(Q28391435)

English

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide

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25 January 2020

Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide (English)

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25 January 2020

computational biology

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5

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25 January 2020

author name string

Benjamin J Killian

1

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25 January 2020

Joslyn Yudenfreund Kravitz

2

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25 January 2020

Sandeep Somani

3

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25 January 2020

Paramita Dasgupta

4

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25 January 2020

Michael K Gilson

6

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25 January 2020

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9 April 2009

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25 January 2020

Journal of Molecular Biology

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25 January 2020

389

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25 January 2020

2

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25 January 2020

315-335

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25 January 2020

Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods

1 reference

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20 March 2017

Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules

1 reference

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20 March 2017

The Amber biomolecular simulation programs

1 reference

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20 March 2017

Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

20 March 2017

Estimating mutual information

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

20 March 2017

Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein

1 reference

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20 March 2017

Announcing the worldwide Protein Data Bank

1 reference

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20 March 2017

Structure of the Tsg101 UEV domain in complex with the PTAP motif of the HIV-1 p6 protein

1 reference

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20 March 2017

Structure and functional interactions of the Tsg101 UEV domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

20 March 2017

Overexpression of the N-terminal domain of TSG101 inhibits HIV-1 budding by blocking late domain function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

20 March 2017

HIV-1 and Ebola virus encode small peptide motifs that recruit Tsg101 to sites of particle assembly to facilitate egress

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

20 March 2017

Tsg101 and the vacuolar protein sorting pathway are essential for HIV-1 budding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

20 March 2017

Tsg101, a homologue of ubiquitin-conjugating (E2) enzymes, binds the L domain in HIV type 1 Pr55(Gag)

1 reference

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20 March 2017

The Protein Data Bank

1 reference

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20 March 2017

Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation

1 reference

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20 March 2017

Extraction of configurational entropy from molecular simulations via an expansion approximation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

6 April 2017

Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association

1 reference

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29 September 2017

Allostery: absence of a change in shape does not imply that allostery is not at play

1 reference

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29 September 2017

Empirical entropic contributions in computational docking: evaluation in APS reductase complexes.

1 reference

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29 September 2017

Induced disorder in protein-ligand complexes as a drug-design strategy

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29 September 2017

A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation

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Enthalpic and entropic contributions in the transesterification of sucrose: computational study of lipases and subtilisin

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29 September 2017

Conformational entropy in molecular recognition by proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

29 September 2017

Ligand configurational entropy and protein binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

29 September 2017

Calculation of protein-ligand binding affinities.

1 reference

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29 September 2017

Conformational heterogeneity and low-frequency vibrational modes of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

29 September 2017

Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

29 September 2017

Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy

1 reference

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29 September 2017

Probing the binding entropy of ligand-protein interactions by NMR.

1 reference

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29 September 2017

Thermodynamic interpretation of protein dynamics from NMR relaxation measurements

1 reference

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29 September 2017

Entropy calculation of HIV-1 Env gp120, its receptor CD4, and their complex: an analysis of configurational entropy changes upon complexation

1 reference

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29 September 2017

Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design

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29 September 2017

Simulation method for calculating the entropy and free energy of peptides and proteins

1 reference

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29 September 2017

Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

1 reference

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29 September 2017

Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A.

1 reference

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29 September 2017

HIV Gag mimics the Tsg101-recruiting activity of the human Hrs protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

29 September 2017

Increased backbone mobility in beta-barrel enhances entropy gain driving binding of N-TIMP-1 to MMP-3.

1 reference

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29 September 2017

Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics

1 reference

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29 September 2017

Membrane transport: ubiquitylation in endosomal sorting.

1 reference

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29 September 2017

Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex

1 reference

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29 September 2017

Estimation of mutual information using kernel density estimators.

1 reference

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29 September 2017

The statistical-thermodynamic basis for computation of binding affinities: a critical review

1 reference

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29 September 2017

Entropy in protein folding and in protein-protein interactions

1 reference

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29 September 2017

Insights into the local residual entropy of proteins provided by NMR relaxation

1 reference

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29 September 2017

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

1 reference

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29 September 2017

Backbone dynamics of the C-terminal domain of Escherichia coli topoisomerase I in the absence and presence of single-stranded DNA.

1 reference

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29 September 2017

Configurational entropy of native proteins

1 reference

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29 September 2017

Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein.

1 reference

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2 June 2018

Evaluating the Accuracy of the Quasiharmonic Approximation

1 reference

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Residual ligand entropy in the binding of p-substituted benzenesulfonamide ligands to bovine carbonic anhydrase II.

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1 reference

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27 November 2018

Evaluating the conformational entropy of macromolecules using an energy decomposition approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2758778

27 November 2018

Direct estimation of entropy loss due to reduced translational and rotational motions upon molecular binding

1 reference

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27 November 2018

New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy.

1 reference

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27 November 2018

Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding

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27 November 2018

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27 November 2018

Coarse-grained model of entropic allostery.

1 reference

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27 November 2018

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1 reference

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27 November 2018

Ubiquitin recognition by the human TSG101 protein

1 reference

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27 November 2018

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27 November 2018

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27 November 2018

15N NMR relaxation studies of free and inhibitor-bound 4-oxalocrotonate tautomerase: backbone dynamics and entropy changes of an enzyme upon inhibitor binding

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12 December 2020

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based on heuristic

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Optimized Monte Carlo data analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/19362095

12 December 2020

based on heuristic

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NMR relaxation studies of the role of conformational entropy in protein stability and ligand binding

1 reference

https://pubmed.ncbi.nlm.nih.gov/19362095

12 December 2020

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1 reference

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12 December 2020

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1 reference

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12 December 2020

based on heuristic

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Increasing the Efficiency of Free Energy Calculations Using Parallel Tempering and Histogram Reweighting

1 reference

https://pubmed.ncbi.nlm.nih.gov/19362095

12 December 2020

based on heuristic

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Identifiers

10.1016/J.JMB.2009.04.003

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25 January 2020

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25 January 2020

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25 January 2020

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