[NMR paper] Integrative approaches for characterizing protein dynamics: NMR, CryoEM, and computer simulations
Integrative approaches for characterizing protein dynamics: NMR, CryoEM, and computer simulations
Proteins are inherently dynamic and their internal motions are essential for biological function. Protein motions cover a broad range of timescales: 10^(-14)-10 s, spanning from sub-picosecond vibrational motions of atoms via microsecond loop conformational rearrangements to millisecond large amplitude domain reorientations. Observing protein dynamics over all timescales and connecting motions and structure to biological mechanisms requires integration of multiple experimental and...
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12-05-2023 11:45 AM
[NMR paper] Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations
Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations
Intrinsically disordered regions of proteins often mediate important protein-protein interactions. However, the folding-upon-binding nature of many polypeptide-protein interactions limits the ability of modeling tools to predict the three-dimensional structures of such complexes. To address this problem, we have taken a tandem approach combining NMR chemical shift data and molecular simulations to determine the structures of peptide-protein complexes. Here,...
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03-31-2023 09:21 AM
[NMR paper] Probing Methyl Group Dynamics in Proteins by NMR Cross-Correlated Dipolar Relaxation and Molecular Dynamics Simulations
Probing Methyl Group Dynamics in Proteins by NMR Cross-Correlated Dipolar Relaxation and Molecular Dynamics Simulations
Nuclear magnetic resonance (NMR) spin relaxation is the most informative approach to experimentally probe the internal dynamics of proteins on the picosecond to nanosecond time scale. At the same time, molecular dynamics (MD) simulations of biological macromolecules are steadily improving through better physical models, enhanced sampling methods, and increased computational power, and they provide exquisite information about flexibility and its role in protein stability...
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations - Science Advances
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations - Science Advances
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations Science AdvancesWe present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are ...
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03-24-2019 10:41 PM
[NMR paper] Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.
Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.
Related Articles Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.
J Biomol Struct Dyn. 2014 Aug 8;:1-10
Authors: Zhang J, Wang F, Zhang Y
Abstract
Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and...
Integrative Molecular Dynamics Simulations Untangle Cross-Linking Data to Unveil Mitochondrial Protein Distributions
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