(Q30380115)

19 August 2017

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding (English)

1 reference

19 August 2017

2

Ivet Bahar

0 references

author name string

Ahmet Bakan

series ordinal

1

1 reference

PMC publication ID

2728110

19 August 2017

language of work or name

English

0 references

publication date

17 August 2009

1 reference

Proceedings of the National Academy of Sciences of the United States of America

19 August 2017

6

1 reference

based on heuristic

inferred from page(s)

published in

1 reference

19 August 2017

106

1 reference

19 August 2017

34

1 reference

19 August 2017

14349-14354

1 reference

Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

A Coupled Equilibrium Shift Mechanism in Calmodulin-Mediated Signal Transduction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Binding-induced folding of a natively unstructured transcription factor.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Flexible ligand docking to multiple receptor conformations: a practical alternative

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Ensemble Refinement of Protein Crystal Structures: Validation and Application

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Molecular basis of MAPK-activated protein kinase 2:p38 assembly

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Efficient molecular docking of NMR structures: application to HIV-1 protease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Relation between native ensembles and experimental structures of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

New tools provide new insights in NMR studies of protein dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

The role of dynamics in allosteric regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

p38 MAP kinases: key signalling molecules as therapeutic targets for inflammatory diseases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Conformational change of proteins arising from normal mode calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Anisotropy of fluctuation dynamics of proteins with an elastic network model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Temperature-dependent equilibrium between the open and closed conformation of the p66 subunit of HIV-1 reverse transcriptase revealed by site-directed spin labelling.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Folding funnels and binding mechanisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Investigating protein dynamics in collective coordinate space

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Mechanisms of cyclin-dependent kinase regulation: structures of Cdks, their cyclin activators, and Cip and INK4 inhibitors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

The structure of mitogen-activated protein kinase p38 at 2.1-A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2728110

Anisotropic network model: systematic evaluation and a new web interface.

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Representing receptor flexibility in ligand docking through relevant normal modes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Effect of a bound non-nucleoside RT inhibitor on the dynamics of wild-type and mutant HIV-1 reverse transcriptase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Protein flexibility in ligand docking and virtual screening to protein kinases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0904214106

Functional modes of proteins are among the most robust

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19706521

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0904214106

1 reference

19 August 2017

0 references

1 reference

PMC publication ID

2728110

19 August 2017

PubMed publication ID

19706521

1 reference

PMC publication ID

2728110