Kinetic characterization of the critical step in HIV-1 protease maturation (Q30530468)

14 August 2017

Kinetic characterization of the critical step in HIV-1 protease maturation (English)

1 reference

14 August 2017

S Kashif Sadiq

1

1 reference

14 August 2017

Frank Noé

series ordinal

2

1 reference

14 August 2017

Gianni De Fabritiis

series ordinal

3

1 reference

14 August 2017

language of work or name

English

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publication date

26 November 2012

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

14 August 2017

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14 August 2017

109

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14 August 2017

50

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14 August 2017

20449-20454

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EMMA: A Software Package for Markov Model Building and Analysis.

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Taming the complexity of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

High-throughput all-atom molecular dynamics simulations using distributed computing.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

The role of dynamic conformational ensembles in biomolecular 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=3528573

Visualizing transient events in amino-terminal autoprocessing of 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=3528573

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 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=3528573

Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained 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=3528573

HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open 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=3528573

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Initial cleavage of the human immunodeficiency virus type 1 GagPol precursor by its activated protease occurs by an intramolecular mechanism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical 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=3528573

Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Molecular dynamics simulations of biomolecules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics 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=3528573

Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of 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=3528573

20 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Kinetics and mechanism of autoprocessing of human immunodeficiency virus type 1 protease from an analog of the Gag-Pol polyprotein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Stability of dimeric retroviral proteases

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3528573

Dissociation and association of the HIV-1 protease dimer subunits: equilibria and rates.

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Influence of flanking sequences on the dimer stability of human immunodeficiency virus type 1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Proteolytic processing of HIV-1 protease precursor, kinetics and mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

A transient precursor of the HIV-1 protease. Isolation, characterization, and kinetics of maturation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Flap opening mechanism of HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Markov models of molecular kinetics: generation and validation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Coarse master equations for peptide folding dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Closing of the flaps of HIV-1 protease induced by substrate binding: a model of a flap closing mechanism in retroviral aspartic proteases

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1210983109

Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23184967

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1210983109

1 reference

14 August 2017

0 references

1 reference

14 August 2017

PubMed publication ID

23184967

1 reference