[NMR paper] Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches.
Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches.
Related ArticlesConformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches.
J Phys Chem B. 2020 Sep 26;:
Authors: Mendelman N, Zerbetto M, Buck M, Meirovitch E
Abstract
A new method for determining conformational entropy in proteins is reported. Proteins prevail as conformational ensembles, p ? exp(-u). By selecting a bond-vector (e.g., N-H) as conformation representative, MD simulations can provide (relative to a reference structure) p as approximate Boltzmann probability density and u as N-H Potential of Mean Force (POMF). The latter is as accurate as the force-field but statistical in character; this limits the insight it can provide, and its utilization. Conformational entropy is given exclusively by u. Deriving it from POMFs renders it accurate but statistical in character. Previously we devised explicit (i.e., analytical but not exact) potentials made of Wigner functions, DL0K, with L
Did you find this post helpful? |
Similar Threads
Thread
Thread Starter
Forum
Replies
Last Post
[NMR paper] Conformational Entropy from Restricted Bond-Vector Motion in Proteins: The Symmetry of the Local Restrictions and Relation to NMR Relaxation.
Conformational Entropy from Restricted Bond-Vector Motion in Proteins: The Symmetry of the Local Restrictions and Relation to NMR Relaxation.
Related Articles Conformational Entropy from Restricted Bond-Vector Motion in Proteins: The Symmetry of the Local Restrictions and Relation to NMR Relaxation.
J Phys Chem B. 2020 May 01;:
Authors: Mendelman N, Meirovitch E
Abstract
Locally-mobile bond-vectors contribute to the conformational entropy of the protein, given by Sk = S/k = -? (Peq ln Peq) d? - ln ? d?. The quantity Peq =...
nmrlearner
Journal club
0
05-03-2020 02:46 PM
[NMR paper] Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Conformational entropy of FK506 binding to FKBP12 determined by NMR relaxation and molecular dynamics simulations.
Biochemistry. 2018 Feb 07;:
Authors: Solomentsev G, Diehl C, Akke M
Abstract
FKBP12 (FK506 binding protein 12 kDa) is an important drug target that attracts a great deal of interest as a model system for computational drug design and studies on the role of protein dynamics in ligand binding. NMR...
nmrlearner
Journal club
0
02-08-2018 04:32 PM
[NMR paper] Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation.
Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7315-19-Wiley_FullText_120x30_orange.png Related Articles Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation.
Chembiochem. 2017 Feb 16;18(4):396-401
...
nmrlearner
Journal club
0
07-05-2017 10:27 AM
[NMR paper] (15)N-H-Related Conformational Entropy Changes Entailed By Plexin-B1 RBD Dimerization: A Combined Molecular Dynamics/NMR Relaxation Approach.
(15)N-H-Related Conformational Entropy Changes Entailed By Plexin-B1 RBD Dimerization: A Combined Molecular Dynamics/NMR Relaxation Approach.
Related Articles (15)N-H-Related Conformational Entropy Changes Entailed By Plexin-B1 RBD Dimerization: A Combined Molecular Dynamics/NMR Relaxation Approach.
J Phys Chem B. 2017 Mar 10;:
Authors: Zerbetto M, Meirovitch E
Abstract
We report on a new method for determining function-related conformational entropy changes in proteins. Plexin-B1 RBD dimerization serves as example, and...
nmrlearner
Journal club
0
03-11-2017 05:12 PM
[NMR paper] Conformational Entropy from NMR Relaxation in Proteins: the SRLS Perspective.
Conformational Entropy from NMR Relaxation in Proteins: the SRLS Perspective.
Related Articles Conformational Entropy from NMR Relaxation in Proteins: the SRLS Perspective.
J Phys Chem B. 2017 Jan 06;:
Authors: Tchaicheeyan O, Meirovitch E
Abstract
Conformational entropy changes associated with bond-vector motions in proteins contribute to the free energy of ligand binding. To derive such contributions we apply the slowly relaxing local structure (SRLS) approach to NMR relaxation from (15)N-H bonds or C-CDH2 moieties of several...
nmrlearner
Journal club
0
01-07-2017 01:27 PM
[NMR paper] Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.
Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.
Related Articles Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.
J Phys Chem Lett. 2016 Jun 14;
Authors: Salvi N, Abyzov A, Blackledge M
Abstract
Intrinsically disordered proteins (IDPs) access highly diverse ensembles of conformations in their functional states. Although this plasticity is essential to their function, little is known about the dynamics underlying...
nmrlearner
Journal club
0
06-15-2016 11:12 PM
[NMR paper] Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.
Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.
Adv Exp Med Biol. 2015;842:217-30
Authors: Zhang Y, Yamaguchi T, Satoh T, Yagi-Utsumi M, Kamiya Y,...
nmrlearner
Journal club
0
05-02-2015 09:41 PM
[NMR paper] Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins.
Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins.
Related Articles Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins.
Chemphyschem. 2001 Sep 17;2(8-9):539-43
Authors: Deschamps M, Bodenhausen G
Abstract
Cross correlations between the fluctuations of dipolar (13) C(?) -(1) H(?) interactions yield information about the relative orientation of successive (13) C(?) -(1) H(?) bond vectors...
Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches.
Linear Mode
