• FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. (researchgate.net)
  • Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations. (ncbs.res.in)
  • We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. (nist.gov)
  • By combining cryo-electron microscopy (cryo-EM) with in vitro reconstitution and molecular dynamics simulations, we show how actin filaments release P i through a 'molecular backdoor' and demonstrate that this arrangement is distorted in a disease-linked actin variant. (nature.com)
  • We are studying the conformational changes of the extracellular domain using a combination of submicrosecond Molecular Dynamics simulations and Elastic Network Models. (ub.es)
  • We combine NMR relaxation experiments with molecular dynamics (MD) simulations to derive a highly detailed picture of how the conformational entropy changes when the protein binds different ligands. (lu.se)
  • The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. (uniroma1.it)
  • These simulations generate conformational ensembles (trajectories) to capture the motion of systems. (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)
  • In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. (lu.se)
  • A more detailed, atomic-level description of the structure, dynamics and compaction of IDPs, may however, be obtained from molecular simulations, but these need to be validated or generated by comparison with experiments. (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)
  • International journal of molecular sciences 2023 0 0. (cdc.gov)
  • Proteins evolve the capacity for conformational proofreading through fine-tuning their geometry, flexibility and chemical interactions with the target. (wikipedia.org)
  • The ribosome is a complex molecular machine that, in order to synthesize proteins during the translation process, has to decode mRNAs by pairing their codons with matching tRNAs. (wikipedia.org)
  • In the current study, a molecular docking approach was employed to explore the interactive behavior of TNFR1 and MADD proteins and their role in the activation of downstream signaling pathways. (uaeu.ac.ae)
  • This DDs interaction mediates some conformational changes in TNFR1 which leads to the activation of mediators proteins in the cellular signaling pathways. (uaeu.ac.ae)
  • 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)
  • On the other hand, computational approaches have been developed to investigate the conformational dynamics in proteins [4,5,6]. (loria.fr)
  • Despite their importance in protein functions, the conformational states of proteins and their changes are often poorly understood, mainly because of the lack of an efficient strategy. (biophysics.org)
  • A higher magnitude of conformational dynamics and variations are expected, especially for multi-domain proteins consisting of multiple structural domains. (biophysics.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)
  • Dynamic and conformational switching in proteins. (rochester.edu)
  • In the present study, through extensive computational docking and multi-ns molecular dynamics (MD) simulation, we evaluated if cyclotides can stably bind to Aβ molecules and/or destabilize the Aβ fibril by preventing conformational changes from α-helical to β-sheet rich structures. (ncbs.res.in)
  • Laser-based gas phase spectroscopy, combined with ab initio calculations, generates precise molecular structural information on molecules such as neurotransmitters that provide a rigorous platform for understanding their behaviour and, ultimately, rationalising drug design. (edu.au)
  • We incorporate this conformational sampling strategy in our alchemical binding free energy estimation protocol and we apply it to a well-known benchmark system: the complex of the L99A mutant of T4 lysozyme with small organic molecules which display varying configurations of protein side chains. (compmolbiophysbc.org)
  • 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)
  • 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)
  • The newer cellulose triacetate dialyzers and the high-flux synthetic dialyzers remove molecules with a higher molecular weight and do a better job of removing beta-2m. (medscape.com)
  • 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)
  • A nuclear magnetic resonance spectroscopy and molecular modeling study. (unthsc.edu)
  • Valence photoelectron spectroscopy of N-2 and CO: Recoil-induced rotational excitation, relative intensities, and atomic orbital composition of molecular orbitals. (uib.no)
  • This is perhaps one reason why protein conformational entropy has not received widespread attention in the field of ligand/drug design, while the often dominant role of solvent entropy is generally taken into account, together with the change in ligand entropy. (lu.se)
  • Both join in Simon´s lab in 2018 for Post-Doctorate and Doctorate, respectively, eager to investigate the connection between protein conformational changes and liquid-liquid phase separation inside living cells. (spp2191.com)
  • In the ideal scenario, we would be able to attribute the contributions from individual molecular groups to the enthalpy and entropy of binding. (lu.se)
  • Arguably, one of the greatest challenges lies in evaluating the conformational entropy of the target protein, which involves a very large number of degrees of freedom. (lu.se)
  • For these reasons, we are interested in the role of the conformational entropy of the target protein in ligand-binding processes. (lu.se)
  • NMR relaxation experiments provide a unique probe of conformational entropy by characterizing bond-vector fluctuations at atomic resolution. (lu.se)
  • By comparing NMR-derived order parameters between the free and ligand-bound protein, we estimate the contributions from conformational entropy to the free energy of ligand binding. (lu.se)
  • In collaboration with experts in computational chemistry, we aim to derive robust protocols for evaluating changes in conformational entropy that have been validated against NMR data. (lu.se)
  • One of those entropies is dihedral conformational entropy by histogramming. (lu.se)
  • Esposito, G. PDB2ENTROPY and PDB2TRENT: Conformational and Translational-Rotational Entropy from Molecular Ensembles. (lu.se)
  • 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)
  • Exploration of the Shared Molecular Mechanisms between COVID-19 and Neurodegenerative Diseases through Bioinformatic Analysis. (cdc.gov)
  • 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)
  • Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. (mdpi.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)
  • Conformational proofreading or conformational selection is a general mechanism of molecular recognition systems, suggested by Yonatan Savir and Tsvi Tlusty, in which introducing an energetic barrier - such as a structural mismatch between a molecular recognizer and its target - enhances the recognition specificity and quality. (wikipedia.org)
  • 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)
  • The computational sequential and structural conformational results revealed that Asp400, Arg58, Arg59 were common residues of TNFR1 and MADD which are involved in the activation of downstream signaling pathways. (uaeu.ac.ae)
  • Structural dimer features which characterize the most stable energetically conformations obtained by molecular and quantum mechanics methods were compared, yielding a unified dimer structure. (upt.ro)
  • The comparison between computed conformational ensembles and NMR and SAXS experiments is, however, not trivial. (lu.se)
  • Target hybridisation past the seed region positions the guide-target heteroduplex into the central binding channel and results in a conformational rearrangement of the REC lobe. (biorxiv.org)
  • Inhibited by human cytomegalovirus US6 glycoprotein, which binds to the lumenal side of the TAP complex and inhibits peptide translocation by specifically blocking ATP-binding to TAP1 and prevents the conformational rearrangement of TAP induced by peptide binding. (lu.se)
  • Thank you for sharing this Molecular Pharmacology article. (aspetjournals.org)
  • Message Body (Your Name) thought you would be interested in this article in Molecular Pharmacology. (aspetjournals.org)
  • 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)
  • Previous studies in our laboratory characterized a panel of highly mutated HIV-specific conformational epitope-targeting antibodies (Abs) from a panel of HIV-infected long-term nonprogressors (LTNPs). (nih.gov)
  • The fact that different amino acids were included in the epitope depending on the targeted protein supports the conclusion that 2C6 targets a native conformational epitope. (nih.gov)
  • conformational epitope. (nih.gov)
  • Predicted philogeny, secondary conformational structure, and epitope antigenicity of immunological sequences in poultry. (geneticsmr.com)
  • The molecular processes that drive MO formation are largely unknown, but recent deletion experiments showed that their formation and function is often associated with intrinsically disordered protein domains. (spp2191.com)
  • Sjoberg P, Politzer P. Use of the electrostatic potential at the molecular surface to interpret and predict nucleophilic processes. (springer.com)
  • Integrated multi-omics approach identified molecular mechanism and pathogenetic processes of COVID-19 that affect patient with Parkinson's disorder. (cdc.gov)
  • Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. (mdpi.com)
  • Molecular modeling is the field of characterizing structure of biomolecules. (loria.fr)
  • 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)
  • In this paper the structure of a diarylazo phosphate was simulated by molecular mechanics methods using the MM+, AMBER and MMFF94s force fields included in the Hyperchem, respectively Omega software. (upt.ro)
  • Methods in Molecular Biology, 903, 65-101. (scirp.org)
  • Methods in molecular biology. (rochester.edu)
  • Marx D, Hutter J. Ab Initio Molecular Dynamics-Basic Theory and Advanced Methods . (springer.com)
  • Develop your entrepreneurial skills while you study molecular biology to enhance your employability. (manchester.ac.uk)
  • The molecular biology and clinical features of amyloid neuropathy. (medlineplus.gov)
  • Current issues in molecular biology 2022 0 0. (cdc.gov)
  • The conformational shape of biomolecules and their interactions with the surrounding environment including water are critical to their functioning. (edu.au)
  • Furthermore, our molecular dynamic simulation results also ensured the stability of the backbone of TNFR1 and MADD death domains (DDs) in binding interactions. (uaeu.ac.ae)
  • Partitioning conformational intermediates between competing refolding and aggregation pathways: insights into transthyretin amyloid disease. (medlineplus.gov)
  • Thus, our findings reveal a crucial role for C12ORF40/REDIC1 in meiotic crossover formation by stabilizing the recombination intermediates, providing prospective molecular targets for the clinical diagnosis and therapy of infertility. (bvsalud.org)
  • Loss of function in phenylketonuria is caused by impaired molecular motions and conformational instability. (drugbank.com)
  • To address this problem, here we test a heating & cooling conformational sampling strategy where we heat the system to enable side chains motions and then cool it before production at room temperature. (compmolbiophysbc.org)
  • We also investigated the conformational dynamics of the same protein by X-ray scattering, neutron scattering, and MD simulation. (biophysics.org)
  • Molecular modelling demonstrated that in 1-nitrosoindolizines, the position of the conformational equilibrium is due to steric effects, while for 3-nitrosoindolizines electronic effects prevail. (rsc.org)
  • 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)
  • TY - JOUR T1 - Carbohydrate specificity and salt-bridge mediated conformational change in acidic winged bean agglutinin. (unboundmedicine.com)
  • Modulation of the Conformational Space of SARS-CoV-2 RNA Quadruplex RG-1 by Cellular Components and the Amyloidogenic Peptides α-Synuclein and hIAPP. (cdc.gov)
  • The mechanism of conformational proofreading is utilized in the system of homologous recombination to discern between similar DNA sequences. (wikipedia.org)
  • for the remaining 10 sequences, 20 conformational structures per sequence were predicted and the most stable sequences were identified by their minimum free energy values. (geneticsmr.com)
  • Conformational proofreading does not require the consumption of energy and may therefore be used in any molecular recognition system. (wikipedia.org)
  • This artificial molecular recognition system has significant advantages such as mechanical/chemical stability, low cost, and ease of preparation, thus have increasingly attracted considerable attention [14,15]. (ebrary.net)
  • Furthermore, the conformational analysis of isoetharine and several beta 2 -adrenergic-stimulating agents made it possible to restrict three dihedral angles so that the molecule was beta 2 -active. (aspetjournals.org)
  • 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)
  • 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)
  • The use of global and local molecular parameters for the analysis of the gas-phase basicity of amines. (springer.com)
  • Electronic population analysis on LCAO-MO molecular wave functions. (springer.com)
  • the need for high sampling density in formamide conformational analysis. (springer.com)
  • C. Bottari , I. Mancini , A. Mele , A. Gessini , C. Masciovecchio , and B. Rossi "Conformational stability of DNA in hydrated ionic liquid by synchrotron-based UV resonance raman", Proc. (spiedigitallibrary.org)
  • analyze classical scrapie, including CH1641-like , from natural goat the conformational stability of CH1641-like isolates, BSE, BSE and experimental sheep 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 structures indicate that incomplete target strand pairing fails to induce the conformational displacements necessary for nuclease domain activation. (biorxiv.org)
  • Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states. (rochester.edu)
  • Water, lipids, and natural moisturizing factor (NMF) influence the molecular structures that affect the properties of SC, including water sorption and binding enthalpy. (cdc.gov)
  • We are excited to collaborate with experts in SPP 2191 to unravel the molecular details and functional aspect of LLPS. (spp2191.com)
  • On completion of the course, students are to have acquired basic knowledge and broad understanding of medicinal chemistry and pharmacological principles from a molecular perspective. (lu.se)
  • Therefore here in this study, we have decided to construct the molecular hybrids based on 1,4-DHP and pyrazole moieties using acyl hydrazone linkage which may possibly circumvent the antiplasmodial drug resistance (Fig. 1 ). (biomedcentral.com)
  • In our study, we exploited a paramagnetic lanthanide ion, Gd 3+ , in electron paramagnetic resonance (EPR) experiments and measured the inter-gadolinium distance distribution that reflects the conformational states of the protein. (biophysics.org)
  • 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)
  • Additional amino acids at sites 524 and 579 were also identified, helping explain its conformational requirement. (nih.gov)
  • 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)
  • Shared molecular signatures between coronavirus infection and neurodegenerative diseases provide targets for broad-spectrum drug development. (cdc.gov)
  • if immediate recombination does not occur, these can manifest as some type of molecular, cellular, or organic system alteration. (cdc.gov)
  • Physical Review A. Atomic, Molecular, and Optical Physics (PRA). (uib.no)
  • Journal of Physics B: Atomic, Molecular and Optical Physics. (uib.no)
  • Unlike non- ionizing radiation (such as microwaves and ultraviolet radiation), which has insufficient energy to eject molecular electrons, ionizing radiation deposits sufficient energy to remove electrons from atomic orbits and create molecular ion pairs along particle tracks. (cdc.gov)
  • Addressing the limitations of conventional molecular imprinting techniques, several research groups have begun to explore alternative approaches for developing new imprinting methodologies. (ebrary.net)