(Q36246465)

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Simulations of HIV capsid protein dimerization reveal the effect of chemistry and topography on the mechanism of hydrophobic protein association

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scholarly article

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Simulations of HIV capsid protein dimerization reveal the effect of chemistry and topography on the mechanism of hydrophobic protein association (English)

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

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based on heuristic

Michael F Hagan

2

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

author name string

Naiyin Yu

1

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Europe PubMed Central

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13 February 2020

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1 September 2012

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Biophysical Journal

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

103

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

6

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Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1363-1369

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

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1 October 2017

Sitting at the edge: how biomolecules use hydrophobicity to tune their interactions and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling

1 reference

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1 October 2017

Mechanisms of kinetic trapping in self-assembly and phase transformation

1 reference

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1 October 2017

Rationally designed interfacial peptides are efficient in vitro inhibitors of HIV-1 capsid assembly with antiviral activity

1 reference

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1 October 2017

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

1 reference

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1 October 2017

Atomic-level modelling of the HIV capsid

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Interfacial thermodynamics of confined water near molecularly rough surfaces

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Disulfide bond stabilization of the hexameric capsomer of human immunodeficiency virus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Understanding the concentration dependence of viral capsid assembly kinetics--the origin of the lag time and identifying the critical nucleus size

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Fluctuations of water near extended hydrophobic and hydrophilic surfaces

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

The capsid protein of human immunodeficiency virus: intersubunit interactions during virus assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

X-ray structures of the hexameric building block of the HIV capsid

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Capsid (CA) protein as a novel drug target: recent progress in the research of HIV-1 CA inhibitors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Mutational analysis and allosteric effects in the HIV-1 capsid protein carboxyl-terminal dimerization domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Molecular structural basis for polymorphism in Alzheimer's -amyloid fibrils

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Dewetting and hydrophobic interaction in physical and biological systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Paired beta-sheet structure of an Abeta(1-40) amyloid fibril revealed by electron microscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Hydrophobicity of protein surfaces: Separating geometry from chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Structure of full-length HIV-1 CA: a model for the mature capsid lattice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Flexibility in HIV-1 Assembly Subunits: Solution Structure of the Monomeric C-Terminal Domain of the Capsid Protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Canonical sampling through velocity rescaling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Dynamic pathways for viral capsid assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Interfaces and the driving force of hydrophobic assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Competing hydrophobic and screened-coulomb interactions in hepatitis B virus capsid assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Assembly properties of the human immunodeficiency virus type 1 CA protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Are weak protein–protein interactions the general rule in capsid assembly?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Diversity of protein-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Functional Surfaces of the Human Immunodeficiency Virus Type 1 Capsid Protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Model-based analysis of assembly kinetics for virus capsids or other spherical polymers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Structures of the HIV-1 capsid protein dimerization domain at 2.6 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Structure of the carboxyl-terminal dimerization domain of the HIV-1 capsid protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Thermodynamic and structural analysis of microtubule assembly: the role of GTP hydrolysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Coupling of local folding to site-specific binding of proteins to DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Solvation energy in protein folding and binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

1 October 2017

Role of water in mediating the assembly of Alzheimer amyloid-beta Abeta16-22 protofilaments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

29 June 2018

Fluctuation-dissipation ratios in the dynamics of self-assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

29 June 2018

An extensive thermodynamic characterization of the dimerization domain of the HIV-1 capsid protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

29 June 2018

Calculation of the free energy of association for protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

29 June 2018

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Studies of reversible capsid shell growth

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Structural mobility of the monomeric C-terminal domain of the HIV-1 capsid protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Observation of a dewetting transition in the collapse of the melittin tetramer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Electrostatic repulsion, compensatory mutations, and long-range non-additive effects at the dimerization interface of the HIV capsid protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Thermodynamic dissection of a low affinity protein-protein interface involved in human immunodeficiency virus assembly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Weak protein-protein interactions are sufficient to drive assembly of hepatitis B virus capsids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Conformational stability of dimeric and monomeric forms of the C-terminal domain of human immunodeficiency virus-1 capsid protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3446662

22 September 2018

Hydration of protein-protein interfaces

1 reference

https://pubmed.ncbi.nlm.nih.gov/22995509

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hydrophobic collapse in multidomain protein folding

1 reference

https://pubmed.ncbi.nlm.nih.gov/22995509

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation

1 reference

https://pubmed.ncbi.nlm.nih.gov/22995509

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mapping hydrophobicity at the nanoscale: applications to heterogeneous surfaces and proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/22995509

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Surface topography dependence of biomolecular hydrophobic hydration

1 reference

https://pubmed.ncbi.nlm.nih.gov/22995509

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Morphology of protein-protein interfaces.

1 reference

https://pubmed.ncbi.nlm.nih.gov/22995509

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1016/J.BPJ.2012.08.016

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22995509%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

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