Brownian dynamics simulation of protein solutions: structural and dynamical properties (Q41151823)

27 September 2017

Brownian dynamics simulation of protein solutions: structural and dynamical properties (English)

1 reference

27 September 2017

1

1 reference

27 September 2017

Razif R Gabdoulline

2

0 references

Rebecca C Wade

object named as

Rebecca C Wade

series ordinal

3

0 references

language of work or name

English

0 references

publication date

1 December 2010

1 reference

27 September 2017

1 reference

27 September 2017

99

1 reference

27 September 2017

11

1 reference

27 September 2017

3782-3791

1 reference

Dependence of protein folding stability and dynamics on the density and composition of macromolecular crowders

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

TCR-peptide-MHC interactions in situ show accelerated kinetics and increased affinity.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Effect of macromolecular crowding on reaction rates: a computational and theoretical study

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Absence of equilibrium cluster phase in concentrated lysozyme solutions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

A consistent experimental and modeling approach to light-scattering studies of protein-protein interactions in solution.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

A mesoscopic model for protein-protein interactions in solution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Macromolecular crowding: obvious but underappreciated

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

The BPTI decamer observed in acidic pH crystal forms pre-exists as a stable species in solution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

27 September 2017

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=2998633

Effect of glycerol on the interactions and solubility of bovine pancreatic trypsin inhibitor

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Decamers observed in the crystals of bovine pancreatic trypsin inhibitor

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

The decameric structure of bovine pancreatic trypsin inhibitor (BPTI) crystallized from thiocyanate at 2.7 A resolution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Protein interactions in solution characterized by light and neutron scattering: comparison of lysozyme and chymotrypsinogen

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Molecular origins of osmotic second virial coefficients of proteins

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Effects of microheterogeneity in hen egg-white lysozyme crystallization

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Brownian dynamics simulation of protein-protein diffusional encounter

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Comparative protein modelling by satisfaction of spatial restraints

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Thermodynamics of BPTI folding

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Nonadditive effects of mixed crowding on protein stability

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Simulation of the diffusional association of barnase and barstar.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Temperature dependence on structure and dynamics of Bovine Pancreatic Trypsin Inhibitor (BPTI): a neutron scattering study

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Influence of macromolecular crowding on protein-protein association rates--a Brownian dynamics study

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Large-scale molecular dynamics simulations of self-assembling systems.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

A small-angle scattering study on equilibrium clusters in lysozyme solutions.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Repartitioning of NaCl and protein impurities in lysozyme crystallization.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Macromolecular diffusion in crowded solutions

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

On the Contributions of Diffusion and Thermal Activation to Electron Transfer betweenPhormidium laminosumPlastocyanin and Cytochromef: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Eve

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998633

Growth of (101) faces of tetragonal lysozyme crystals: measured growth-rate trends

2 December 2018

1 reference

12 December 2020

Measured and calculated effects of mutations in bacteriophage T4 lysozyme on interactions in solution

1 reference

12 December 2020

Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme

1 reference

12 December 2020

Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems

1 reference

12 December 2020

Exploring bovine pancreatic trypsin inhibitor phase transitions

1 reference

12 December 2020

Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular crowding

1 reference

12 December 2020

The concentration dependence of the diffusion coefficient for bovine pancreatic trypsin inhibitor: a dynamic light scattering study of a small protein

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

12 December 2020

Effect of salt concentration on the pKa of acidic residues in lysozyme

1 reference

12 December 2020

A pulsed-field gradient NMR study of bovine pancreatic trypsin inhibitor self-association

1 reference

12 December 2020

Dynamics of hard-sphere suspensions

1 reference

12 December 2020

10.1016/J.BPJ.2010.10.035

Identifiers

DOI

1 reference

27 September 2017

1 reference

27 September 2017

1 reference

PMCID

2998633