• This tutorial review provides first a brief discussion of the main principles of ECD spectroscopy and related methods for interpretation of spectra , with special reference to conformational aspects. (rsc.org)
  • Finally, the review presents the relatively less common but very interesting application of ECD spectroscopy for conformational analyses of organic compounds. (rsc.org)
  • We study the influence of the molecular environment (N2) on the Cs-C2 equilibrium of tetrahydrofuran in the [email protected]2 system utilizing nitrogen matrix isolation infrared spectroscopy. (researchgate.net)
  • Conformations and aggregation of PBLG were studied by vibrational circular dichroism spectroscopy (VCD) at various concentrations or acidities. (chemicke-listy.cz)
  • Fluorescence correlation spectroscopy (FCS) is a sensitive analytical tool that allows dynamics and hydrodynamics of biomolecules to be studied under a broad range of experimental conditions. (biu.ac.il)
  • Infrared spectroscopy (IR) and quantum chemistry calculations that are based on the density functional theory (DFT) have been used to study the structure and molecular interactions of the nematic and twist-bend phases of thioether -linked dimers. (bvsalud.org)
  • A nuclear magnetic resonance spectroscopy and molecular modeling study. (unthsc.edu)
  • The recent improvements of such parameters have made them suitable for the analysis of nucleic acids and for characterizing conformational changes in RNA molecules. (loria.fr)
  • Molecular dynamics simulations of covalently modified surfaces provide models of conformational details that depend on chain length, chain density, and temperature. (nist.gov)
  • A molecular understanding of interrelationship between dynamics, function and conformational stability of immunoglobulins, both in solution and in presence of co-solutes, can be important for their pharmaceutical development. (ku.edu)
  • Therefore, a better understanding of interactions that govern protein structure, dynamics and conformational stability at low and high concentrations and in presence of excipients should aid in designing, optimizing and developing rational formulation conditions for protein based therapeutics. (ku.edu)
  • A variety of experimental methods sensitive to structure, dynamics and conformational stability of proteins in solution were employed in these studies. (ku.edu)
  • Different monoclonal antibodies within IgG1 isotype were used to investigate interrelationships between protein dynamics and conformational stability in absence and presence of co-solutes. (ku.edu)
  • These studies provide evidence that immunoglobulins belonging to the same IgG1 subtype can have notable differences in their conformational stability, dynamics, aggregation propensity, hydration properties and their response to co-solutes. (ku.edu)
  • In addition, alterations in protein dynamics (at a global protein level and in local regions with differences in solvent exposures) by stabilizing or destabilizing excipients were found to modulate the conformational stability of a monoclonal antibody. (ku.edu)
  • The work presented in this dissertation provides evidence that factors modulating protein dynamics and those governing intra- and intermolecular interactions can influence the conformational stability, aggregation and viscosity of proteins in solution. (ku.edu)
  • FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. (researchgate.net)
  • We probe the open conformation of human Hsp90α for druggable sites that overlap with these allosteric control elements, and identify three putative natural compound allosteric modulators: Cephalostatin 17, 20(29)-Lupene-3β-isoferulate and 3′-Bromorubrolide F. We assess the allosteric potential of these ligands by examining their effect on the conformational dynamics of the protein. (nature.com)
  • The main goal of this PhD project is to elucidate the conformational dynamics of protein-RNA complexes and to develop a method for understanding their allosteric communications. (loria.fr)
  • The candidate will be supervised by Yasaman Karami (Inria researcher) with expertise in analyzing proteins conformational dynamics and drug design [1,2], and Malika SmailTabonne (associate professor, University of Lorraine) expert in machine learning. (loria.fr)
  • Therefore, characterizing the structure, dynamics and conformational changes of biomolecules can help understand the molecular mechanisms of underlying diseases, and hopefully prevent them by designing drugs. (loria.fr)
  • While major improvements have been introduced with the breakthrough of artificial intelligence (AlphaFold2 [3]), predicting conformational dynamics of biomolecules is still challenging. (loria.fr)
  • In this PhD the goal is to design and implement a method for characterizing the conformational dynamics of protein-RNA complexes using the set of trajectories generated from MD simulations in a systematic way. (loria.fr)
  • On the other hand, computational approaches have been developed to investigate the conformational dynamics in proteins [4,5,6]. (loria.fr)
  • A higher magnitude of conformational dynamics and variations are expected, especially for multi-domain proteins consisting of multiple structural domains. (biophysics.org)
  • The trajectory of the inter-gadolinium distance as predicted by molecular dynamics (MD) simulation is shown at the bottom, depicting drastic conformational changes of MurD. (biophysics.org)
  • We also investigated the conformational dynamics of the same protein by X-ray scattering, neutron scattering, and MD simulation. (biophysics.org)
  • Our studies are performed using hybrid molecular dynamics/Monte Carlo simulations and theoretical modelling. (reading.ac.uk)
  • Our recent studies of the moving contact-line problem via molecular dynamics simulations have shown that the dynamic contact angle effect (Lukyanov, Likhtman 2013) is essentially conditioned by the microscopic processes in a small region, several atoms wide, around the contact line, basically at nanoscale. (reading.ac.uk)
  • We performed targeted molecular dynamics simulation to obtain trajectory of conformational change from inactive to active form. (intechopen.com)
  • Molecular dynamics studied by NMR relaxation experiments. (lu.se)
  • Protein dynamics studied by NMR spin relaxation. (lu.se)
  • Protein dynamics studied by NMR. (lu.se)
  • Using a series of diverse virology and computational methods, as well as molecular dynamics simulations for conformational mobility, the researchers showed that hypervariable region 1 (HVR1) acts as a "safety catch" that regulates entry. (who.int)
  • Structural basis for ligand modulation of the CCR2 conformational landscape. (iasp-pain.org)
  • We find evidence for the selective allosteric activation and inhibition of Hsp90's conformational transition toward the closed state in response to ligand binding and shed valuable insight to further the understanding of allosteric drug design and Hsp90's complex allosteric mechanism of action. (nature.com)
  • The data show that the protein enzyme MurD exists in a wide variety of the conformational states that were eliminated by ligand binding. (biophysics.org)
  • Also, the ligand s reorganization capacity and its conformational space have been investigated. (upt.ro)
  • With the aim of identifying new pathological relevant AβO structural variants and conformational epitopes, we are investigating post-mortem human brains from patients affected by Alzheimer's disease, also in condition of co-morbidities, at different stages of pathology and in several areas of brain cortex, by different approaches of microscopy and biochemistry. (ebri.it)
  • Signal transduction in biology relies on the transfer of information across biomolecules by concerted conformational changes that cannot currently be characterized experimentally at high resolution. (europa.eu)
  • analyze classical scrapie, including CH1641-like , from natural goat the conformational stability of CH1641-like isolates, BSE, BSE and experimental sheep BSE. (cdc.gov)
  • A novel human prion disease, variant CJD, was reveal strain-specifi ed PrPSc conformational stability in reported in 1995 and postulated to be caused by eating sheep isolates because it enabled discrimination of Nor98 beef infected with BSE. (cdc.gov)
  • Commission to increase the search for BSE infections in We thus sought to determine the conformational stability small ruminants. (cdc.gov)
  • The findings suggest that the topological conformational changes in the HPV L1 gene DNA residues bound to the AAHS adjuvant may be genotype-related. (scirp.org)
  • We examined the conformational preferences of dipeptide fragments Ac-D-Ser-Pro*-NHMe (in both free and TBS protected side chains of D-Ser and Pro* residues) using computational studies. (lsu.edu)
  • To investigate the conformational change of c-Src tyrosine kinase, we applied network analysis to time series of correlation among residues. (intechopen.com)
  • The time series of correlation between residues during the conformational change generated by targeted molecular dynamic simulation. (intechopen.com)
  • With centrality measures such as betweenness centrality, degree centrality, and closeness centrality, we observed a few important residues that significantly contribute to the conformational change of c-Src tyrosine kinase for the different time steps. (intechopen.com)
  • Comparison of the effect of the introduced mutations on the effectiveness of interaction between HlyIICTD and HlyIIC-20 and a control antibody recognizing a non-overlapping epitope enabled identifying the amino acid residues N339, K340 included in the conformational antigenic determinant rec-ognized by HlyIIC-20. (bvsalud.org)
  • NMR studies on these peptides in CDCl3 clearly indicate that the NH group of dehydroalanine is involved in an intramolecular hydrogen bond. (iisc.ac.in)
  • Peptides have become valuable as catalysts for a variety of different reactions, but little is known about the conformational properties of peptidic catalysts. (unibas.ch)
  • Conformational equilibria were dependent on the solvent of choice, either methanol-d(4) or chloroform-d, with mainly C-4(1) and C-1(4) conformations present but also skew conformations to some extent. (lu.se)
  • On base of highly biased conformational equilibria, the temperature-dependent populations of stable local minima for four studied dimethylcyclohexanes were obtained by utilizing Boltzmann distribution within 300-2500 K. Moreover, two unique interconversion processes for them, including inversion and topomerization, were fully investigated, and their potential energy surfaces were illustrated with the rigorous descriptions in two or three-dimensional schemes for clarify. (authorea.com)
  • The unique high sensitivity of ECD towards conformation, as well as of other chiroptical spectroscopies, renders these techniques a useful alternative or complement to standard spectroscopic tools for conformational investigations, such as NMR . (rsc.org)
  • More specific examples of conformational isomerism are detailed elsewhere: Ring conformation Cyclohexane conformations, including with chair and boat conformations among others. (wikipedia.org)
  • Nuclear Overhauser effect (NOE) studies are also accommodative of an inverse -turn-type of conformation that is characterised by conformational angles of -70° and +70° around the X residue, and a C[stack i+1 ]H-Ni+2H interproton distance of 2.5 Å. (iisc.ac.in)
  • The study used travelling-wave ion mobility with quadrupole and orthogonal time-of-flight mass spectrometry to quantify the extent of metal ion labeling of lysozyme as a function of pH, charge state and conformation. (tamuc.edu)
  • Novoselsky, A & Glaser, R 2002, ' Solid-state CP/MAS 13 C NMR studies on conformational polymorphism in sertraline hydrochloride, an antidepressant drug ', Magnetic Resonance in Chemistry , vol. 40, no. 11, pp. 723-728. (bgu.ac.il)
  • Predicting how the conformational phase behavior of tethered chain molecules depends on external variables is challenging. (nist.gov)
  • These systems undergo conformational changes in response to different environmental conditions, such as mutations, changes in temperature or electrostatic potential, and binding to other molecules. (loria.fr)
  • To set the stage for FCS studies of unfolded proteins, we first show that the diffusion coefficients of small molecules as well as proteins can be determined accurately even in the presence of high concentrations of co-solutes that change the solution refractive index significantly. (biu.ac.il)
  • In the basis of these calculations, the axial conformer was more stable than equatorial conformer in the studied molecules. (magiran.com)
  • 100 references, on organotin(IV) complexes of the carboxylic acid derivatives are presented with special reference to their methods of synthesis, spectroscopic and structural studies and their biological activities. (degruyter.com)
  • Synthesis and conformational analysis of a bridged anabasine and related compounds. (unthsc.edu)
  • Dive into the research topics of 'Synthesis and conformational analysis of a bridged anabasine and related compounds. (unthsc.edu)
  • Study of the Experimental and Simulated Vibrational Spectra Together with Conformational Analysis of Thioether Cyanobiphenyl-Based Liquid Crystal Dimers. (bvsalud.org)
  • The C(2) isotropic chemical shift values in solid-state CP/MAS 13 C NMR spectra of conformational polymorphs Form I (δ 28.5) and III (δ 22.9) of (1S,4S)-sertraline HCl (1) were correlated with a γ-gauche effect resulting from the respective 162.6° antiperiplanar and 68.8° (+)-synclinal C(2)-C(1)-N-CH 3 torsion angles as measured by X-ray crystallography. (bgu.ac.il)
  • We are performing studies on subcellular mechanisms of formation, trafficking and action of endogenous Aβ O in human primary cells derived from patients and ex vivo reprogrammed induced Pluripotent Stem Cells (iPSCs), with a main focus on mechanisms driven by the Endoplasmic Reticulum. (ebri.it)
  • In addition, conformational analysis can be used to predict and explain product selectivity, mechanisms, and rates of reactions. (wikipedia.org)
  • Because multi-domain proteins often undergo drastic conformational changes during their functional processes, information about their dynamic properties is essential to understand the mechanisms. (biophysics.org)
  • The 1,3-dimethylcyclohexane and 1,4-dimethylcyclohexane in both cis- and trans-configurations were focused here to unravel their conformational inversion-topomerization mechanisms. (authorea.com)
  • To honor Michael, we invite submissions for this Special Issue of Viruses focusing on Michael's interests: virus structures and assembly mechanisms, conformational transitions and structure-function relationships, and genome packaging and virus infection mechanisms. (mdpi.com)
  • Also, this review focuses on studies related to micelle formation, attraction between metal ions and micelles, and recovery of surfactants for future research. (degruyter.com)
  • The conformational analysis was performed utilizing FT-IR matrix isolation technique and theoretical methods such as density functional theory and ab initio calculations. (researchgate.net)
  • During the conformational analysis the envelope (E) and twisted (T) ring shapes with the position of the fluorine atom and chloromethyl group in terms of axial/equatorial and cis/trans/gauche-/gauche+ positions were investigated utilizing MP2/aug-cc-pVTZ and DFT/B3LYP/aug-cc-pVTZ level of theory. (researchgate.net)
  • The study of the energetics between different conformations is referred to as conformational analysis. (wikipedia.org)
  • Conformational analysis also plays an important role in rational, structure-based drug design. (wikipedia.org)
  • With respect to quantum results, the conformational analysis was conducted to gain insight into the determination, thermodynamic stabilities, and relative energies of distinct molecular geometric structures. (authorea.com)
  • Conformational Analysis of Some Hydrazinecarbothioamide Derivatives with In Vitro Antimicrobial Activity. (upt.ro)
  • In the present study a conformational analysis has been performed for N-allyl-2-(5-fluoro-2-oxo-1-(piperidin-1- ylmethyl)indolin-3-ylidene) hydrazinecarbothioamide in order to determine the possible global and local minima on the potential energy surface (PES). (upt.ro)
  • The analysis has been carried out using molecular mechanics (AMBER96) and semiempirical (AM1 and PM3) methods and the results were compared to identify the best possible approach to be used for studying the conformational space of the title compound. (upt.ro)
  • The conformational analysis of the title compound has been carried out with Conformational Search Module implemented in HyperChem 7.5 software package. (upt.ro)
  • Application in conformational analysis. (iitk.ac.in)
  • the need for high sampling density in formamide conformational analysis. (springer.com)
  • These problems can be handled either by taking into account the whole conformational ensemble or by considering rigid derivatives prepared ad hoc . (rsc.org)
  • The conformational ensemble of the enamine is still dominated by the β-turn, but the backbone and the side chain of the glutamic acid residue are more dynamic. (unibas.ch)
  • Our study demonstrated that gadolinium tagging of specific positions on the protein enables EPR distance measurements for probing the conformational ensemble of the protein. (biophysics.org)
  • Receptor fragment approach to the binding between CCK8 peptide and cholecystokinin receptors: a fluorescence study on type B receptor fragment CCK(B)-R (352-379). (uni-bielefeld.de)
  • Prior to my surface study work, I used planar laser induced fluorescence (PLIF) and optical emission techniques to investigate the gas-phase chemistry behavior in fluorocarbon plasmas used in semiconductor oxide etching. (nist.gov)
  • Design, setting, and participants: Tibial (cortical) and patellar (trabecular) bone lead levels were measured by K x-ray fluorescence between 1991 and 1999 in a subset of participants in the Normative Aging Study (NAS), a Boston-based longitudinal study of aging in men. (cdc.gov)
  • In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). (wikipedia.org)
  • The ring-flip of substituted cyclohexanes constitutes another common form of conformational isomerism. (wikipedia.org)
  • In this study, the stabilities of trans-2,3- and trans-2,5-dihalo-1,4-dioxanes conformers were investigated at the LC-BLYP/6-311+G(d,p) theory level. (magiran.com)
  • To determine how variables such as temperature, chain density, chain length, surface interactions, etc., impact the conformational phase behavior of tethered chains. (nist.gov)
  • To date, we have investigated the impact of surface interactions, chain stiffness, and tethering geometry on conformational phase behavior. (nist.gov)
  • Studying these interactions at the single-molecule level contributes significantly to our understanding of biological phenomena. (biophysics.org)
  • The intrinsic disorder and flexibility of IDPs grant them a number of advantages with respect to ordered proteins, such as conformational plasticity to bind several targets, a large interaction surface, involvement in high specificity/low affinity interactions, enhanced binding kinetics. (edu.pl)
  • We have developed a computational modeling framework for studying this process, where the combined effects of mechanical and genetic interactions are analyzed within the context of proliferating cells. (lu.se)
  • These simulations generate conformational ensembles (trajectories) to capture the motion of systems. (loria.fr)
  • This work concerns the typical conformational behaviors for di-substituted cyclohexanes that inherently depend on spatial orientations of side chains in flexible cyclic ring. (authorea.com)
  • Conformational isomers are thus distinct from the other classes of stereoisomers (i. e. configurational isomers) where interconversion necessarily involves breaking and reforming of chemical bonds. (wikipedia.org)
  • Disulfide reduced lysozyme exhibited four distinct conformational families in the gas-phase termed as the highly folded, folded, partially unfolded and unfolded. (tamuc.edu)
  • While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers. (wikipedia.org)
  • Studying an enzyme's kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism , how its activity is controlled, and how a drug or a modifier ( inhibitor or activator ) might affect the rate. (wikipedia.org)
  • Enzyme kinetics is the study of the rates of enzyme-catalysed chemical reactions . (wikipedia.org)
  • This rate-determining step may be a chemical reaction or a conformational change of the enzyme or substrates, such as those involved in the release of product(s) from the enzyme. (wikipedia.org)
  • Enzyme engineering and modification are also studied, for their application to biotechnological processes in industry. (upc.edu)
  • Overall, the study enhances the understanding of BTK's activation mechanism, autoinhibition, and allosteric control, challenging previous assumptions about BTK. (elifesciences.org)
  • Despite extensive studies, the precise mechanism of target DNA binding and on-/off-target discrimination remains incompletely understood. (biorxiv.org)
  • This study provides new evidence on the mechanism by which HCV, one of the main causes of liver cancer worldwide, evades immunity and enters cells. (who.int)
  • Density functional studies on photophysical properties and chemical reactivities of the triarylboranes: effect of the constraint of planarity. (springer.com)
  • The structures indicate that incomplete target strand pairing fails to induce the conformational displacements necessary for nuclease domain activation. (biorxiv.org)
  • We have investigated the conformational phase behavior of tethered chain systems using temperature expanded Monte Carlo techniques at thousands of state points, covering densities from the isolated chains to the thin film limit, and a broad range of temperatures. (nist.gov)
  • We have demonstrated that simulation may be used as an effective guide to understanding the conformational phase behavior of tethered chain systems. (nist.gov)
  • The similarity of the solution-state C(2) chemical shifts in CD 2 Cl 2 (δ 22.8) and DMSO-d 6 (δ 23.4) with that for Form III (and other polymorphs having C(2)-C(1)-N-CH 3 (+)-synclinal angles) strongly suggests that a conformational bias about the C(1)-N bond exists for 1 in both solvents. (bgu.ac.il)
  • Coordinadora del grup d'investigació "Biomimetic Supramolecular Chemistry and Materials", desenvolupa la seua activitat investigadora en el àmbit dels materials orgànics supramoleculars amb especial interés en els materials biomimetics i en la seua aplicació en biomedicina i en catàlisi. (uji.es)
  • Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. (lu.se)
  • Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. (elifesciences.org)
  • Single-particle cryo-electron microscopy (cryo-EM) has emerged over the last two decades as a technique capable of studying the structure of challenging systems. (nature.com)
  • Most previous structural studies on S protein have been conducted at pH 8.0, but knowledge of the conformational propensities under both physiological and endosomal pH conditions is important to inform vaccine development. (nih.gov)
  • This study presents convincing evidence, utilizing various biophysical techniques, to support a model for BTK activation that will be valuable for the field. (elifesciences.org)
  • The cover image for the 120/15 issue of Biophysical Journal conceptually shows the investigation of the conformational variation of a multidomain protein, MurD, based on the inter-gadolinium distance measurements. (biophysics.org)
  • In this work , we studied 16 mutant forms of HlyIICTD. (bvsalud.org)
  • ATP hydrolysis and the subsequent release of ADP from the NTD initiate a conformational return to the native apo open state and client release. (nature.com)
  • As Hulka has so clearly stated, "the most important current limitation in many epidemiological studies is the relative inac- curacy of methods for measuring the exposure variable" (2). (cdc.gov)
  • In silico binding study of compound 5d with plasmodial cysteine protease falcipain-2 indicated the inhibition of falcipain-2 as the probable reason for the antimalarial potency of compound 5d . (biomedcentral.com)
  • Multiple independent studies confirmed the findings of Honeyman et al by demonstrating the presence of the fusion gene in FLCs. (medscape.com)
  • Beyond imaging for scoliosis and dyspnea, imaging studies are of little help in making the diagnosis. (medscape.com)