized than the native state; and (3) In the more stable, disulfide-engineered V42C/R52C (Delta Delta G(d)(50 degrees C) = +1 kcal/mole; Delta T(m) = +17 degrees C), the native state is more stabilized than the denatured state. These results show that a cross-link stabilizes both native and denatured states, and differential stabilization of the two states causes either loss or gain in protein stability. Removal of hydrogen

Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

Energy Technology Data Exchange (ETDEWEB)

Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

2012-12-15

We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

In situ ultra-small-angle X-ray scattering study under uniaxial stretching of colloidal crystals prepared by silica nanoparticles bearing hydrogen-bonding polymer grafts

Directory of Open Access Journals (Sweden)

Ryohei Ishige

2016-05-01

Full Text Available A molded film of single-component polymer-grafted nanoparticles (SPNP, consisting of a spherical silica core and densely grafted polymer chains bearing hydrogen-bonding side groups capable of physical crosslinking, was investigated by in situ ultra-small-angle X-ray scattering (USAXS measurement during a uniaxial stretching process. Static USAXS revealed that the molded SPNP formed a highly oriented twinned face-centered cubic (f.c.c. lattice structure with the [11−1] plane aligned nearly parallel to the film surface in the initial state. Structural analysis of in situ USAXS using a model of uniaxial deformation induced by rearrangement of the nanoparticles revealed that the f.c.c. lattice was distorted in the stretching direction in proportion to the macroscopic strain until the strain reached 35%, and subsequently changed into other f.c.c. lattices with different orientations. The lattice distortion and structural transition behavior corresponded well to the elastic and plastic deformation regimes, respectively, observed in the stress–strain curve. The attractive interaction of the hydrogen bond is considered to form only at the top surface of the shell and then plays an effective role in cross-linking between nanoparticles. The rearrangement mechanism of the nanoparticles is well accounted for by a strong repulsive interaction between the densely grafted polymer shells of neighboring particles.

Gas phase detection of the NH-P hydrogen bond and importance of secondary interactions

DEFF Research Database (Denmark)

Møller, Kristian Holten; Hansen, Anne Schou; Kjærgaard, Henrik Grum

2015-01-01

bond compared to secondary interactions. We find that B3LYP favors the hydrogen bond and M06-2X favors the secondary interactions leading to under- and overestimation, respectively, of the hydrogen bond angle relative to a DF-LCCSD(T)-F12a calculated angle. The remaining functionals tested, B3LYP-D3, B......3LYP-D3BJ, CAM-B3LYP, and ωB97X-D, as well as MP2, show comparable contributions from the hydrogen bond and the secondary interactions and are close to DF-LCCSD(T)-F12a results....

Verification of anti-fatigue effect of anserine by angle fatigue indicator based on median frequency changes of electromyograms

Directory of Open Access Journals (Sweden)

Hirohisa Kishi

2013-10-01

Full Text Available ABSTRACT: Objective: Anserine, which is abundant in avian species and in a wide range of fish such as bonito and tuna, is reported to have anti-fatigue effect. Although chicken soup and bonito soup is traditionally used to recover from physical fatigue, it is generally difficult to verify the effect in humans. This study was to directly demonstrate the anti-fatigue effect of oceanic anserine in humans. Methods: Edible-grade anserine was purified from fish extract with food-grade reagents. Subjects were 17 healthy male volunteers (35.5 ± 5 yr., 75.5 ± 5.0 kg. Each subject performed the isometric exercise tolerance test (ETT on the rectus femoris muscle twice (Ex_1, Ex_2 both for anserine and water conditions on a different day. Median frequency changes (MDF during Functional Foods in Health and Disease 2013; 3(10 389-399 ETTs were calculated and regression curves were calculated over a frequency range of 21-214 Hz. The difference, or angle, between the slopes of Ex_1 and Ex_2 MDF regression curves, which corresponds to the degree of fatigue, was defined as an angle fatigue index and compared between anserine and water intake conditions. Results: MDF decreased during ETTs in most patients and the slopes of regression curves were larger in Ex_2 than in Ex_1. Angle fatigue index for water (control was significantly larger than that for anserine (p<0.01, paired t-test, n=17. The result indicates that anserine have an anti-fatigue effect on skeletal muscle in humans. Conclusions: We proposed the angle fatigue index as a touchstone of the muscle fatigue. The index indicates that anserine is effective to reduce the muscle fatigue in humans.

Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed by Neutron Crystallography

Energy Technology Data Exchange (ETDEWEB)

Gerlits, Oksana O. [UT/ORNL; Coates, Leighton [Biology; Woods, Robert J. [Complex; Kovalevsky, Andrey [Biology

2017-08-30

Plant lectins are carbohydrate-binding proteins with various biomedical applications. Concanavalin A (Con A) holds promise in treating cancerous tumors. To better understand the Con A carbohydrate binding specificity, we obtained a room-temperature neutron structure of this legume lectin in complex with a disaccharide Manα1–2Man, mannobiose. The neutron structure afforded direct visualization of the hydrogen bonding between the protein and ligand, showing that the ligand is able to alter both protonation states and interactions for residues located close to and distant from the binding site. An unprecedented low-barrier hydrogen bond was observed forming between the carboxylic side chains of Asp28 and Glu8, with the D atom positioned equidistant from the oxygen atoms having an O···D···O angle of 101.5°.

Pulsed-High Field/High-Frequency EPR Spectroscopy

Science.gov (United States)

Fuhs, Michael; Moebius, Klaus

Pulsed high-field/high-frequency electron paramagnetic resonance (EPR) spectroscopy is used to disentangle many kinds of different effects often obscured in continuous wave (cw) EPR spectra at lower magnetic fields/microwave frequencies. While the high magnetic field increases the resolution of G tensors and of nuclear Larmor frequencies, the high frequencies allow for higher time resolution for molecular dynamics as well as for transient paramagnetic intermediates studied with time-resolved EPR. Pulsed EPR methods are used for example for relaxation-time studies, and pulsed Electron Nuclear DOuble Resonance (ENDOR) is used to resolve unresolved hyperfine structure hidden in inhomogeneous linewidths. In the present article we introduce the basic concepts and selected applications to structure and mobility studies on electron transfer systems, reaction centers of photosynthesis as well as biomimetic models. The article concludes with an introduction to stochastic EPR which makes use of an other concept for investigating resonance systems in order to increase the excitation bandwidth of pulsed EPR. The limited excitation bandwidth of pulses at high frequency is one of the main limitations which, so far, made Fourier transform methods hardly feasible.

The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.

Science.gov (United States)

Zhou, Alice Qinhua; O'Hern, Corey S; Regan, Lynne

2012-05-16

The energy functions used to predict protein structures typically include both molecular-mechanics and knowledge-based terms. In contrast, our approach is to develop robust physics- and geometry-based methods. Here, we investigate to what extent simple hard-sphere models can be used to predict side-chain conformations. The distributions of the side-chain dihedral angle χ(1) of Val and Thr in proteins of known structure show distinctive features: Val side chains predominantly adopt χ(1) = 180°, whereas Thr side chains typically adopt χ(1) = 60° and 300° (i.e., χ(1) = ±60° or g- and g(+) configurations). Several hypotheses have been proposed to explain these differences, including interresidue steric clashes and hydrogen-bonding interactions. In contrast, we show that the observed side-chain dihedral angle distributions for both Val and Thr can be explained using only local steric interactions in a dipeptide mimetic. Our results emphasize the power of simple physical approaches and their importance for future advances in protein engineering and design. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Experimental investigation of bond strength under high loading rates

Directory of Open Access Journals (Sweden)

Michal Mathias

2015-01-01

Full Text Available The structural behaviour of reinforced concrete is governed significantly by the transmission of forces between steel and concrete. The bond is of special importance for the overlapping joint and anchoring of the reinforcement, where rigid bond is required. It also plays an important role in the rotational capacity of plastic hinges, where a ductile bond behaviour is preferable. Similar to the mechanical properties of concrete and steel also the characteristics of their interaction changes with the velocity of the applied loading. For smooth steel bars with its main bond mechanisms of adhesion and friction, nearly no influence of loading rate is reported in literature. In contrast, a high rate dependence can be found for the nowadays mainly used deformed bars. For mechanical interlock, where ribs of the reinforcing steel are bracing concrete material surrounding the bar, one reason can be assumed to be in direct connection with the increase of concrete compressive strength. For splitting failure of bond, characterized by the concrete tensile strength, an even higher dynamic increase is observed. For the design of Structures exposed to blast or impact loading the knowledge of a rate dependent bond stress-slip relationship is required to consider safety and economical aspects at the same time. The bond behaviour of reinforced concrete has been investigated with different experimental methods at the University of the Bundeswehr Munich (UniBw and the Joint Research Centre (JRC in Ispra. Both static and dynamic tests have been carried out, where innovative experimental apparatuses have been used. The bond stress-slip relationship and maximum pull-out-forces for varying diameter of the bar, concrete compressive strength and loading rates have been obtained. It is expected that these experimental results will contribute to a better understanding of the rate dependent bond behaviour and will serve for calibration of numerical models.

Crystallochemistry of rhenium compounds with metal-metal bonds

International Nuclear Information System (INIS)

Koz'min, P.A.; Surazhskaya, M.D.

1980-01-01

A review is presented including a brief description of atomic structure of 59 coordination rhenium compounds with metal-metal bond. The most important bond lengths and valent angles are presented for each compound. The dependence of rhenium-rhenium bond length on its multiplicity is discussed and possible causes of deviations from this dependence (namely, axial ligand presence, steric repulsion of ligands) are considered. On the basis of qualitative comparison of electronegativity of ligands in dimer compounds with quarternary bond of rhenium-rhenium a supposition is made on the influence of formal charge of atomic group and summary electro-negativity of ligands on the possibility of the metal-metal bond formation

Amino Acid Patterns around Disulfide Bonds

Directory of Open Access Journals (Sweden)

Brett Drury

2010-11-01

Full Text Available Disulfide bonds provide an inexhaustible source of information on molecular evolution and biological specificity. In this work, we described the amino acid composition around disulfide bonds in a set of disulfide-rich proteins using appropriate descriptors, based on ANOVA (for all twenty natural amino acids or classes of amino acids clustered according to their chemical similarities and Scheffé (for the disulfide-rich proteins superfamilies statistics. We found that weakly hydrophilic and aromatic amino acids are quite abundant in the regions around disulfide bonds, contrary to aliphatic and hydrophobic amino acids. The density distributions (as a function of the distance to the center of the disulfide bonds for all defined entities presented an overall unimodal behavior: the densities are null at short distances, have maxima at intermediate distances and decrease for long distances. In the end, the amino acid environment around the disulfide bonds was found to be different for different superfamilies, allowing the clustering of proteins in a biologically relevant way, suggesting that this type of chemical information might be used as a tool to assess the relationship between very divergent sets of disulfide-rich proteins.

Coplanar stripline components for high frequency application

Science.gov (United States)

Goverdhanam, Kavita; Simons, Rainee N.; Dib, Nihad; Katehi, Linda P. B.

1996-01-01

In this paper, coplanar stripline discontinuities such as a slit, a right angle bend and a T-junction are characterized and their performance is parameterized with respect to frequency and geometry. Lumped equivalent circuits are presented for some of them. The element values are obtained from the measured discontinuity scattering (S) parameters. The experimental results are compared with theoretical data obtained using the Finite Difference Time Domain (FD-TD) technique for validation and show very good agreement.

X-ray-absorption fine structure determination of pressure-induced bond-angle changes in ReO3

International Nuclear Information System (INIS)

Houser, B.; Ingalls, R.

2000-01-01

We report here on a Marquardt-type method to fit the x-ray absorption fine structure (XAFS) of ReO 3 . We find that, when the ambient-pressure structure of ReO 3 is used as a starting point, the pressure dependence of the angle of the Re-O-Re bond in ReO 3 is fairly straightforwardly and robustly determined using FEFF curved-wave, multiple-scattering programs and is accurate to about ±1.5 degree sign or better. We present an argument that XAFS and scattering experiments fundamentally differ in what they measure in the case of nearly linear atomic bridges. Focussed multiple-scattering paths involving the Re-O-Re bridge make a contribution to the XAFS spectrum that is sensitive to the rms deviation of oxygen from the [100]-type directions. Fits to simulated spectra back up our contention that for XAFS experiments the effective position of the oxygen atom is its rms displacement whether the average displacement is zero or not. (c) 2000 The American Physical Society

High-frequency instabilities of stationary crossflow vortices in a hypersonic boundary layer

Science.gov (United States)

Li, Fei; Choudhari, Meelan; Paredes, Pedro; Duan, Lian

2016-09-01

Hypersonic boundary layer flows over a circular cone at moderate incidence angle can support strong crossflow instability in between the windward and leeward rays on the plane of symmetry. Due to more efficient excitation of stationary crossflow vortices by surface roughness, such boundary layer flows may transition to turbulence via rapid amplification of the high-frequency secondary instabilities of finite-amplitude stationary crossflow vortices. The amplification characteristics of these secondary instabilities are investigated for crossflow vortices generated by an azimuthally periodic array of roughness elements over a 7° half-angle circular cone in a Mach 6 free stream. The analysis is based on both quasiparallel stability theory in the form of a partial-differential-equation-based eigenvalue analysis and plane marching parabolized stability equations that account for the effects of the nonparallel basic state on the growth of secondary disturbances. Depending on the local amplitude of the stationary crossflow mode, the most unstable high-frequency disturbances either originate from the second (i.e., Mack) mode instabilities of the unperturbed boundary layer or correspond to genuine secondary instabilities that reduce to stable disturbances at sufficiently small amplitudes of the stationary crossflow vortex. The predicted frequencies of the dominant secondary disturbances of either type are similar to those measured during wind tunnel experiments at Purdue University and the Technical University of Braunschweig, Germany. Including transverse surface curvature within the quasiparallel predictions does not alter the topology of the unstable modes; however, the resulting changes in both mode shape and disturbance growth rate are rather significant and curvature can be either stabilizing or destabilizing depending on the disturbance frequency and mode type. Nonparallel effects are shown to be strongly destabilizing for secondary instabilities originating from

Effect of pressure on the solution structure and hydrogen bond properties of aqueous N-methylacetamide

International Nuclear Information System (INIS)

Sarma, Rahul; Paul, Sandip

2012-01-01

Highlights: ► NMA molecules are associated mostly through their hydrophobic methyl groups. ► High pressure reduces association propensity causing dispersion of these moieties. ► Orientational polarization of vicinal water molecules near O and H atoms of NMA. ► NMA prefers to be a H-bond acceptor rather than a donor in interaction with water. ► Energy of these hydrogen bonds reduces slightly at high pressure. -- Abstract: Effects of high pressure on hydrophobic and hydrogen bonding interactions are investigated by employing molecular dynamics (MD) simulations of aqueous N-methylacetamide (NMA) solutions. Such systems are of interest mainly because high pressure causes protein denaturation and NMA is a computationally effective model to understand the atomic-level picture of pressure-induced structural transitions of protein. Simulations are performed for five different pressure values ranging from 1 atm to 8000 atm. We find that NMA molecules are associated mostly through their hydrophobic methyl groups and high pressure reduces this association propensity, causing dispersion of these moieties. At high pressure, structural void decreases and the packing efficiency of water molecules around NMA molecules increases. Hydrogen bond properties calculations show favorable NMA–NMA hydrogen bonds as compared to those of NMA–water hydrogen bonds and preference of NMA to be a hydrogen bond acceptor rather than a donor in interaction with water.

BOA valence bonding with f-character in highly coordinated actinides

International Nuclear Information System (INIS)

Carter, F.L.

1979-01-01

The addition of f character to bidirectional orbitals enhances their flexibility significantly. The resultant Cf and Gf orbitals are applied to some common high coordinations of the actinides. The valence bond approach implies d and f orbital radial splitting into bonding hybrids and either contracted localized or extended supra-valent d and f orbitals

75 FR 81284 - Nationwide Use of High Frequency and Ultra High Frequency Active SONAR Technology; Draft...

Science.gov (United States)

2010-12-27

... Frequency and Ultra High Frequency Active SONAR Technology; Draft Programmatic Environmental Assessment and... Programmatic Environmental Assessment (PEA) for the Nationwide Use of High Frequency (HF) and Ultra High... potential impacts of each alternative on the human and natural environments. DATES: Comments and related...

Accounting for thermodynamic non-ideality in the Guinier region of small-angle scattering data of proteins.

Science.gov (United States)

Scott, David J

2016-12-01

Hydrodynamic studies of the solution properties of proteins and other biological macromolecules are often hard to interpret when the sample is present at a reasonably concentrated solution. The reason for this is that solutions exhibit deviations from ideal behaviour which is manifested as thermodynamic non-ideality. The range of concentrations at which this behaviour typically is exhibited is as low as 1-2 mg/ml, well within the range of concentrations used for their analysis by techniques such as small-angle scattering. Here we discuss thermodynamic non-ideality used previously used in the context of light scattering and sedimentation equilibrium analytical ultracentrifugation and apply it to the Guinier region of small-angle scattering data. The results show that there is a complementarity between the radially averaged structure factor derived from small-angle X-ray scattering/small-angle neutron scattering studies and the second virial coefficient derived from sedimentation equilibrium analytical ultracentrifugation experiments.

Stimulation of Protein Expression Through the Harmonic Resonance of Frequency-Specific Music.

Science.gov (United States)

Orhan, Ibrahim Y; Gulbahar, Burak A

2016-12-01

The use of specific frequencies for specific individual amino acids may increase the potential energy of protein molecules in the medium [1]. The resonance would also increase the movement of particles in the cytosol, increasing the collisions necessary for the conduction of protein expression. The clash of two waves that share frequencies will exhibit an increase in energy through an increase in amplitude [2]. The increase in energy would in turn increase the number of collisions forming the tRNA-amino acid, increasing the amino acid acquiry for ribosomes to improve intracellular efficiency in gene expression. To test the hypothesis, Red Fluorescent Protein (RFP) in transformated BL-21 strains of E. coli and p53 protein of MCF-7 were examined after exposure to sounds of specific frequencies. Through the exposure of the experimental systems to a sequence of sounds that match the frequencies of specific amino acids, the levels of RFP exhibition respective to the control groups in the bacterial medium increased two-fold in terms of RFU. The experiments that targeted the p53 protein with the 'music' showed a decrease in the cell prevalence in the MCF-7 type breast cancer cells by 28%, by decreasing the speed of tumour formation. Exposure to 'music' that was designed through assigning a musical note for every single one of the twenty unique amino acids, produced both an analytical and a visible shift in protein synthesis, making it as potential tool for reducing procedural time uptake.

Limits to Arbitrage in Sovereign Bonds Price and Liquidity Discovery in High Frequency Quote Driven Markets

DEFF Research Database (Denmark)

Pelizzon, Loriana; Subrahmanyam, Marti G.; Tomio, Davide

The progressively stronger linkages across markets, due to faster access to information and trade execution, cause market liquidity to be rapidly transmitted across markets. In contrast to the resultant commonality of liquidity across markets that are affected by common market-wide factors...... between markets, and liquidity discovery, the transmission of liquidity shocks, through changes in the quotes posted by market makers and the reactions of arbitrageurs. Our analysis is in the context of the Italian sovereign bond cash and future markets, during the recent Euro-zone sovereign bond crisis...... discovery, the cash market leads the futures market in liquidity discovery, i.e., the willingness of the market makers to trade (measured by market depth as the key liquidity measure). More specifically, the liquidity in the cash market also has a significant impact on the changes in the basis (and...

Aggregation of bovine serum albumin upon cleavage of its disulfide bonds, studied by the time-resolved small-angle X-ray scattering technique with synchrotron radiation

Energy Technology Data Exchange (ETDEWEB)

Ueki, Tatzuo; Inoko, Yoji; Hiragi, Yuzuru; Kataoka, Mikio; Amemiya, Yoshiyuki; Izumi, Yoshinobu; Tagawa, Hiroyuki; Muroga, Yoshio

1985-11-01

A rapid mixing system of the stopped-flow type, used with small-angle X-ray scattering equipment using synchrotron radiation, is described. The process of aggregation of bovine serum albumin was traced with a time interval of 50s, initiated upon cleavage of its disulfide bonds by reduction with dithiothreitol. The results indicate that a 218-fold molar excess of dithiothreitol over the number of moles of disulfide bonds in bovine serum albumin is sufficient to initiate the reaction immediately after mixing, which reaches equilibrium in about 15 min. On the other hand, half this amount is not sufficient to initiate the reaction, so that the reaction is delayed by about 150s. Such a single-shot time-resolved experiment showed that experiments with a time interval of 100 ms are possible with repeated multi-shot runs. 26 refs.; 8 figs.

Aggregation of bovine serum albumin upon cleavage of its disulfide bonds, studied by the time-resolved small-angle X-ray scattering technique with synchrotron radiation

International Nuclear Information System (INIS)

Ueki, Tatzuo; Inoko, Yoji; Izumi, Yoshinobu; Tagawa, Hiroyuki; Muroga, Yoshio

1985-01-01

A rapid mixing system of the stopped-flow type, used with small-angle X-ray scattering equipment using synchrotron radiation, is described. The process of aggregation of bovine serum albumin was traced with a time interval of 50 s, initiated upon cleavage of its disulfide bonds by reduction with dithiothreitol. The results indicate that a 218-fold molar excess of dithiothreitol over the number of moles of disulfide bonds in bovine serum albumin is sufficient to initiate the reaction immediately after mixing, which reaches equilibrium in about 15 min. On the other hand, half this amount is not sufficient to initiate the reaction, so that the reaction is delayed by about 150 s. Such a single-shot time-resolved experiment showed that experiments with a time interval of 100 ms are possible with repeated multi-shot runs. (Auth.)

Artificial membranes with selective nanochannels for protein transport

KAUST Repository

Sutisna, Burhannudin

2016-09-05

A poly(styrene-b-tert-butoxystyrene-b-styrene) copolymer was synthesized by anionic polymerization and hydrolyzed to poly(styrene-b-4-hydroxystyrene-b-styrene). Lamellar morphology was confirmed in the bulk after annealing. Membranes were fabricated by self-assembly of the hydrolyzed copolymer in solution, followed by water induced phase separation. A high density of pores of 4 to 5 nm diameter led to a water permeance of 40 L m−2 h−1 bar−1 and molecular weight cut-off around 8 kg mol−1. The morphology was controlled by tuning the polymer concentration, evaporation time, and the addition of imidazole and pyridine to stabilize the terpolymer micelles in the casting solution via hydrogen bond complexes. Transmission electron microscopy of the membrane cross-sections confirmed the formation of channels with hydroxyl groups beneficial for hydrogen-bond forming sites. The morphology evolution was investigated by time-resolved grazing incidence small angle X-ray scattering experiments. The membrane channels reject polyethylene glycol with a molecular size of 10 kg mol−1, but are permeable to proteins, such as lysozyme (14.3 kg mol−1) and cytochrome c (12.4 kg mol−1), due to the right balance of hydrogen bond interactions along the channels, electrostatic attraction, as well as the right pore sizes. Our results demonstrate that artificial channels can be designed for protein transport via block copolymer self-assembly using classical methods of membrane preparation.

Artificial membranes with selective nanochannels for protein transport

KAUST Repository

Sutisna, Burhannudin; Polymeropoulos, Georgios; Mygiakis, E.; Musteata, Valentina-Elena; Peinemann, Klaus-Viktor; Smilgies, D. M.; Hadjichristidis, Nikolaos; Nunes, Suzana Pereira

2016-01-01

A poly(styrene-b-tert-butoxystyrene-b-styrene) copolymer was synthesized by anionic polymerization and hydrolyzed to poly(styrene-b-4-hydroxystyrene-b-styrene). Lamellar morphology was confirmed in the bulk after annealing. Membranes were fabricated by self-assembly of the hydrolyzed copolymer in solution, followed by water induced phase separation. A high density of pores of 4 to 5 nm diameter led to a water permeance of 40 L m−2 h−1 bar−1 and molecular weight cut-off around 8 kg mol−1. The morphology was controlled by tuning the polymer concentration, evaporation time, and the addition of imidazole and pyridine to stabilize the terpolymer micelles in the casting solution via hydrogen bond complexes. Transmission electron microscopy of the membrane cross-sections confirmed the formation of channels with hydroxyl groups beneficial for hydrogen-bond forming sites. The morphology evolution was investigated by time-resolved grazing incidence small angle X-ray scattering experiments. The membrane channels reject polyethylene glycol with a molecular size of 10 kg mol−1, but are permeable to proteins, such as lysozyme (14.3 kg mol−1) and cytochrome c (12.4 kg mol−1), due to the right balance of hydrogen bond interactions along the channels, electrostatic attraction, as well as the right pore sizes. Our results demonstrate that artificial channels can be designed for protein transport via block copolymer self-assembly using classical methods of membrane preparation.

Structural investigation of ribonuclease A conformational preferences using high pressure protein crystallography

Energy Technology Data Exchange (ETDEWEB)

Kurpiewska, Katarzyna, E-mail: kurpiews@chemia.uj.edu.pl [Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Protein Crystallography Group, Ingardena 3, 30-060 Kraków (Poland); Dziubek, Kamil; Katrusiak, Andrzej [Adam Mickiewicz University, Faculty of Chemistry, Department of Materials Chemistry, Umultowska 89b, 61-61 Poznań (Poland); Font, Josep [School of Medical Science, University of Sydney, NSW 2006 (Australia); Ribò, Marc; Vilanova, Maria [Universitat de Girona, Laboratorid’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Campus de Montilivi, 17071 Girona (Spain); Lewiński, Krzysztof [Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Protein Crystallography Group, Ingardena 3, 30-060 Kraków (Poland)

2016-04-01

Highlights: • A unique crystallographic studies of wild-type and mutated form of the same protein under high pressure. • Compressibility of RNase A molecule is significantly affected by a single amino acid substitution. • High pressure protein crystallography helps understanding protein flexibility and identify conformational substrates. - Abstract: Hydrostatic pressure in range 0.1–1.5 GPa is used to modify biological system behaviour mostly in biophysical studies of proteins in solution. Due to specific influence on the system equilibrium high pressure can act as a filter that enables to identify and investigate higher energy protein conformers. The idea of the presented experiments is to examine the behaviour of RNase A molecule under high pressure before and after introduction of destabilizing mutation. For the first time crystal structures of wild-type bovine pancreatic ribonuclease A and its markedly less stable variant modified at position Ile106 were determined at different pressures. X-ray diffraction experiments at high pressure showed that the secondary structure of RNase A is well preserved even beyond 0.67 GPa at room temperature. Detailed structural analysis of ribonuclease A conformation observed under high pressure revealed that pressure influences hydrogen bonds pattern, cavity size and packing of molecule.

Structural investigation of ribonuclease A conformational preferences using high pressure protein crystallography

International Nuclear Information System (INIS)

Kurpiewska, Katarzyna; Dziubek, Kamil; Katrusiak, Andrzej; Font, Josep; Ribò, Marc; Vilanova, Maria; Lewiński, Krzysztof

2016-01-01

Highlights: • A unique crystallographic studies of wild-type and mutated form of the same protein under high pressure. • Compressibility of RNase A molecule is significantly affected by a single amino acid substitution. • High pressure protein crystallography helps understanding protein flexibility and identify conformational substrates. - Abstract: Hydrostatic pressure in range 0.1–1.5 GPa is used to modify biological system behaviour mostly in biophysical studies of proteins in solution. Due to specific influence on the system equilibrium high pressure can act as a filter that enables to identify and investigate higher energy protein conformers. The idea of the presented experiments is to examine the behaviour of RNase A molecule under high pressure before and after introduction of destabilizing mutation. For the first time crystal structures of wild-type bovine pancreatic ribonuclease A and its markedly less stable variant modified at position Ile106 were determined at different pressures. X-ray diffraction experiments at high pressure showed that the secondary structure of RNase A is well preserved even beyond 0.67 GPa at room temperature. Detailed structural analysis of ribonuclease A conformation observed under high pressure revealed that pressure influences hydrogen bonds pattern, cavity size and packing of molecule.

Small angle X-ray scattering and transmission electron microscopy study of the Lactobacillus brevis S-layer protein

Energy Technology Data Exchange (ETDEWEB)

Jaeaeskelaeinen, Pentti [Department of Biomedical Engineering and Computational Science, PO Box 2200, FI-02015 Aalto University School of Science and Technology (Finland); Engelhardt, Peter [Haartman Institute, Department of Pathology, PO Box 21, FIN-00014 University of Helsinki (Finland); Hynoenen, Ulla; Palva, Airi [Department of Basic Veterinary Sciences, Division of Microbiology, FIN-00014 University of Helsinki (Finland); Torkkeli, Mika; Serimaa, Ritva, E-mail: ritva.serimaa@helsinki.f [Department of Physics, POB 64, 00014 University of Helsinki (Finland)

2010-10-01

The structure of self-assembly domain containing recombinant truncation mutants of Lactobacillus brevis surface layer protein SlpA in aqueous solution was studied using small-angle X-ray scattering and transmission electron microscopy. The proteins were found out to interact with each other forming stable globular oligomers of about 10 monomers. The maximum diameter of the oligomers varied between 75 A and 435 A.

Protection of MOS capacitors during anodic bonding

Science.gov (United States)

Schjølberg-Henriksen, K.; Plaza, J. A.; Rafí, J. M.; Esteve, J.; Campabadal, F.; Santander, J.; Jensen, G. U.; Hanneborg, A.

2002-07-01

We have investigated the electrical damage by anodic bonding on CMOS-quality gate oxide and methods to prevent this damage. n-type and p-type MOS capacitors were characterized by quasi-static and high-frequency CV-curves before and after anodic bonding. Capacitors that were bonded to a Pyrex wafer with 10 μm deep cavities enclosing the capacitors exhibited increased leakage current and interface trap density after bonding. Two different methods were successful in protecting the capacitors from such damage. Our first approach was to increase the cavity depth from 10 μm to 50 μm, thus reducing the electric field across the gate oxide during bonding from approximately 2 × 105 V cm-1 to 4 × 104 V cm-1. The second protection method was to coat the inside of a 10 μm deep Pyrex glass cavity with aluminium, forming a Faraday cage that removed the electric field across the cavity during anodic bonding. Both methods resulted in capacitors with decreased interface trap density and unchanged leakage current after bonding. No change in effective oxide charge or mobile ion contamination was observed on any of the capacitors in the study.

Accurate Angle Estimator for High-Frame-rate 2-D Vector Flow Imaging

DEFF Research Database (Denmark)

Villagómez Hoyos, Carlos Armando; Stuart, Matthias Bo; Lindskov Hansen, Kristoffer

2016-01-01

This paper presents a novel approach for estimating 2-D flow angles using a high-frame-rate ultrasound method. The angle estimator features high accuracy and low standard deviation (SD) over the full 360° range. The method is validated on Field II simulations and phantom measurements using...

Ester carbonyl vibration as a sensitive probe of protein local electric field.

Science.gov (United States)

Pazos, Ileana M; Ghosh, Ayanjeet; Tucker, Matthew J; Gai, Feng

2014-06-10

The ability to quantify the local electrostatic environment of proteins and protein/peptide assemblies is key to gaining a microscopic understanding of many biological interactions and processes. Herein, we show that the ester carbonyl stretching vibration of two non-natural amino acids, L-aspartic acid 4-methyl ester and L-glutamic acid 5-methyl ester, is a convenient and sensitive probe in this regard, since its frequency correlates linearly with the local electrostatic field for both hydrogen-bonding and non-hydrogen-bonding environments. We expect that the resultant frequency-electric-field map will find use in various applications. Furthermore, we show that, when situated in a non-hydrogen-bonding environment, this probe can also be used to measure the local dielectric constant (ε). For example, its application to amyloid fibrils formed by Aβ(16-22) revealed that the interior of such β-sheet assemblies has an ε value of approximately 5.6. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development and implementation of an empirical frequency map for use in MD simulations of isotope-edited proteins, and, Development, implementation, and evaluation of an online student portal as a textbook replacement in an advanced general chemistry course

Science.gov (United States)

Shorb, Justin Matthew

The first portion of this thesis describes an extension of work done in the Skinner group to develop an empirical frequency map for N-methylacetamide (NMA) in water. NMA is a peptide bond capped on either side by a methyl group and is therefore a common prototypical molecule used when studying complicated polypeptides and proteins. This amide bond is present along the backbone of every protein as it connects individual component amino acids. This amide bond also has a strong observable frequency in the IR due to the Amide-I mode (predominantly carbon-oxygen stretching motion). This project describes the simplification of the prior model for mapping the frequency of the Amide-I mode from the electric field due to the environment and develops a parallel implementation of this algorithm for use in larger biological systems, such as the trans-membrane portion of the tetrameric polypeptide bundle protein CD3zeta. The second portion of this thesis describes the development, implementation and evaluation of an online textbook within the context of a cohesive theoretical framework. The project begins by describing what is meant when discussing a digital textbook, including a survey of various types of digital media being used to deliver textbook-like content. This leads into the development of a theoretical framework based on constructivist pedagogical theory, hypertext learning theory, and chemistry visualization and representation frameworks. The implementation and design of ChemPaths, the general chemistry online text developed within the Chemistry Education Digital Library (ChemEd DL) is then described. The effectiveness of ChemPaths being used as a textbook replacement in an advanced general chemistry course is evaluated within the developed theoretical framework both qualitatively and quantitatively.

High frequency energy measurements

International Nuclear Information System (INIS)

Stotlar, S.C.

1981-01-01

High-frequency (> 100 MHz) energy measurements present special problems to the experimenter. Environment or available electronics often limit the applicability of a given detector type. The physical properties of many detectors are frequency dependent and in some cases, the physical effect employed can be frequency dependent. State-of-the-art measurements generally involve a detection scheme in association with high-speed electronics and a method of data recording. Events can be single or repetitive shot requiring real time, sampling, or digitizing data recording. Potential modification of the pulse by the detector and the associated electronics should not be overlooked. This presentation will review typical applications, methods of choosing a detector, and high-speed detectors. Special considerations and limitations of some applications and devices will be described

Acousto-ultrasonic evaluation of adhesively bonded CFRP-aluminum joints

International Nuclear Information System (INIS)

Lee, Seung Hwan; Kwon, Oh Yang

1997-01-01

Correlation between the amount of artificial defects in bonded region and the acousto-ultrasonic parameters(AUPs) including signal amplitude and then the static strength of adhesively bonded joints of carbon fiber reinforced plastic(CFRP) laminates and Al6061 plates has been investigated. The effect of the frequency content and the bandwidth of input signals were studied using 200 kHz, 650 kHz, 1 MHz, 2 MHz pulses and 1 MHz tone-burst signals. With increasing fraction of defects, the signal amplitude and AUP1 were decreased whereas AUP2 was increased. This result has been attributed to the energy transfer characteristics of bonded joints with delamination-type defects and the change of spectral content due to the defects. Considering the nature of high attenuation, a pulse signal with major frequency content at the third harmonic of thickness mode resonance, 650 kHz for the dimension of specimens used in this study, has been found optimal for acousto-ultrasonic testing of CFRP-aluminum joints.

Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

International Nuclear Information System (INIS)

Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

2004-01-01

A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

Effect of high-frequency excitation on natural frequencies of spinning discs

DEFF Research Database (Denmark)

Hansen, Morten Hartvig

2000-01-01

The effect of high-frequency, non-resonant parametric excitation on the low-frequency response of spinning discs is considered. The parametric excitation is obtained through a non-constant rotation speed, where the frequency of the pulsating overlay is much higher than the lowest natural frequenc......The effect of high-frequency, non-resonant parametric excitation on the low-frequency response of spinning discs is considered. The parametric excitation is obtained through a non-constant rotation speed, where the frequency of the pulsating overlay is much higher than the lowest natural...

Investigation of energy losses in low-coercivity resin-bonded magnets in alternating magnetic fields

Science.gov (United States)

Milov, E. V.; Sipin, I. A.; Milov, V. N.; Andreenko, A. S.; Balan, I. A.

2017-01-01

Energy losses during alternating remagnetization of low-coercitivity resin-bonded magnets and commercially produced electrical steels were studied experimentally. The studies were conducted on several samples of resin-bonded magnets with different manufacturing technologies and samples of electrical steel sheets of various thicknesses. The static and dynamic magnetic properties of the samples were measured on a vibration magnetometer and a specially designed apparatus, respectively. It was found that the studied samples of bonded magnets have a relatively high level of hysteresis losses associated with high coercivity, which reaches a value of 4-5 Oe. At the same time, the remagnetization losses due to the Foucault currents in the bonded magnets are considerably lower than in electrical steels. The measurement results show that bonded magnets at high frequencies of remagnetization, especially in high-rpm motors, can be competitive in comparison with electrical steels.

Crystallographic Studies Evidencing the High Energy Tolerance to Disrupting the Interface Disulfide Bond of Thioredoxin 1 from White Leg Shrimp Litopenaeus vannamei

Directory of Open Access Journals (Sweden)

Adam A. Campos-Acevedo

2014-12-01

Full Text Available Thioredoxin (Trx is a small 12-kDa redox protein that catalyzes the reduction of disulfide bonds in proteins from different biological systems. A recent study of the crystal structure of white leg shrimp thioredoxin 1 from Litopenaeus vannamei (LvTrx revealed a dimeric form of the protein mediated by a covalent link through a disulfide bond between Cys73 from each monomer. In the present study, X-ray-induced damage in the catalytic and the interface disulfide bond of LvTrx was studied at atomic resolution at different transmission energies of 8% and 27%, 12.8 keV at 100 K in the beamline I-24 at Diamond Light Source. We found that at an absorbed dose of 32 MGy, the X-ray induces the cleavage of the disulfide bond of each catalytic site; however, the interface disulfide bond was cleaved at an X-ray adsorbed dose of 85 MGy; despite being the most solvent-exposed disulfide bond in LvTrx (~50 Å2. This result clearly established that the interface disulfide bond is very stable and, therefore, less susceptible to being reduced by X-rays. In fact, these studies open the possibility of the existence in solution of a dimeric LvTrx.

Crystallographic studies evidencing the high energy tolerance to disrupting the interface disulfide bond of thioredoxin 1 from white leg shrimp Litopenaeus vannamei.

Science.gov (United States)

Campos-Acevedo, Adam A; Rudiño-Piñera, Enrique

2014-12-15

Thioredoxin (Trx) is a small 12-kDa redox protein that catalyzes the reduction of disulfide bonds in proteins from different biological systems. A recent study of the crystal structure of white leg shrimp thioredoxin 1 from Litopenaeus vannamei (LvTrx) revealed a dimeric form of the protein mediated by a covalent link through a disulfide bond between Cys73 from each monomer. In the present study, X-ray-induced damage in the catalytic and the interface disulfide bond of LvTrx was studied at atomic resolution at different transmission energies of 8% and 27%, 12.8 keV at 100 K in the beamline I-24 at Diamond Light Source. We found that at an absorbed dose of 32 MGy, the X-ray induces the cleavage of the disulfide bond of each catalytic site; however, the interface disulfide bond was cleaved at an X-ray adsorbed dose of 85 MGy; despite being the most solvent-exposed disulfide bond in LvTrx (~50 Å2). This result clearly established that the interface disulfide bond is very stable and, therefore, less susceptible to being reduced by X-rays. In fact, these studies open the possibility of the existence in solution of a dimeric LvTrx.

Large-angle theory for pion-nucleus scattering at high energies

International Nuclear Information System (INIS)

Hoock, D.W. Jr.

1978-01-01

An approximate solution for high-energy, projectile-nucleus, multiple scattering is developed from the exact Watson series and applied to pion scattering for 12 C and 4 He. Agreement with measured differential cross sections available from the literature for the range 150 to 260 MeV pion laboratory energies is surprisingly good. The approximation method expands the propagators of the Watson series about the transverse component of the momentum transfer. Contributions of each of the first two terms to double scattering from a Gaussian potential are compared to the exact solution. The purely plane-wave propagation produces a scattering amplitude that agrees to order (k 0 a) -1 with the exact solution at the forward and backward directions at high energies. The second (off-axis) propagation term produces an amplitude that is one order smaller at forward angles and two orders smaller at 180 0 than the exact amplitude. At intermediate angles it is of the same order. The general multiple-scattering series is approximated with selection of plane-wave propagation as the fundamental process at large and small angles. This model suggests that a single nucleon accepts most of the momentum transfer for backward scattering. The resulting multiple-scattering formula agrees with the well-known high-energy eikonal theory at small angles and the backward-angle scattering formula of Chen at exactly 180 0 . A lowest-order formula that includes off-axis propagation is also derived. Predicted differential cross sections are found to be sensitive to nucleon motion and binding. For 4 He the effect of the nuclear potential on the pion kinetic energy is also examined and found to produce significant changes in the predicted cross sections

Methacrylate-bonded covalent-organic framework monolithic columns for high performance liquid chromatography.

Science.gov (United States)

Liu, Li-Hua; Yang, Cheng-Xiong; Yan, Xiu-Ping

2017-01-06

Covalent-organic frameworks (COFs) are a newfangled class of intriguing microporous materials. Considering their unique properties, COFs should be promising as packing materials for high performance liquid chromatography (HPLC). However, the irregular shape and sub-micrometer size of COFs synthesized via the traditional methods render the main obstacles for the application of COFs in HPLC. Herein, we report the preparation of methacrylate-bonded COF monolithic columns for HPLC to overcome the above obstacles. The prepared COF bonded monolithic columns not only show good homogeneity and permeability, but also give high column efficiency, good resolution and precision for HPLC separation of small molecules including polycyclic aromatic hydrocarbons, phenols, anilines, nonsteroidal anti-inflammatory drugs and benzothiophenes. Compared with the bare polymer monolithic column, the COF bonded monolithic columns show enhanced hydrophobic, π-π and hydrogen bond interactions in reverse phase HPLC. The results reveal the great potential of COF bonded monoliths for HPLC and COFs in separation sciences. Copyright © 2016 Elsevier B.V. All rights reserved.

Association of fatty acid-binding protein 2 and fat mass and obesity-associated gene polymorphism with primary open-angle glaucoma

Science.gov (United States)

Abbas, Shania; Raza, Syed Tasleem; Chandra, Anu; Singh, Luxmi; Mahdi, Farzana

2017-01-01

PURPOSE: The present study was carried out to investigate the association of fatty acid-binding protein 2 (FABP2) and fat mass and obesity-associated (FTO) gene polymorphism with primary open-angle glaucoma (POAG) cases and controls. MATERIALS AND METHODS: This study includes 122 POAG cases and 112 controls. FABP2 and FTO gene polymorphisms in cases and controls were evaluated by polymerase chain reaction-restriction fragment length polymorphism method. RESULTS: The mean ages were 49.88 ± 12.34 and 53.74 ± 11.87 years in POAG cases and control groups, respectively. The FABP2 gene AA, AT, TT genotype frequencies were 12.90%, 62.40%, 24.80% in POAG cases and 20.60%, 64.70%, 14.70% in healthy controls, respectively. The frequencies of A and T allele in POAG cases were 44.06% and 55.94% as compared to 52.94% and 47.06% in the controls. The FTO gene AA, AT, TT genotype frequencies were 2.00%, 79.20%, 18.80% in cases and 0%, 75.50%, 24.50% in healthy controls, respectively. The frequencies of A and T allele in POAG cases were 41.58% and 58.42% as compared to 37.75% and 62.25% in the controls. No significant difference in the frequencies of FABP2 and FTO genotype was found between POAG cases and controls. CONCLUSION: We could not identify the possible association of FABP2 and FTO gene polymorphism with POAG; however, further studies with larger sample size in different population are require to clarify the role of FABP2 and FTO genes in susceptibility to POAG. PMID:29034152

One-dimensional low spatial frequency LIPSS with rotating orientation on fused silica

Energy Technology Data Exchange (ETDEWEB)

Schwarz, Simon, E-mail: simon.schwarz@h-ab.de; Rung, Stefan; Hellmann, Ralf

2017-07-31

Highlights: • Generation of one-dimensional low spatial frequency LIPSS on transparent material. • Varying the angle of incidence results in a rotation of the one-dimensional LSFL. • Rotation angle of LSFL decreases with increasing the applied fluence. • Orientation of the LSFL is mirror-inverted when reversing the scanning direction. - Abstract: We report on the generation of one-dimensional low spatial frequency LIPSS on transparent material. The influence of the applied laser fluence and angle of incidence on the periodicity, orientation and quality of the one-dimensional low spatial frequency LIPSS is investigated, facilitating the generation of highly uniform LIPSS alongside a line. Most strikingly, however, we observe a previously unreported effect of a pronounced rotation of the one-dimensional low spatial frequency LIPSS for varying angle of incidence upon inclined laser irradiation.

Atmospheric-radiation boundary conditions for high-frequency waves in time-distance helioseismology

Science.gov (United States)

Fournier, D.; Leguèbe, M.; Hanson, C. S.; Gizon, L.; Barucq, H.; Chabassier, J.; Duruflé, M.

2017-12-01

The temporal covariance between seismic waves measured at two locations on the solar surface is the fundamental observable in time-distance helioseismology. Above the acoustic cut-off frequency ( 5.3 mHz), waves are not trapped in the solar interior and the covariance function can be used to probe the upper atmosphere. We wish to implement appropriate radiative boundary conditions for computing the propagation of high-frequency waves in the solar atmosphere. We consider recently developed and published radiative boundary conditions for atmospheres in which sound-speed is constant and density decreases exponentially with radius. We compute the cross-covariance function using a finite element method in spherical geometry and in the frequency domain. The ratio between first- and second-skip amplitudes in the time-distance diagram is used as a diagnostic to compare boundary conditions and to compare with observations. We find that a boundary condition applied 500 km above the photosphere and derived under the approximation of small angles of incidence accurately reproduces the "infinite atmosphere" solution for high-frequency waves. When the radiative boundary condition is applied 2 Mm above the photosphere, we find that the choice of atmospheric model affects the time-distance diagram. In particular, the time-distance diagram exhibits double-ridge structure when using a Vernazza Avrett Loeser atmospheric model.

Geographies of High Frequency Trading

DEFF Research Database (Denmark)

Grindsted, Thomas Skou

2016-01-01

This paper investigates the geographies of high frequency trading. Today shares shift hands within micro seconds, giving rise to a form of financial geographies termed algorithmic capitalism. This notion refers to the different spatio-temporalities produced by high frequency trading, under...... the valuation of time. As high frequency trading accelerates financial markets, the paper examines the spatio-temporalities of automated trading by the ways in which the speed of knowledge exploitation in financial markets is not only of interest, but also the expansion between different temporalities....... The paper demonstrates how the intensification of time-space compression produces radical new dynamics in the financial market and develops information rent in HFT as convertible to a time rent and a spatio-temporal rent. The final section discusses whether high frequency trading only responds to crises...

Study of optical shuttering action in supramolecular hydrogen bonded nematogens

Science.gov (United States)

Kavitha, C.; Pongali Sathya Prabu, N.; Madhu Mohan, M. L. N.

2012-11-01

Supramolecular hydrogen bonded mesogens are formed between p-n-undecyloxy benzoic acid (11BAO) and p-n-alkyl benzoic acids (nBA, where n = 2-8). The isolated mesogens are characterized by distinct techniques in order to appreciate the optical, thermal, electrical, and dielectric properties. The optical tilt angle measurement is studied for all the members of this homologous series and is found to concur with the mean field theory predicted value. An interesting factor to notice is the observation of optical shuttering action in nematic phase of the entire series which privilege these materials to be used as light modulators. Dielectric measurements were carried out and the dispersion curves were discussed in terms of relaxation frequency and activation energies.

Direct, simple derivatization of disulfide bonds in proteins with organic mercury in alkaline medium without any chemical pre-reducing agents

Energy Technology Data Exchange (ETDEWEB)

Campanella, Beatrice; Onor, Massimo [National Research Council of Italy, C.N.R., Istituto di Chimica dei Composti Organo Metallici-ICCOM- UOS Pisa, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy); Ferrari, Carlo [National Research Council of Italy, C.N.R., Istituto Nazionale di Ottica, INO-UOS Pisa, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy); D’Ulivo, Alessandro [National Research Council of Italy, C.N.R., Istituto di Chimica dei Composti Organo Metallici-ICCOM- UOS Pisa, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy); Bramanti, Emilia, E-mail: bramanti@pi.iccom.cnr.it [National Research Council of Italy, C.N.R., Istituto di Chimica dei Composti Organo Metallici-ICCOM- UOS Pisa, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy)

2014-09-16

Highlights: • A simple procedure for the derivatization of proteins disulfide bonds. • Cysteine groups in several proteins derivatised with pHMB in alkaline media. • 75–100% labelling of cysteines in proteins with pHMB. - Abstract: In this work we have studied the derivatization of protein disulfide bonds with p-Hydroxymercurybenzoate (pHMB) in strong alkaline medium without any preliminary reduction. The reaction has been followed by the determination of the protein–pHMB complex using size exclusion chromatography coupled to a microwave/UV mercury oxidation system for the on-line oxidation of free and protein-complexed pHMB and atomic fluorescence spectrometry (SEC–CVG–AFS) detection. The reaction has been optimized by an experimental design using lysozyme as a model protein and applied to several thiolic proteins. The proposed method reports, for the first time, that it is possible to label 75–100% cysteines of proteins and, thus, to determine thiolic proteins without the need of any reducing step to obtain reduced -SH groups before mercury labelling. We obtained a detection limit of 100 nmol L{sup −1} based on a signal-to-noise ratio of 3 for unbound and complexed pHMB, corresponding to a detection limit of proteins ranged between 3 and 360 nmol L{sup −1}, depending on the number of cysteines in the protein sequence.

Direct, simple derivatization of disulfide bonds in proteins with organic mercury in alkaline medium without any chemical pre-reducing agents

International Nuclear Information System (INIS)

Campanella, Beatrice; Onor, Massimo; Ferrari, Carlo; D’Ulivo, Alessandro; Bramanti, Emilia

2014-01-01

Highlights: • A simple procedure for the derivatization of proteins disulfide bonds. • Cysteine groups in several proteins derivatised with pHMB in alkaline media. • 75–100% labelling of cysteines in proteins with pHMB. - Abstract: In this work we have studied the derivatization of protein disulfide bonds with p-Hydroxymercurybenzoate (pHMB) in strong alkaline medium without any preliminary reduction. The reaction has been followed by the determination of the protein–pHMB complex using size exclusion chromatography coupled to a microwave/UV mercury oxidation system for the on-line oxidation of free and protein-complexed pHMB and atomic fluorescence spectrometry (SEC–CVG–AFS) detection. The reaction has been optimized by an experimental design using lysozyme as a model protein and applied to several thiolic proteins. The proposed method reports, for the first time, that it is possible to label 75–100% cysteines of proteins and, thus, to determine thiolic proteins without the need of any reducing step to obtain reduced -SH groups before mercury labelling. We obtained a detection limit of 100 nmol L −1 based on a signal-to-noise ratio of 3 for unbound and complexed pHMB, corresponding to a detection limit of proteins ranged between 3 and 360 nmol L −1 , depending on the number of cysteines in the protein sequence

High-strength high-conductivity Cu-Nb microcomposite sheet fabricated via multiple roll bonding

International Nuclear Information System (INIS)

Jha, S.C.; Delagi, R.G.; Forster, J.A.; Krotz, P.D.

1993-01-01

Copper-niobium microcomposites are a new class of high-strength high-conductivity materials that have attractive properties for room- and elevated-temperature applications. Since Nb has little solid solubility in Cu, addition of Nb to Cu does not affect its conductivity. Copper-niobium microcomposites are melted and cast so that the microstructure of cast Cu-Nb ingots consists of 1- to 10 μm Nb dendrites uniformly distributed within the copper matrix. Extensive wire drawing with a true processing strain (η> 12) of Cu-Nb alloy leads to refinement and elongation of Nb dendrites into 1- to 10 nm-thick filaments. The presence of such fine Nb filaments causes a significant increase in the strength of Cu-Nb wires. The tensile strength of heavily drawn Cu-Nb wires was determined to be significantly higher than the values predicted by the rule of mixtures. This article reports the fabrication of high-strength Cu-Nb microcomposite sheet by multiple roll bonding. It is difficult and impractical to attain high processing strains (η>3) by simple cold rolling. In most practical cold-rolling operation, the thickness reduction does not exceed 90 pct (η ≅2). Therefore, innovative processing is required to generate high strength in Cu-Nb microcomposite sheet. Multiple roll bonding of Cu-Nb has been utilized to store high processing strain ( η>10) in the material and refine the Nb particle size within the copper matrix. This article describes the microstructure, mechanical properties, and thermal stability of roll-bonded Cu-Nb microcomposite sheet

Effect of Pd Surface Roughness on the Bonding Process and High Temperature Reliability of Au Ball Bonds

Science.gov (United States)

Huang, Y.; Kim, H. J.; McCracken, M.; Viswanathan, G.; Pon, F.; Mayer, M.; Zhou, Y. N.

2011-06-01

A 0.3- μm-thick electrolytic Pd layer was plated on 1 μm of electroless Ni on 1 mm-thick polished and roughened Cu substrates with roughness values ( R a) of 0.08 μm and 0.5 μm, respectively. The rough substrates were produced with sand-blasting. Au wire bonding on the Ni/Pd surface was optimized, and the electrical reliability was investigated under a high temperature storage test (HTST) during 800 h at 250°C by measuring the ball bond contact resistance, R c. The average value of R c of optimized ball bonds on the rough substrate was 1.96 mΩ which was about 40.0% higher than that on the smooth substrate. The initial bondability increased for the rougher surface, so that only half of the original ultrasonic level was required, but the reliability was not affected by surface roughness. For both substrate types, HTST caused bond healing, reducing the average R c by about 21% and 27%, respectively. Au diffusion into the Pd layer was observed in scanning transmission electron microscopy/ energy dispersive spectroscopy (STEM-EDS) line-scan analysis after HTST. It is considered that diffusion of Au or interdiffusion between Au and Pd can provide chemically strong bonding during HTST. This is supported by the R c decrease measured as the aging time increased. Cu migration was indicated in the STEM-EDS analysis, but its effect on reliability can be ignored. Au and Pd tend to form a complete solid solution at the interface and can provide reliable interconnection for high temperature (250°C) applications.

Multiple exchange and high-energy fixed-angle scattering

CERN Document Server

Halliday, I G; Orzalesi, C A; Tau, M

1975-01-01

The application of the eikonal ansatz to fermion fermion elastic scattering with Abelian vector gluon exchanges is discussed. The behaviours of the elastic scattering amplitude and the elastic form factor are considered and an important mechanism for fixed angle high energy elastic scattering is identified. (6 refs).

CO2·- radical induced cleavage of disulfide bonds in proteins. A gamma-ray and pulse radiolysis mechanistic investigation

International Nuclear Information System (INIS)

Favaudon, V.; Tourbez, H.; Lhoste, J-M.; Houee-Levin, C.

1990-01-01

Disulfide bond reduction by the CO 2 ·- radical was investigated in aponeocarzinostatin, aporiboflavin-binding protein, and bovine immunoglobulin. Protein-bound cysteine free thiols were formed under γ-ray irradiation in the course of a pH-dependent and protein concentration dependent chain reaction. The chain efficiency increased upon acidification of the medium, with an apparent pK a around 5, and decreased abruptly below pH 3.6. It decreased also at neutral pH as cysteine accumulated. From pulse radiolysis analysis, CO 2 ·- proved able to induce rapid one-electron oxidation of thiols and of tyrosine phenolic groups in addition to one-electron donation to exposed disulfide bonds. The bulk rate constant of CO 2 ·- uptake by the native proteins was 5- to 10-fold faster at pH 3 than at pH 8, and the protonated form of the disulfide radical anion, appeared to be the major protein radical species formed under acidic conditions. Formation of the disulfide radical cation, phenoxyl radical Tyr-O · disproportionation, and phenoxyl radical induced oxidation of preformed thiol groups should also be taken into consideration to explain the fate of the oxygen-centered phenoxyl radical

Looking for the best experimental conditions to detail the protein solvation shell in a binary aqueous solvent via small angle scattering

International Nuclear Information System (INIS)

Ortore, Maria Grazia; Sinibaldi, Raffaele; Spinozzi, Francesco; Carbini, Andrea; Carsughi, Flavio; Mariani, Paolo

2009-01-01

Protein hydration features attract particular interest in different fields, from biology up to physics, crossing chemistry and medicine. Particular attention is devoted to proteins dissolved in binary aqueous mixtures, since the presence of cosolvent can induce modifications in structural and functional properties. We have recently developed a methodology to obtain a quantitative description on protein solvation shell by a set of in-solution small angle scattering experiments, simultaneously analysed by a global-fit approach. In this paper, numerical simulations of small angle scattering curves are presented to figure out the sensitivity of the technique to different experimental conditions. Simulations concern two model proteins of different molecular weights and an unique cosolvent. A reliability test is introduced in order to find the best experimental conditions to be investigated, together with the most suitable scattering probe (neutrons or X-rays).

Two-Photon Absorption Properties of Gold Fluorescent Protein: A Combined Molecular Dynamics and Quantum Chemistry Study.

Science.gov (United States)

Simsek, Yusuf; Brown, Alex

2018-05-09

Molecular dynamic (MD) simulations were carried out to obtain the conformational changes of the chromophore in the gold fluorescent protein (PDB ID: 1OXF). To obtain two-photon absorption (TPA) cross-sections, time dependent density functional theory (TD-DFT) computations were performed for chromophore geometries sampled along the trajectory. The TD-DFT computations used the CAM-B3LYP functional and 6-31+G(d) basis set with the conductor-like polarizable continuum model (PCM) with parameters for water. Results showed that two dihedral angles change remarkably over the simulation time. TPA cross-sections were found to average 20 GM for the excitation to S1 between 430 and 460 nm; however, the maximal and minimal values were 35GM and 5GM, respectively. Besides the effects of the dihedrals on the spectroscopic properties, some bond lengths affected the excitation energies and the TPA cross-sections significantly (up to ±25-30%) while the effects of bond angles were smaller (±5%). Overall the present results provide insight in the effects of conformational exibility on TPA (with gold fluorescent protein as a specific example) and suggest that further experimental measurements of TPA for gold fluorescent protein should be undertaken.

Cα and Cβ Carbon-13 Chemical Shifts in Proteins From an Empirical Database

International Nuclear Information System (INIS)

Iwadate, Mitsuo; Asakura, Tetsuo; Williamson, Michael P.

1999-01-01

We have constructed an extensive database of 13C Cα and Cβ chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal structure has been shown to be essentially identical to the solution structure. There is no systematic effect of temperature, reference compound, or pH on reported shifts, but there appear to be differences in reported shifts arising from referencing differences of up to 4.2 ppm. The major factor affecting chemical shifts is the backbone geometry, which causes differences of ca. 4 ppm between typical α- helix and β-sheet geometries for Cα, and of ca. 2 ppm for Cβ. The side-chain dihedral angle χ1 has an effect of up to 0.5 ppm on the Cα shift, particularly for amino acids with branched side-chains at Cβ. Hydrogen bonding to main-chain atoms has an effect of up to 0.9 ppm, which depends on the main- chain conformation. The sequence of the protein and ring-current shifts from aromatic rings have an insignificant effect (except for residues following proline). There are significant differences between different amino acid types in the backbone geometry dependence; the amino acids can be grouped together into five different groups with different φ,ψ shielding surfaces. The overall fit of individual residues to a single non-residue-specific surface, incorporating the effects of hydrogen bonding and χ1 angle, is 0.96 ppm for both Cα and Cβ. The results from this study are broadly similar to those from ab initio studies, but there are some differences which could merit further attention

Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C’ scalar couplings (3hbJNC’)

NARCIS (Netherlands)

Bonvin, A.M.J.J.; Houben, K.; Guenneugues, M.N.L.; Kaptein, R.; Boelens, R.

2001-01-01

The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small alpha/beta protein

Dual-band and high-efficiency polarization converter based on metasurfaces at microwave frequencies

Science.gov (United States)

Liu, Yajun; Xia, Song; Shi, Hongyu; Zhang, Anxue; Xu, Zhuo

2016-06-01

We present a dual-band and high-efficiency polarization converter in microwave regime. The proposed converter can convert a linearly polarized wave to its cross-polarized wave for two distinct bands: Ku (11.5-20.0 GHz) and Ka (28.8-34.0 GHz). It can also convert the linearly polarized wave to a circularly polarized wave at four other frequencies. The experimental results are in good agreement with simulation results for both frequency bands. The polarization conversion ratio is above 0.94 for the Ku-band and 0.90 for the Ka-band. Furthermore, the converter can achieve dual-band and high-efficiency polarization conversion over angles of incidence up to 45°. The converter is also polarization-selective in that only the x- and y-polarized waves can be converted. The physical mechanism of the dual-band polarization conversion effect is interpreted via decomposed electric field components that couple with different plasmon resonance modes of the structure.

The electronic donation and frequency shifts on the YCCH⋯BH4- boron-bonded complexes (Y = H, CH3, CF3 and CCl3)

Science.gov (United States)

Pordeus, Renato Q.; Rego, Danilo G.; Oliveira, Boaz G.

2015-06-01

In this theoretical work, the tetrahydroborate ion (BH4-) was used as proton acceptor in the formation of the YCC-H⋯BH4- complexes (Y = H, CH3, CCl3 and CF3). Using B3LYP/6-311++G(d,p) level of theory, the results of structure corroborate with the analyses of infrared spectra showing that the changes in the bond lengths are in good agreement with the frequency shifts of the HCC-H, H3CCC-H, Cl3CCC-H and F3CCC-H proton donors. Based on the calculations carried out by the Quantum Theory of Atoms in Molecules (QTAIM), the reductions of electronic density corroborate with the red shifts in the frequencies of the C-H bonds. In addition to that, the C-H bonds are polarized because the contributions of s orbital diminish whereas of p increase. In line with this, the variations on the atomic radii computed via QTAIM calculations show that carbon outweigh hydrogen as follows (ΔrC > ΔrH). This scenario is indirectly supported by the Bent's rule of the chemical bonding. Although the interaction energies (corrected with BSSE and ZPE) vary between -19 and -67 kJ mol-1, these complexes interact without covalent character.

Adhesive bond strength evaluation in composite materials by laser-generated high amplitude ultrasound

International Nuclear Information System (INIS)

Perton, M; Blouin, A; Monchalin, J-P

2011-01-01

Adhesive bonding of composites laminates is highly efficient but is not used for joining primary aircraft structures, since there is presently no nondestructive inspection technique to ensure the quality of the bond. We are developing a technique based on the propagation of high amplitude ultrasonic waves to evaluate the adhesive bond strength. Large amplitude compression waves are generated by a short pulse powerful laser under water confinement and are converted after reflection by the assembly back surface into tensile waves. The resulting tensile stresses can cause a delamination inside the laminates or at the bond interfaces. The adhesion strength is evaluated by increasing the laser pulse energy until disbond. A good bond is unaffected by a certain level of stress whereas a weaker one is damaged. The method is shown completely non invasive throughout the whole composite assembly. The sample back surface velocity is measured by an optical interferometer and used to estimate stress history inside the sample. The depth and size of the disbonds are revealed by a post-test inspection by the well established laser-ultrasonic technique. Experimental results show that the proposed method is able to differentiate weak bond from strong bonds and to estimate quantitatively their bond strength.

Spectral editing at ultra-fast magic-angle-spinning in solid-state NMR: facilitating protein sequential signal assignment by HIGHLIGHT approach

Energy Technology Data Exchange (ETDEWEB)

Wang, Songlin; Matsuda, Isamu; Long, Fei; Ishii, Yoshitaka, E-mail: yishii@uic.edu [University of Illinois at Chicago, Department of Chemistry (United States)

2016-02-15

This study demonstrates a novel spectral editing technique for protein solid-state NMR (SSNMR) to simplify the spectrum drastically and to reduce the ambiguity for protein main-chain signal assignments in fast magic-angle-spinning (MAS) conditions at a wide frequency range of 40–80 kHz. The approach termed HIGHLIGHT (Wang et al., in Chem Comm 51:15055–15058, 2015) combines the reverse {sup 13}C, {sup 15}N-isotope labeling strategy and selective signal quenching using the frequency-selective REDOR pulse sequence under fast MAS. The scheme allows one to selectively observe the signals of “highlighted” labeled amino-acid residues that precede or follow unlabeled residues through selectively quenching {sup 13}CO or {sup 15}N signals for a pair of consecutively labeled residues by recoupling {sup 13}CO–{sup 15}N dipolar couplings. Our numerical simulation results showed that the scheme yielded only ∼15 % loss of signals for the highlighted residues while quenching as much as ∼90 % of signals for non-highlighted residues. For lysine-reverse-labeled micro-crystalline GB1 protein, the 2D {sup 15}N/{sup 13}C{sub α} correlation and 2D {sup 13}C{sub α}/{sup 13}CO correlation SSNMR spectra by the HIGHLIGHT approach yielded signals only for six residues following and preceding the unlabeled lysine residues, respectively. The experimental dephasing curves agreed reasonably well with the corresponding simulation results for highlighted and quenched residues at spinning speeds of 40 and 60 kHz. The compatibility of the HIGHLIGHT approach with fast MAS allows for sensitivity enhancement by paramagnetic assisted data collection (PACC) and {sup 1}H detection. We also discuss how the HIGHLIGHT approach facilitates signal assignments using {sup 13}C-detected 3D SSNMR by demonstrating full sequential assignments of lysine-reverse-labeled micro-crystalline GB1 protein (∼300 nmol), for which data collection required only 11 h. The HIGHLIGHT approach offers valuable

Small-angle X-ray scattering studies of thermally-induced globular protein gels

International Nuclear Information System (INIS)

Clark, A.H.; Tuffnell, C.D.

1980-01-01

Small-angle X-ray scattering has been applied to gels formed by heating globular proteins, in aqueous solution, above their unfolding temperatures. A number of BSA gels, previously characterised by electron microscopy, have been studied, and by setting up theoretical models for the scattering process, the X-ray data have been shown to be consistent with the microscope conclusions regarding network structure. It is concluded that the networks form by a linearly-directed aggregation of unfolded, disc-like, protein molecules, three-dimensional geometry being achieved by occasional branching, and/or cross-linking. Long-range inhomogeneities in network structure, easily observed by electron microscopy, and correlated with variations in pH or ionic strength, have an effect on X-ray scattering, and hence the X-ray method is sensitive not only to different network strand thicknesses, but to different degrees of uniformity as well. (author)

In vitro folding of inclusion body proteins.

Science.gov (United States)

Rudolph, R; Lilie, H

1996-01-01

Insoluble, inactive inclusion bodies are frequently formed upon recombinant protein production in transformed microorganisms. These inclusion bodies, which contain the recombinant protein in an highly enriched form, can be isolated by solid/liquid separation. After solubilization, native proteins can be generated from the inactive material by using in vitro folding techniques. New folding procedures have been developed for efficient in vitro reconstitution of complex hydrophobic, multidomain, oligomeric, or highly disulfide-bonded proteins. These protocols take into account process parameters such as protein concentration, catalysis of disulfide bond formation, temperature, pH, and ionic strength, as well as specific solvent ingredients that reduce unproductive side reactions. Modification of the protein sequence has been exploited to improve in vitro folding.

Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

Energy Technology Data Exchange (ETDEWEB)

Dai, Shuyan; Sun, Cancan; Tan, Kemin; Ye, Sheng; Zhang, Rongguang

2017-09-01

Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystal structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.

Binaural beats at high frequencies.

Science.gov (United States)

McFadden, D; Pasanen, E G

1975-10-24

Binaural beats have long been believed to be audible only at low frequencies, but an interaction reminiscent of a binaural beat can sometimes be heard when different two-tone complexes of high frequency are presented to the two ears. The primary requirement is that the frequency separation in the complex at one ear be slightly different from that in the other--that is, that there be a small interaural difference in the envelope periodicities. This finding is in accord with other recent demonstrations that the auditory system is not deaf to interaural time differences at high frequencies.

Photoinduced High-Frequency Charge Oscillations in Dimerized Systems

Science.gov (United States)

Yonemitsu, Kenji

2018-04-01

Photoinduced charge dynamics in dimerized systems is studied on the basis of the exact diagonalization method and the time-dependent Schrödinger equation for a one-dimensional spinless-fermion model at half filling and a two-dimensional model for κ-(bis[ethylenedithio]tetrathiafulvalene)2X [κ-(BEDT-TTF)2X] at three-quarter filling. After the application of a one-cycle pulse of a specifically polarized electric field, the charge densities at half of the sites of the system oscillate in the same phase and those at the other half oscillate in the opposite phase. For weak fields, the Fourier transform of the time profile of the charge density at any site after photoexcitation has peaks for finite-sized systems that correspond to those of the steady-state optical conductivity spectrum. For strong fields, these peaks are suppressed and a new peak appears on the high-energy side, that is, the charge densities mainly oscillate with a single frequency, although the oscillation is eventually damped. In the two-dimensional case without intersite repulsion and in the one-dimensional case, this frequency corresponds to charge-transfer processes by which all the bonds connecting the two classes of sites are exploited. Thus, this oscillation behaves as an electronic breathing mode. The relevance of the new peak to a recently found reflectivity peak in κ-(BEDT-TTF)2X after photoexcitation is discussed.

Financial system loss as an example of high consequence, high frequency events

Energy Technology Data Exchange (ETDEWEB)

McGovern, D.E.

1996-07-01

Much work has been devoted to high consequence events with low frequency of occurrence. Characteristic of these events are bridge failure (such as that of the Tacoma Narrows), building failure (such as the collapse of a walkway at a Kansas City hotel), or compromise of a major chemical containment system (such as at Bhopal, India). Such events, although rare, have an extreme personal, societal, and financial impact. An interesting variation is demonstrated by financial losses due to fraud and abuse in the money management system. The impact can be huge, entailing very high aggregate costs, but these are a result of the contribution of many small attacks and not the result of a single (or few) massive events. Public awareness is raised through publicized events such as the junk bond fraud perpetrated by Milikin or gross mismanagement in the failure of the Barings Bank through unsupervised trading activities by Leeson in Singapore. These event,s although seemingly large (financial losses may be on the order of several billion dollars), are but small contributors to the estimated $114 billion loss to all types of financial fraud in 1993. This paper explores the magnitude of financial system losses and identifies new areas for analysis of high consequence events including the potential effect of malevolent intent.

Geometry and evolution of low-angle normal faults (LANF) within a Cenozoic high-angle rift system, Thailand: Implications for sedimentology and the mechanisms of LANF development

Science.gov (United States)

Morley, Chris K.

2009-10-01

At least eight examples of large (5-35 km heave), low-angle normal faults (LANFs, 20°-30° dip) occur in the Cenozoic rift basins of Thailand and laterally pass into high-angle extensional fault systems. Three large-displacement LANFs are found in late Oligocene-Miocene onshore rift basins (Suphan Buri, Phitsanulok, and Chiang Mai basins), they have (1) developed contemporaneous with, or after the onset of, high-angle extension, (2) acted as paths for magma and associated fluids, and (3) impacted sedimentation patterns. Displacement on low-angle faults appears to be episodic, marked by onset of lacustrine conditions followed by axial progradation of deltaic systems that infilled the lakes during periods of low or no displacement. The Chiang Mai LANF is a low-angle (15°-25°), high-displacement (15-35 km heave), ESE dipping LANF immediately east of the late early Miocene Doi Inthanon and Doi Suthep metamorphic core complexes. Early Cenozoic transpressional crustal thickening followed by the northward motion of India coupled with Burma relative to east Burma and Thailand (˜40-30 Ma) caused migmatization and gneiss dome uplift in the late Oligocene of the core complex region, followed by LANF activity. LANF displacement lasted 4-6 Ma during the early Miocene and possibly transported a late Oligocene-early Miocene high-angle rift system 35 km east. Other LANFs in Thailand have lower displacements and no associated metamorphic core complexes. The three LANFs were initiated as low-angle faults, not by isostatic rotation of high-angle faults. The low-angle dips appear to follow preexisting low-angle fabrics (thrusts, shear zones, and other low-angle ductile foliations) predominantly developed during Late Paleozoic and early Paleogene episodes of thrusting and folding.

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

Science.gov (United States)

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

ALMA High Frequency Techniques

Science.gov (United States)

Meyer, J. D.; Mason, B.; Impellizzeri, V.; Kameno, S.; Fomalont, E.; Chibueze, J.; Takahashi, S.; Remijan, A.; Wilson, C.; ALMA Science Team

2015-12-01

The purpose of the ALMA High Frequency Campaign is to improve the quality and efficiency of science observing in Bands 8, 9, and 10 (385-950 GHz), the highest frequencies available to the ALMA project. To this end, we outline observing modes which we have demonstrated to improve high frequency calibration for the 12m array and the ACA, and we present the calibration of the total power antennas at these frequencies. Band-to-band (B2B) transfer and bandwidth switching (BWSW), techniques which improve the speed and accuracy of calibration at the highest frequencies, are most necessary in Bands 8, 9, and 10 due to the rarity of strong calibrators. These techniques successfully enable increased signal-to-noise on the calibrator sources (and better calibration solutions) by measuring the calibrators at lower frequencies (B2B) or in wider bandwidths (BWSW) compared to the science target. We have also demonstrated the stability of the bandpass shape to better than 2.4% for 1 hour, hidden behind random noise, in Band 9. Finally, total power observing using the dual sideband receivers in Bands 9 and 10 requires the separation of the two sidebands; this procedure has been demonstrated in Band 9 and is undergoing further testing in Band 10.

Diffusion bonding and brazing of high purity copper for linear collider accelerator structures

Directory of Open Access Journals (Sweden)

J. W. Elmer

2001-05-01

Full Text Available Diffusion bonding and brazing of high purity copper were investigated to develop procedures for joining precision machined copper components for the Next Linear Collider (NLC. Diffusion bonds were made over a range of temperatures from 400 °C to 1000 °C, under two different loading conditions [3.45 kPa (0.5 psi and 3.45 MPa (500 psi], and on two different diamond machined surface finishes. Brazes were made using pure silver, pure gold, and gold-nickel alloys, and different heating rates produced by both radiation and induction heating. Braze materials were applied by both physical vapor deposition (PVD and conventional braze alloy shims. Results of the diffusion bonding experiments showed that bond strengths very near that of the copper base metal could be made at bonding temperatures of 700 °C or higher at 3.45 MPa bonding pressure. At lower temperatures, only partial strength diffusion bonds could be made. At low bonding pressures (3.45 kPa, full strength bonds were made at temperatures of 800 °C and higher, while no bonding (zero strength was observed at temperatures of 700 °C and lower. Observations of the fracture surfaces of the diffusion bonded samples showed the effects of surface finish on the bonding mechanism. These observations clearly indicate that bonding began by point asperity contact, and flatter surfaces resulted in a higher percentage of bonded area under similar bonding conditions. Results of the brazing experiments indicated that pure silver worked very well for brazing under both conventional and high heating rate scenarios. Similarly, pure silver brazed well for both the PVD layers and the braze alloy shims. The gold and gold-containing brazes had problems, mainly due to the high diffusivity of gold in copper. These problems led to the necessity of overdriving the temperature to ensure melting, the presence of porosity in the joint, and very wide braze joints. Based on the overall findings of this study, a two

Short Carboxylic Acid–Carboxylate Hydrogen Bonds Can Have Fully Localized Protons

Energy Technology Data Exchange (ETDEWEB)

Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A.

2017-01-17

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15–0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor–acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O–O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O–O distance with increasing H-bond donor pK_a. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid–carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

On the photostability of the disulfide bond

DEFF Research Database (Denmark)

Stephansen, Anne Boutrup; Larsen, Martin Alex Bjørn; Klein, Liv Bærenholdt

2014-01-01

Photostability is an essential property of molecular building blocks of nature. Disulfides are central in the structure determination of proteins, which is in striking contradiction to the result that the S-S bond is a photochemically labile structural entity that cleaves to form free radicals upon...... on a sub 50 fs timescale without further ado. In a cyclic motif resembling the cysteine-disulfide bond in proteins, light can perturb the S-S bond to generate short-lived diradicaloid species, but the sulfur atoms are conformationally restricted by the ring that prevents the sulfur atoms from flying apart...... the photostability of disulfide-bonds must be ascribed a cyclic structural arrangement....

A study on poly (N-vinyl-2-pyrrolidone covalently bonded NiTi surface for inhibiting protein adsorption

Directory of Open Access Journals (Sweden)

Hongyan Yu

2016-12-01

Full Text Available Near equiatomic NiTi alloys have been extensively applied as biomaterials owing to its unique shape memory effect, superelasticity and biocompatibility. It has been demonstrated that surfaces capable of preventing plasma protein adsorption could reduce the reactivity of biomaterials with human blood. This motivated a lot of researches on the surface modification of NiTi alloy. In the present work, following heat and alkaline treatment and silanization by trichlorovinylsilane (TCVS, coating of poly (N-vinyl-2-pyrrolidone (PVP was produced on the NiTi alloy by gamma ray induced chemical bonding. The structures and properties of modified NiTi were characterized and in vitro biocompatibility of plasma protein adsorption was investigated. The results indicated that heat treatment at 823 K for 1 h could result in the formation of a protective TiO2 layer with “Ni-free” zone on NiTi surface. It was found that PVP was covalently bonded on NiTi surface to create a hydrophilic layer for inhibiting protein adsorption on the surface. The present work offers a green approach to introduce a bioorganic surface on metal and other polymeric or inorganic substrates by gamma irradiation.

X-ray diffraction and chemical bonding

International Nuclear Information System (INIS)

Bats, J.W.

1976-01-01

Chemical bonds are investigated in sulfamic acid (H 3 N-SO 3 ), sodium sulfonlate dihydrate (H 2 NC 6 H 4 SO 3 Na.2H 2 O), 2,5-dimercaptothiadiazole (HS-C 2 N 2 S-SH), sodium cyanide dihydrate (NaCN.2H 2 O), sodium thiocyanate (NaSCN) and ammonium thiocyanate (NH 4 SCN) by X-ray diffraction, and if necessary completed with neutron diffraction. Crystal structures and electron densities are determined together with bond length and angles. Also the effects of thermal motion are discussed

High-frequency Trader Subjectivity

DEFF Research Database (Denmark)

Borch, Christian; Lange, Ann-Christina

2017-01-01

In this article, we examine the recent shift in financial markets toward high-frequency trading (HFT). This turn is being legitimized with reference to how algorithms are allegedly more rational and efficient than human traders, and less prone to emotionally motivated decisions. We argue......-techniques of the ideal high-frequency trader. We demonstrate that these traders face the challenge of avoiding emotional interference in their algorithms and that they deploy a set of disciplinary self-techniques to curb the importance of emotional attachment....

Use of multi-frequency, multi-polarization, multi-angle airborne radars for class discrimination in a southern temperature forest

Science.gov (United States)

Mehta, N. C.

1984-01-01

The utility of radar scatterometers for discrimination and characterization of natural vegetation was investigated. Backscatter measurements were acquired with airborne multi-frequency, multi-polarization, multi-angle radar scatterometers over a test site in a southern temperate forest. Separability between ground cover classes was studied using a two-class separability measure. Very good separability is achieved between most classes. Longer wavelength is useful in separating trees from non-tree classes, while shorter wavelength and cross polarization are helpful for discrimination among tree classes. Using the maximum likelihood classifier, 50% overall classification accuracy is achieved using a single, short-wavelength scatterometer channel. Addition of multiple incidence angles and another radar band improves classification accuracy by 20% and 50%, respectively, over the single channel accuracy. Incorporation of a third radar band seems redundant for vegetation classification. Vertical transmit polarization is critically important for all classes.

Flight test of the X-29A at high angle of attack: Flight dynamics and controls

Science.gov (United States)

Bauer, Jeffrey E.; Clarke, Robert; Burken, John J.

1995-01-01

The NASA Dryden Flight Research Center has flight tested two X-29A aircraft at low and high angles of attack. The high-angle-of-attack tests evaluate the feasibility of integrated X-29A technologies. More specific objectives focus on evaluating the high-angle-of-attack flying qualities, defining multiaxis controllability limits, and determining the maximum pitch-pointing capability. A pilot-selectable gain system allows examination of tradeoffs in airplane stability and maneuverability. Basic fighter maneuvers provide qualitative evaluation. Bank angle captures permit qualitative data analysis. This paper discusses the design goals and approach for high-angle-of-attack control laws and provides results from the envelope expansion and handling qualities testing at intermediate angles of attack. Comparisons of the flight test results to the predictions are made where appropriate. The pitch rate command structure of the longitudinal control system is shown to be a valid design for high-angle-of-attack control laws. Flight test results show that wing rock amplitude was overpredicted and aileron and rudder effectiveness were underpredicted. Flight tests show the X-29A airplane to be a good aircraft up to 40 deg angle of attack.

Fallspeed measurement and high-resolution multi-angle photography of hydrometeors in freefall

OpenAIRE

T. J. Garrett; C. Fallgatter; K. Shkurko; D. Howlett

2012-01-01

We describe here a new instrument for imaging hydrometeors in freefall. The Multi-Angle Snowflake Camera (MASC) captures high resolution photographs of hydrometeors from three angles while simultaneously measuring their fallspeed. Based on the stereoscopic photographs captured over the two months of continuous measurements obtained at a high altitude location within the Wasatch Front in Utah, we derive statistics for fallspeed, hydrometeor size, shape, orientation and aspect ratio. From a sel...

Gauche effect in 1,2-difluoroethane. Hyperconjugation, bent bonds, steric repulsion.

Science.gov (United States)

Goodman, Lionel; Gu, Hongbing; Pophristic, Vojislava

2005-02-17

Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.

Angle-resolved reflection spectroscopy of high-quality PMMA opal crystal

Science.gov (United States)

Nemtsev, Ivan V.; Tambasov, Igor A.; Ivanenko, Alexander A.; Zyryanov, Victor Ya.

2018-02-01

PMMA opal crystal was prepared by a simple hybrid method, which includes sedimentation, meniscus formation and evaporation. We investigated three surfaces of this crystal by angle-resolved reflective light spectroscopy and SEM study. The angle-resolved reflective measurements were carried out in the 400-1100 nm range. We have determined the high-quality ordered surface of the crystal region. Narrow particle size distribution of the surface has been revealed. The average particle diameter obtained with SEM was nearly 361 nm. The most interesting result was that reflectivity of the surface turned out up to 98% at normal light incidence. Using a fit of dependences of the maximum reflectivity wavelength from an angle based on the Bragg-Snell law, the wavelength of maximum 0° reflectivity, the particle diameter and the fill factor have been determined. For the best surface maximum reflectivity wavelength of a 0° angle was estimated to be 869 nm. The particle diameter and fill factor were calculated as 372 nm and 0.8715, respectively. The diameter obtained by fitting is in excellent agreement with the particle diameter obtained with SEM. The reflectivity maximum is assumed to increase significantly when increasing the fill factor. We believe that using our simple approach to manufacture PMMA opal crystals will significantly increase the fabrication of high-quality photonic crystal templates and thin films.

Immersion angle dependence of the resonant-frequency shift of the quartz crystal microbalance in a liquid: effects of longitudinal wave.

Science.gov (United States)

Yoshimoto, Minoru; Kobirata, Satoshi; Aizawa, Hideo; Kurosawa, Shigeru

2007-06-19

We investigated the effects of the longitudinal wave on the immersion angle dependence of the resonant-frequency shift, deltaF, of the quartz crystal microbalance, QCM. In order to study exactly the effects, we employed the three types of cells: normal cell, cell with the glass beads and cell with sponge. The longitudinal wave exists in the normal cell. On the other hand, both the cell with the glass beads and the cell with sponge eliminate the longitudinal wave. As results, we have found that the tendencies of deltaF are the same in the three types of cells. That is, we conclude that the longitudinal wave does not have effects on the immersion angle dependence of deltaF.

Enhanced production of a single domain antibody with an engineered stabilizing extra disulfide bond.

Science.gov (United States)

Liu, Jinny L; Goldman, Ellen R; Zabetakis, Dan; Walper, Scott A; Turner, Kendrick B; Shriver-Lake, Lisa C; Anderson, George P

2015-10-09

Single domain antibodies derived from the variable region of the unique heavy chain antibodies found in camelids yield high affinity and regenerable recognition elements. Adding an additional disulfide bond that bridges framework regions is a proven method to increase their melting temperature, however often at the expense of protein production. To fulfill their full potential it is essential to achieve robust protein production of these stable binding elements. In this work, we tested the hypothesis that decreasing the isoelectric point of single domain antibody extra disulfide bond mutants whose production fell due to the incorporation of the extra disulfide bond would lead to recovery of the protein yield, while maintaining the favorable melting temperature and affinity. Introduction of negative charges into a disulfide bond mutant of a single domain antibody specific for the L1 antigen of the vaccinia virus led to approximately 3.5-fold increase of protein production to 14 mg/L, while affinity and melting temperature was maintained. In addition, refolding following heat denaturation improved from 15 to 70 %. It also maintained nearly 100 % of its binding function after heating to 85 °C for an hour at 1 mg/mL. Disappointingly, the replacement of neutral or positively charged amino acids with negatively charged ones to lower the isoelectric point of two anti-toxin single domain antibodies stabilized with a second disulfide bond yielded only slight increases in protein production. Nonetheless, for one of these binders the charge change itself stabilized the structure equivalent to disulfide bond addition, thus providing an alternative route to stabilization which is not accompanied by loss in production. The ability to produce high affinity, stable single domain antibodies is critical for their utility. While the addition of a second disulfide bond is a proven method for enhancing stability of single domain antibodies, it frequently comes at the cost of reduced

Analyzing the installation angle error of a SAW torque sensor

International Nuclear Information System (INIS)

Fan, Yanping; Ji, Xiaojun; Cai, Ping

2014-01-01

When a torque is applied to a shaft, normal strain oriented at ±45° direction to the shaft axis is at its maximum, which requires two one-port SAW resonators to be bonded to the shaft at ±45° to the shaft axis. In order to make the SAW torque sensitivity high enough, the installation angle error of two SAW resonators must be confined within ±5° according to our design requirement. However, there are few studies devoted to the installation angle analysis of a SAW torque sensor presently and the angle error was usually obtained by a manual method. Hence, we propose an approximation method to analyze the angle error. First, according to the sensitive mechanism of the SAW device to torque, the SAW torque sensitivity is deduced based on the linear piezoelectric constitutive equation and the perturbation theory. Then, when a torque is applied to the tested shaft, the stress condition of two SAW resonators mounted with an angle deviating from ±45° to the shaft axis, is analyzed. The angle error is obtained by means of the torque sensitivities of two orthogonal SAW resonators. Finally, the torque measurement system is constructed and the loading and unloading experiments are performed twice. The torque sensitivities of two SAW resonators are obtained by applying average and least square method to the experimental results. Based on the derived angle error estimation function, the angle error is estimated about 3.447°, which is close to the actual angle error 2.915°. The difference between the estimated angle and the actual angle is discussed. The validity of the proposed angle error analysis method is testified to by the experimental results. (technical design note)

High-frequency energy in singing and speech

Science.gov (United States)

Monson, Brian Bruce

While human speech and the human voice generate acoustical energy up to (and beyond) 20 kHz, the energy above approximately 5 kHz has been largely neglected. Evidence is accruing that this high-frequency energy contains perceptual information relevant to speech and voice, including percepts of quality, localization, and intelligibility. The present research was an initial step in the long-range goal of characterizing high-frequency energy in singing voice and speech, with particular regard for its perceptual role and its potential for modification during voice and speech production. In this study, a database of high-fidelity recordings of talkers was created and used for a broad acoustical analysis and general characterization of high-frequency energy, as well as specific characterization of phoneme category, voice and speech intensity level, and mode of production (speech versus singing) by high-frequency energy content. Directionality of radiation of high-frequency energy from the mouth was also examined. The recordings were used for perceptual experiments wherein listeners were asked to discriminate between speech and voice samples that differed only in high-frequency energy content. Listeners were also subjected to gender discrimination tasks, mode-of-production discrimination tasks, and transcription tasks with samples of speech and singing that contained only high-frequency content. The combination of these experiments has revealed that (1) human listeners are able to detect very subtle level changes in high-frequency energy, and (2) human listeners are able to extract significant perceptual information from high-frequency energy.

The Effect of Bond Albedo on Venus' Atmospheric and Surface Temperatures

Science.gov (United States)

Bullock, M. A.; Limaye, S. S.; Grinspoon, D. H.; Way, M.

2017-12-01

In spite of Venus' high planetary albedo, sufficient solar energy reaches the surface to drive a powerful greenhouse effect. The surface temperature is three times higher than it would be without an atmosphere. However, the details of the energy balance within Venus' atmosphere are poorly understood. Half of the solar energy absorbed within the clouds, where most of the solar energy is absorbed, is due to an unknown agent. One of the challenges of modeling Venus' atmosphere has been to account for all the sources of opacity sufficient to generate a globally averaged surface temperature of 735 K, when only 2% of the incoming solar energy is deposited at the surface. The wavelength and spherically integrated albedo, or Bond albedo, has typically been cited as between 0.7 and 0.82 (Colin 1983). Yet, recent photometry of Venus at extended phase angles between 2 and 179° indicate a Bond albedo of 0.90 (Mallama et al., 2006). The authors note an increase in cloud top brightness at phase angles fixed. Figure 1b (right). Venus surface temperature as Bond Albedo changes. Radiative-convective equilibrium models predict the correct globally averaged surface temperature at a=0.81. Calculations here show that a Bond albedo of a=0.9 would yield a surface temperature of 666.4 K, about 70 K too low, unless there is additional thermal absorption within the atmosphere that is not understood. Colin, L.,, Venus, University of Arizona Press, Tucson, 1983, pp 10-26. Mallama, A., et al., 2006. Icarus. 182, 10-22.

Protein resonance assignment at MAS frequencies approaching 100 kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods

Energy Technology Data Exchange (ETDEWEB)

Penzel, Susanne; Smith, Albert A.; Agarwal, Vipin; Hunkeler, Andreas [ETH Zürich, Physical Chemistry (Switzerland); Org, Mai-Liis; Samoson, Ago, E-mail: ago.samoson@ttu.ee [Tallinn University of Technology, NMR Instituut, Tartu Teadus, Tehnomeedikum (Estonia); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [UMR 5086 CNRS/Université de Lyon 1, Institut de Biologie et Chimie des Protéines (France); Ernst, Matthias, E-mail: maer@ethz.ch; Meier, Beat H., E-mail: beme@ethz.ch [ETH Zürich, Physical Chemistry (Switzerland)

2015-10-15

We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T{sub 2}′ times and a site-specific comparison of T{sub 2}′ at 93 kHz versus 60 kHz MAS frequency. A quantitative analysis of transfer efficiencies of building blocks, as they are used for typical 3D experiments, was performed. To do this, we compared dipolar-coupling and J-coupling based transfer steps. The building blocks were then combined into 3D experiments for sequential resonance assignment, where we evaluated signal-to-noise ratio and information content of the different 3D spectra in order to identify the best assignment strategy. Based on this comparison, six experiments were selected to optimally assign the model protein ubiquitin, solely using spectra acquired at 93 kHz MAS. Within 3 days of instrument time, the required spectra were recorded from which the backbone resonances have been assigned to over 96 %.

Note: high precision angle generator using multiple ultrasonic motors and a self-calibratable encoder.

Science.gov (United States)

Kim, Jong-Ahn; Kim, Jae Wan; Kang, Chu-Shik; Jin, Jonghan; Eom, Tae Bong

2011-11-01

We present an angle generator with high resolution and accuracy, which uses multiple ultrasonic motors and a self-calibratable encoder. A cylindrical air bearing guides a rotational motion, and the ultrasonic motors achieve high resolution over the full circle range with a simple configuration. The self-calibratable encoder can compensate the scale error of a divided circle (signal period: 20") effectively by applying the equal-division-averaged method. The angle generator configures a position feedback control loop using the readout of the encoder. By combining the ac and dc operation mode, the angle generator produced stepwise angular motion with 0.005" resolution. We also evaluated the performance of the angle generator using a precision angle encoder and an autocollimator. The expanded uncertainty (k = 2) in the angle generation was estimated less than 0.03", which included the calibrated scale error and the nonlinearity error. © 2011 American Institute of Physics

Water-Protein Hydrogen Exchange in the Micro-Crystalline Protein Crh as Observed by Solid State NMR Spectroscopy

International Nuclear Information System (INIS)

Boeckmann, Anja; Juy, Michel; Bettler, Emmanuel; Emsley, Lyndon; Galinier, Anne; Penin, Francois; Lesage, Anne

2005-01-01

We report site-resolved observation of hydrogen exchange in the micro-crystalline protein Crh. Our approach is based on the use of proton T 2 ' -selective 1 H- 13 C- 13 C correlation spectra for site-specific assignments of carbons nearby labile protein protons. We compare the proton T 2 ' selective scheme to frequency selective water observation in deuterated proteins, and discuss the impacts of deuteration on 13 C linewidths in Crh. We observe that in micro-crystalline proteins, solvent accessible hydroxyl and amino protons show comparable exchange rates with water protons as for proteins in solution, and that structural constraints, such as hydrogen bonding or solvent accessibility, more significantly reduce exchange rates

Characterization of bond line discontinuities in a high-Mn TWIP steel pipe welded by HF-ERW

Energy Technology Data Exchange (ETDEWEB)

Park, Gitae; Kim, Bongyoon; Kang, Yongjoon [Division of Materials Science and Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763 (Korea, Republic of); Kang, Heewoong [RD Team, Husteel, 131 Bugokgongdan-ro, Songak-eup, Dangjin-si, Chungnam 31721 (Korea, Republic of); Lee, Changhee, E-mail: chlee@hanyang.ac.kr [Division of Materials Science and Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763 (Korea, Republic of)

2016-08-15

In this work, the microstructure and defects in a high-frequency electrical resistance welded (HF-ERW) pipe of high-Mn twinning-induced plasticity (TWIP) steel were characterized. The microstructure of the base metal and the bond line were examined using both optical microscopy and scanning electron microscopy. The features of the bond line were similar to those of conventional steel. Simultaneously, the circumferential ductility was evaluated via a flaring test. It was concluded that the deterioration of the circumferential ductility in a high-Mn TWIP steel pipe was caused by irregular shaped oxide defects and a penetrator that had been formed during welding. Specifically, the penetrator, which is composed of MnO and Mn{sub 2}SiO{sub 4}, was found to be the most influential on the circumferential ductility of the welded pipe. The penetrator was analyzed using both an electron probe micro analyzer and transmission electron microscopy, and the formation sequence of the penetrator was evaluated. - Highlights: •This study focused on applying the HF-ERW process to the seam welding of expandable pipe using TWIP steels. •For improvement of the circumferential ductility, deterioration factors were characterized. •Penetrator which would mainly deteriorate the circumferential ductility consisted of round MnO and Mn{sub 2}SiO{sub 4}. •Metallurgical evidence of existing theory regarding the mechanism of defect formation during the HF-ERW was characterized.

Angle-selective all-dielectric Huygens’ metasurfaces

Science.gov (United States)

Arslan, D.; Chong, K. E.; Miroshnichenko, A. E.; Choi, D.-Y.; Neshev, D. N.; Pertsch, T.; Kivshar, Y. S.; Staude, I.

2017-11-01

We experimentally and numerically study the angularly resolved transmission properties of dielectric metasurfaces consisting of silicon nanodisks which support electric and magnetic dipolar Mie-type resonances in the near-infrared spectral range. First, we concentrate on Huygens’ metasurfaces which are characterised by a spectral overlap of the fundamental electric and magnetic dipole resonances of the silicon nanodisks at normal incidence. Huygens’ metasurfaces exhibit a high transmitted intensity over the spectral width of the resonances due to impedance matching, while the transmitted phase shows a variation of 2π as the wavelength is swept across the width of the resonances. We observe that the transmittance of the Huygens’ metasurfaces depends on the incidence angle and is sensitive to polarisation for non-normal incidence. As the incidence angle is increased starting from normal incidence, the two dipole resonances are shifted out of the spectral overlap and the resonant features appear as pronounced transmittance minima. Next, we consider a metasurface with an increased nanodisk radius as compared to the Huygens’ metasurface, which supports spectrally separate electric and magnetic dipole resonances at normal incidence. We show that for TM polarisation, we can shift the resonances of this metasurface into spectral overlap and regain the high resonant transmittance characteristic of Huygens’ metasurfaces at a particular incidence angle. Furthermore, both metasurfaces are demonstrated to reject all TM polarised light incident under angles other than the design overlap angle at their respective operation frequency. Our experimental observations are in good qualitative agreement with numerical calculations.

Creation of the {pi} angle standard for the flat angle measurements

Energy Technology Data Exchange (ETDEWEB)

Giniotis, V; Rybokas, M, E-mail: gi@ap.vtu.l, E-mail: MRybokas@gama.l [Department of Information Technologies, Vilnius Gediminas Technical University, Sauletekio al. 11, 10223 Vilnius-40 (Lithuania)

2010-07-01

Angle measurements are based mainly on multiangle prisms - polygons with autocollimators, rotary encoders for high accuracy and circular scales as the standards of the flat angle. Traceability of angle measurements is based on the standard of the plane angle - prism (polygon) calibrated at an appropriate accuracy. Some metrological institutions have established their special test benches (comparators) equipped with circular scales or rotary encoders of high accuracy and polygons with autocollimators for angle calibration purposes. Nevertheless, the standard (etalon) of plane angle - polygon has many restrictions for the transfer of angle unit - radian (rad) and other units of angle. It depends on the number of angles formed by the flat sides of the polygon that is restricted by technological and metrological difficulties related to the production and accuracy determination of the polygon. A possibility to create the standard of the angle equal to {pi} rad or half the circle or the full angle is proposed. It can be created by the circular scale with the rotation axis of very high accuracy and two precision reading instruments, usually, photoelectric microscopes (PM), placed on the opposite sides of the circular scale using the special alignment steps. A great variety of angle units and values can be measured and its traceability ensured by applying the third PM on the scale. Calibration of the circular scale itself and other scale or rotary encoder as well is possible using the proposed method with an implementation of {pi} rad as the primary standard angle. The method proposed enables to assure a traceability of angle measurements at every laboratory having appropriate environment and reading instruments of appropriate accuracy together with a rotary table with the rotation axis of high accuracy - rotation trajectory (runout) being in the range of 0.05 {mu}m. Short information about the multipurpose angle measurement test bench developed is presented.

A novel bonding method for large scale poly(methyl methacrylate) micro- and nanofluidic chip fabrication

Science.gov (United States)

Qu, Xingtian; Li, Jinlai; Yin, Zhifu

2018-04-01

Micro- and nanofluidic chips are becoming increasing significance for biological and medical applications. Future advances in micro- and nanofluidics and its utilization in commercial applications depend on the development and fabrication of low cost and high fidelity large scale plastic micro- and nanofluidic chips. However, the majority of the present fabrication methods suffer from a low bonding rate of the chip during thermal bonding process due to air trapping between the substrate and the cover plate. In the present work, a novel bonding technique based on Ar plasma and water treatment was proposed to fully bond the large scale micro- and nanofluidic chips. The influence of Ar plasma parameters on the water contact angle and the effect of bonding conditions on the bonding rate and the bonding strength of the chip were studied. The fluorescence tests demonstrate that the 5 × 5 cm2 poly(methyl methacrylate) chip with 180 nm wide and 180 nm deep nanochannels can be fabricated without any block and leakage by our newly developed method.

Improving the bonding between henequen fibers and high density polyethylene using atmospheric pressure ethylene-plasma treatments

Directory of Open Access Journals (Sweden)

A. Aguilar-Rios

2014-07-01

Full Text Available In order to improve the bonding between henequen fibers (Agave fourcroydes and High Density Polyethylene (HDPE, they were treated in an ethylene-dielectric barrier discharge (DBD plasma operating at atmospheric pressure. A 23 factorial experimental design was used to study the effects of the plasma operational parameters, namely, frequency, flow rate and exposure time, over the fiber tensile mechanical properties and its adhesion to HDPE. The fiber-matrix Interfacial Shear Strength (IFSS was evaluated by means of the single fiber pull-out test. The fiber surface chemical changes were assessed by photoacoustic Fourier transform infrared spectroscopy (PAS-FTIR and the changes in surface morphology with scanning electron microscopy (SEM. The results indicate that individual operational parameters in the DBD plasma treatment have different effects on the tensile properties of the henequen fibers and on its bonding to HDPE. The SEM results show that the plasma treatment increased the roughness of the fiber surface. The FTIR result seems to indicate the presence of a hydrocarbon-like polymer film, bearing some vinyl groups deposited onto the fibers. These suggests that the improvement in the henequen-HDPE bonding could be the result of the enhancement of the mechanical interlocking, due the increment in roughness, and the possible reaction of the vinyl groups on the film deposited onto the fiber with the HDPE.

Bifurcation analysis and stability design for aircraft longitudinal motion with high angle of attack

Directory of Open Access Journals (Sweden)

Xin Qi

2015-02-01

Full Text Available Bifurcation analysis and stability design for aircraft longitudinal motion are investigated when the nonlinearity in flight dynamics takes place severely at high angle of attack regime. To predict the special nonlinear flight phenomena, bifurcation theory and continuation method are employed to systematically analyze the nonlinear motions. With the refinement of the flight dynamics for F-8 Crusader longitudinal motion, a framework is derived to identify the stationary bifurcation and dynamic bifurcation for high-dimensional system. Case study shows that the F-8 longitudinal motion undergoes saddle node bifurcation, Hopf bifurcation, Zero-Hopf bifurcation and branch point bifurcation under certain conditions. Moreover, the Hopf bifurcation renders series of multiple frequency pitch oscillation phenomena, which deteriorate the flight control stability severely. To relieve the adverse effects of these phenomena, a stabilization control based on gain scheduling and polynomial fitting for F-8 longitudinal motion is presented to enlarge the flight envelope. Simulation results validate the effectiveness of the proposed scheme.

Alkaline transition of pseudoazurin Met16X mutant proteins: protein stability influenced by the substitution of Met16 in the second sphere coordination.

Science.gov (United States)

Abdelhamid, Rehab F; Obara, Yuji; Kohzuma, Takamitsu

2008-01-01

Several blue copper proteins are known to change the active site structure at alkaline pH (alkaline transition). Spectroscopic studies of Met16Phe, Met16Tyr, Met16Trp, and Met16Val pseudoazurin variants were performed to investigate the second sphere role through alkaline transition. The visible electronic absorption and resonance Raman spectra of Met16Phe, Met16Tyr, and Met16Trp variants showed the increasing of axial component at pH approximately 11 like wild-type PAz. The visible electronic absorption and far-UV CD spectra of Met16Val demonstrated that the destabilization of the protein structure was triggered at pH>11. Resonance Raman (RR) spectra of PAz showed that the intensity-weighted averaged Cu-S(Cys) stretching frequency was shifted to higher frequency region at pH approximately 11. The higher frequency shift of Cu-S(Cys) bond is implied the stronger Cu-S(Cys) bond at alkaline transition pH approximately 11. The visible electronic absorption and far-UV CD spectra of Met16X PAz revealed that the Met16Val variant is denatured at pH>11, but Met16Phe, Met16Tyr, and Met16Trp mutant proteins are not denatured even at pH>11. These observations suggest that Met16 is important to maintain the protein structure through the possible weak interaction between methionine -SCH3 part and coordinated histidine imidazole moiety. The introduction of pi-pi interaction in the second coordination sphere may be contributed to the enhancement of protein structure stability.

Edge Detection from High Resolution Remote Sensing Images using Two-Dimensional log Gabor Filter in Frequency Domain

International Nuclear Information System (INIS)

Wang, K; Yu, T; Meng, Q Y; Wang, G K; Li, S P; Liu, S H

2014-01-01

Edges are vital features to describe the structural information of images, especially high spatial resolution remote sensing images. Edge features can be used to define the boundaries between different ground objects in high spatial resolution remote sensing images. Thus edge detection is important in the remote sensing image processing. Even though many different edge detection algorithms have been proposed, it is difficult to extract the edge features from high spatial resolution remote sensing image including complex ground objects. This paper introduces a novel method to detect edges from the high spatial resolution remote sensing image based on frequency domain. Firstly, the high spatial resolution remote sensing images are Fourier transformed to obtain the magnitude spectrum image (frequency image) by FFT. Then, the frequency spectrum is analyzed by using the radius and angle sampling. Finally, two-dimensional log Gabor filter with optimal parameters is designed according to the result of spectrum analysis. Finally, dot product between the result of Fourier transform and the log Gabor filter is inverse Fourier transformed to obtain the detections. The experimental result shows that the proposed algorithm can detect edge features from the high resolution remote sensing image commendably

The Valency Theory: The Human Bond From A New Psychoanalytic Perspective

OpenAIRE

Med Hafsi

2008-01-01

The present paper discusses some psychoanalytical conceptions concerning what links people to each other, or the human bond. Psychoanalysis, can be regarded as a science dealing basically with, although not directly, the human bond or link linking the person with his external and internal objects. The fact that this bond is in perpetualtransformation, and therefore can be apprehended from different angles has led to various psychoanalytical conceptions or theories which are more complementary...

Combination of acoustic levitation with small angle scattering techniques and synchrotron radiation circular dichroism. Application to the study of protein solutions.

Science.gov (United States)

Cristiglio, Viviana; Grillo, Isabelle; Fomina, Margarita; Wien, Frank; Shalaev, Evgenyi; Novikov, Alexey; Brassamin, Séverine; Réfrégiers, Matthieu; Pérez, Javier; Hennet, Louis

2017-01-01

The acoustic levitation technique is a useful sample handling method for small solid and liquids samples, suspended in air by means of an ultrasonic field. This method was previously used at synchrotron sources for studying pharmaceutical liquids and protein solutions using x-ray diffraction and small angle x-ray scattering (SAXS). In this work we combined for the first time this containerless method with small angle neutron scattering (SANS) and synchrotron radiation circular dichroism (SRCD) to study the structural behavior of proteins in solutions during the water evaporation. SANS results are also compared with SAXS experiments. The aggregation behavior of 45μl droplets of lysozyme protein diluted in water was followed during the continuous increase of the sample concentration by evaporating the solvent. The evaporation kinetics was followed at different drying stage by SANS and SAXS with a good data quality. In a prospective work using SRCD, we also studied the evolution of the secondary structure of the myoglobin protein in water solution in the same evaporation conditions. Acoustic levitation was applied for the first time with SANS and the high performances of the used neutron instruments made it possible to monitor fast container-less reactions in situ. A preliminary work using SRCD shows the potentiality of its combination with acoustic levitation for studying the evolution of the protein structure with time. This multi-techniques approach could give novel insights into crystallization and self-assembly phenomena of biological compound with promising potential applications in pharmaceutical, food and cosmetics industry. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo. Copyright © 2016 Elsevier B.V. All rights reserved.

Peripheral Protein Unfolding Drives Membrane Bending.

Science.gov (United States)

Siaw, Hew Ming Helen; Raghunath, Gokul; Dyer, R Brian

2018-06-20

Dynamic modulation of lipid membrane curvature can be achieved by a number of peripheral protein binding mechanisms such as hy-drophobic insertion of amphipathic helices and membrane scaffolding. Recently, an alternative mechanism was proposed in which crowding of peripherally bound proteins induces membrane curvature through steric pressure generated by lateral collisions. This effect was enhanced using intrinsically disordered proteins that possess high hydrodynamic radii, prompting us to explore whether membrane bending can be triggered by the folding-unfolding transition of surface-bound proteins. We utilized histidine-tagged human serum albumin bound to Ni-NTA-DGS containing liposomes as our model system to test this hypothesis. We found that reduction of the disulfide bonds in the protein resulted in unfolding of HSA, which subsequently led to membrane tubule formation. The frequency of tubule formation was found to be significantly higher when the proteins were unfolded while being localized to a phase-separated domain as opposed to randomly distributed in fluid phase liposomes, indicating that the steric pressure generated from protein unfolding is directly responsible for membrane deformation. Our results are critical for the design of peripheral membrane protein-immobilization strategies and open new avenues for exploring mechanisms of membrane bending driven by conformational changes of peripheral membrane proteins.

Econometrics of financial high-frequency data

CERN Document Server

Hautsch, Nikolaus

2011-01-01

This book covers major approaches in high-frequency econometrics. It discusses implementation details, provides insights into properties of high-frequency data as well as institutional settings and presents applications.

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables.

Science.gov (United States)

Wako, Hiroshi; Endo, Shigeru

2013-06-01

We have developed a computer program, named PDBETA, that performs normal mode analysis (NMA) based on an elastic network model that uses dihedral angles as independent variables. Taking advantage of the relatively small number of degrees of freedom required to describe a molecular structure in dihedral angle space and a simple potential-energy function independent of atom types, we aimed to develop a program applicable to a full-atom system of any molecule in the Protein Data Bank (PDB). The algorithm for NMA used in PDBETA is the same as the computer program FEDER/2, developed previously. Therefore, the main challenge in developing PDBETA was to find a method that can automatically convert PDB data into molecular structure information in dihedral angle space. Here, we illustrate the performance of PDBETA with a protein-DNA complex, a protein-tRNA complex, and some non-protein small molecules, and show that the atomic fluctuations calculated by PDBETA reproduce the temperature factor data of these molecules in the PDB. A comparison was also made with elastic-network-model based NMA in a Cartesian-coordinate system. Copyright © 2013 Elsevier Ltd. All rights reserved.

Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories

KAUST Repository

Chikalov, Igor

2011-02-15

Background: Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor.Methods: This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration ?. We model dependence of the output variable on the predictors by a regression tree.Results: Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings.Conclusions: We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone. 2011 Chikalov et al; licensee BioMed Central Ltd.

Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond.

Science.gov (United States)

Lu, Norman; Chung, Wei-Cheng; Ley, Rebecca M; Lin, Kwan-Yu; Francisco, Joseph S; Negishi, Ei-Ichi

2016-03-03

Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

Science.gov (United States)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Chip bonding of low-melting eutectic alloys by transmitted laser radiation

Science.gov (United States)

Hoff, Christian; Venkatesh, Arjun; Schneider, Friedrich; Hermsdorf, Jörg; Bengsch, Sebastian; Wurz, Marc C.; Kaierle, Stefan; Overmeyer, Ludger

2017-06-01

Present-day thermode bond systems for the assembly of radio-frequency identification (RFID) chips are mechanically inflexible, difficult to control, and will not meet future manufacturing challenges sufficiently. Chip bonding, one of the key processes in the production of integrated circuits (ICs), has a high potential for optimization with respect to process duration and process flexibility. For this purpose, the technologies used, so far, are supposed to be replaced by a transmission laser-bonding process using low-melting eutectic alloys. In this study, successful bonding investigations of mock silicon chips and of RFID chips on flexible polymer substrates are presented using the low-melting eutectic alloy, 52In48Sn, and a laser with a wavelength of 2 μm.

Transforming between discrete and continuous angle distribution models: application to protein χ1 torsions

International Nuclear Information System (INIS)

Schmidt, Jürgen M.

2012-01-01

Two commonly employed angular-mobility models for describing amino-acid side-chain χ 1 torsion conformation, the staggered-rotamer jump and the normal probability density, are discussed and performance differences in applications to scalar-coupling data interpretation highlighted. Both models differ in their distinct statistical concepts, representing discrete and continuous angle distributions, respectively. Circular statistics, introduced for describing torsion-angle distributions by using a universal circular order parameter central to all models, suggest another distribution of the continuous class, here referred to as the elliptic model. Characteristic of the elliptic model is that order parameter and circular variance form complementary moduli. Transformations between the parameter sets that describe the probability density functions underlying the different models are provided. Numerical aspects of parameter optimization are considered. The issues are typified by using a set of χ 1 related 3 J coupling constants available for FK506-binding protein. The discrete staggered-rotamer model is found generally to produce lower order parameters, implying elevated rotatory variability in the amino-acid side chains, whereas continuous models tend to give higher order parameters that suggest comparatively less variation in angle conformations. The differences perceived regarding angular mobility are attributed to conceptually different features inherent to the models.

A new hydrocarbon empirical potential in angle bending calculation for the molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Ping, Tan Ai; Hoe, Yeak Su [Department of Mathematical Sciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor Bahru, Johor Darul Takzim (Malaysia)

2014-07-10

Typically, short range potential only depends on neighbouring atoms and its parameters function can be categorized into bond stretching, angle bending and bond rotation potential. In this paper, we present our work called Angle Bending (AB) potential, whereas AB potential is the extension of our previous work namely Bond Stretching (BS) potential. Basically, potential will tend to zero after truncated region, potential in specific region can be represented by different piecewise polynomial. We proposed the AB piecewise potential which is possible to solve a system involving three atoms. AB potential able to handle the potential of covalent bonds for three atoms as well as two atoms cases due to its degeneracy properties. Continuity for the piecewise polynomial has been enforced by coupling with penalty methods. There are still plenty of improvement spaces for this AB potential. The improvement for three atoms AB potential will be studied and further modified into torsional potential which are the ongoing current research.

Aggregation in concentrated protein solutions: Insights from rheology, neutron scattering and molecular simulations

Science.gov (United States)

Castellanos, Maria Monica

Aggregation of therapeutic proteins is currently one of the major challenges in the bio-pharmaceutical industry, because aggregates could induce immunogenic responses and compromise the quality of the product. Current scientific efforts, both in industry and academia, are focused on developing rational approaches to screen different drug candidates and predict their stability under different conditions. Moreover, aggregation is promoted in highly concentrated protein solutions, which are typically required for subcutaneous injection. In order to gain further understanding about the mechanisms that lead to aggregation, an approach that combined rheology, neutron scattering, and molecular simulations was undertaken. Two model systems were studied in this work: Bovine Serum Albumin in surfactant-free Phosphate Buffered Saline at pH = 7.4 at concentrations from 11 mg/mL up to ˜519 mg/mL, and a monoclonal antibody in 20 mM Histidine/Histidine Hydrochloride at pH = 6.0 with 60 mg/mL trehalose and 0.2 mg/mL polysorbate-80 at concentrations from 53 mg/mL up to ˜220 mg/mL. The antibody used here has three mutations in the CH2 domain, which result in lower stability upon incubation at 40 °C with respect to the wild-type protein, based on size-exclusion chromatography assays. This temperature is below 49 °C, where unfolding of the least stable, CH2 domain occurs, according to differential scanning calorimetry. This dissertation focuses on identifying the role of aggregation on the viscosity of protein solutions. The protein solutions of this work show an increase in the low shear viscosity in the absence of surfactants, because proteins adsorb at the air/water interface forming a viscoelastic film that affects the measured rheology. Stable surfactant-laden protein solutions behave as simple Newtonian fluids. However, the surfactant-laden antibody solution also shows an increase in the low shear viscosity from bulk aggregation, after prolonged incubation at 40 °C. Small-angle

ISIS 1 measurements of high-frequency backscatter inside the ionosphere

International Nuclear Information System (INIS)

James, H.G.

1989-01-01

A study has been made of high-frequency backscatter observed by the ISIS 1 topside sounder at orbital heights from approximately 600 to 800 km. Signals are detected during high-latitude passes at radar ranges x of up to about 400 km and at frequencies from about the X mode cutoff at the spacecraft (usually around 5 MHz) up to 10 MHz typically and 18 MHz occasionally. The signals are interpreted as coherent aspect-sensitive scatter. The absolute power of return signals at high latitudes usually varies as x -2 for x ≤ 150 km. This implies that the scattering cross-section density σ is constant for all azimuths about the magnetic field and for ranges out to 150 km or, in other words, that irregularity patches have a constant σ over cross-field dimensions of 300 km. At larger ranges the signal often falls off more sharply with x, indicating azimuthal variations in σ. The cross section scaled from the data using the radar equation is found to have values centered near 10 -8 to 10 -7 m -1 for the most intense signals, referred to an assumed polar-aspect angle sensitivity. However, the magnitude of σ drops by about 2 orders of magnitude in the frequency range 5-15 MHz. Previous statistical studies have established that strong backscatter is restricted to auroral latitudes. Here the polar distribution of backscatter has been plotted for two sets of passes over the south pole, one collected during austral winter and the other during summer. The strongest backscatter is located at invariant latitudes around 80 degree. Backscatter is significantly stronger and distributed more extensively over the polar cap in winter than in summer

Effects of hydrogen bonds on solid state TATB, RDX, and DATB under high pressures