(Q33395463)

26 July 2017

Protein side-chain dynamics and residual conformational entropy (English)

1 reference

26 July 2017

Nikola Trbovic

1

1 reference

26 July 2017

Jae-Hyun Cho

2

1 reference

26 July 2017

Robert Abel

3

1 reference

26 July 2017

Richard A Friesner

4

1 reference

26 July 2017

Mark Rance

5

1 reference

26 July 2017

Arthur G Palmer

6

1 reference

26 July 2017

language of work or name

English

0 references

publication date

1 January 2009

1 reference

Journal of the American Chemical Society

26 July 2017

1 reference

26 July 2017

131

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26 July 2017

2

1 reference

26 July 2017

615-622

1 reference

Quantitative lid dynamics of MDM2 reveals differential ligand binding modes of the p53-binding cleft.

26 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Evaluating rotational diffusion from protein MD simulations

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Conformational entropy in molecular recognition by proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Heteronuclear NMR spectroscopy for lysine NH(3) groups in proteins: unique effect of water exchange on (15)N transverse relaxation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

An inserted Gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases H

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Comparison of multiple Amber force fields and development of improved protein backbone parameters

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

The origin of protein sidechain order parameter distributions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

AANT: the Amino Acid-Nucleotide Interaction Database

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Protein dynamics from solution NMR: theory and applications

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

An improved hydrogen bond potential: impact on medium resolution protein structures.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Arginine side-chain dynamics in the HIV-1 rev-RRE complex

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

The penultimate rotamer library

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Calculations of NMR dipolar coupling strengths in model peptides

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Anatomy of hot spots in protein interfaces

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-correlation NMR experiments: application to the N-terminal SH3 domain from drk.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Backbone and side chain dynamics of lac repressor headpiece (1-56) and its complex with DNA.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Spectral density function mapping using 15N relaxation data exclusively

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Empirical scale of side-chain conformational entropy in protein folding

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Dynamics of beta-CH and beta-CH2 Groups of Amino Acid Side Chains in Proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Multiple-timescale dynamics of side-chain carboxyl and carbonyl groups in proteins by 13C nuclear spin relaxation.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Retention of conformational flexibility in HIV-1 Rev-RNA complexes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Measurement of dipolar cross-correlation in methylene groups in uniformly 13C-, 15N-labeled proteins

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Cross-correlation suppressed T1 and NOE experiments for protein side-chain 13CH2 groups.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Dynamics of ribonuclease H: temperature dependence of motions on multiple time scales.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

31 October 2018

Ion-pairs in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2683258

Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI

31 October 2018

1 reference

12 December 2020

General Framework for Studying the Dynamics of Folded and Nonfolded Proteins by NMR Relaxation Spectroscopy and MD Simulation

1 reference

12 December 2020

A simple method to measure 13CH2 heteronuclear dipolar cross-correlation spectral densities

1 reference

12 December 2020

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

1 reference

12 December 2020

Structural and Dynamic Characterization of the Phosphotyrosine Binding Region of an Src Homology 2 Domain-Phosphopeptide Complex by NMR Relaxation, Proton Exchange, and Chemical Shift Approaches

1 reference

12 December 2020

Structural Determinants of Protein Dynamics: Analysis of 15N NMR Relaxation Measurements for Main-Chain and Side-Chain Nuclei of Hen Egg White Lysozyme

1 reference

12 December 2020

Differential modulation of binding loop flexibility and stability by Arg50 and Arg52 in Cucurbita maxima trypsin inhibitor-V deduced by trypsin-catalyzed hydrolysis and NMR spectroscopy

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA806475K

1 reference

26 July 2017

1 reference

26 July 2017

1 reference