The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics (Q33987369)

30 July 2017

title

The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics (English)

1 reference

30 July 2017

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics (English)

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

9 December 2024

1 reference

molecular dynamics simulation

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:21829336

9 December 2024

4

M. Neal Waxham

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:21829336

9 December 2024

5

Margaret S. Cheung

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:21829336

9 December 2024

author name string

Qian Wang

1

1 reference

30 July 2017

Kao-Chen Liang

2

1 reference

30 July 2017

Arkadiusz Czader

3

1 reference

30 July 2017

language of work or name

English

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21829336

9 December 2024

publication date

28 July 2011

1 reference

full work available at URL

30 July 2017

https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002114&type=printable

file format

Portable Document Format

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:21829336

https://europepmc.org/articles/PMC3145654

9 December 2024

file format

HyperText Markup Language

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:21829336

https://europepmc.org/articles/PMC3145654?pdf=render

9 December 2024

file format

Portable Document Format

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC:MED AND EXT_ID:21829336

http://dx.plos.org/10.1371/journal.pcbi.1002114

9 December 2024

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

PLOS Computational Biology

9 December 2024

published in

1 reference

30 July 2017

volume

7

1 reference

30 July 2017

issue

7

1 reference

30 July 2017

page(s)

e1002114

1 reference

Creative Commons Attribution 4.0 International

30 July 2017

copyright license

start time

28 July 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

All-atom empirical potential for molecular modeling and dynamics studies of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Effects of macromolecular crowding on protein conformational changes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Intra- and interdomain effects due to mutation of calcium-binding sites in calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

The effect of calcium ions and peptide ligands on the relative stabilities of the calmodulin dumbbell and compact structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Single-molecule force spectroscopy distinguishes target binding modes of calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Folding, stability and shape of proteins in crowded environments: experimental and computational approaches

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Crowded, cell-like environment induces shape changes in aspherical protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

The influence of macromolecular crowding on HIV-1 protease internal dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Protein grabs a ligand by extending anchor residues: molecular simulation for Ca2 binding to calmodulin loop

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Molecular crowding enhances native state stability and refolding rates of globular proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Mechanical unfolding of RNA hairpins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

NMR and molecular dynamics studies of the interaction of melatonin with calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Structure, dynamics and interaction with kinase targets: computer simulations of calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Calmodulin signaling via the IQ motif

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Macromolecular crowding: an important but neglected aspect of the intracellular environment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Ligand binding and thermodynamic stability of a multidomain protein, calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Calmodulin: a prototypical calcium sensor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide spin label and two-dimensional NMR study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Structure and dynamics of calmodulin in solution.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Interactions between domains of apo calmodulin alter calcium binding and stability.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Theory of protein folding: the energy landscape perspective

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

The Role of β-Sheet Interactions in Domain Stability, Folding, and Target Recognition Reactions of Calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Calcium binding decreases the stokes radius of calmodulin and mutants R74A, R90A, and R90G

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

VMD: visual molecular dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Pre-formation of the semi-open conformation by the apo-calmodulin C-terminal domain and implications binding IQ-motifs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Blocking the Ca2 -induced conformational transitions in calmodulin with disulfide bonds

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Kinetics and thermodynamics of folding in model proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

The Merck Frosst Award Lecture 1994. Calmodulin: a versatile calcium mediator protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Solution structure of calcium-free calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Calcium-induced conformational transition revealed by the solution structure of apo calmodulin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3145654

Probing Ca2 -induced conformational changes in porcine calmodulin by H/D exchange and ESI-MS: effect of cations and ionic strength

5 July 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Modulation of calmodulin plasticity by the effect of macromolecular crowding

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Thermal unfolding simulations of apo-calmodulin using leap-dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Multiscale investigation of chemical interference in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome c.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Charge-charge interactions influence the denatured state ensemble and contribute to protein stability

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Computational modeling predicts the structure and dynamics of chromatin fiber

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Role of the N- and C-lobes of calmodulin in the activation of Ca(2 )/calmodulin-dependent protein kinase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Excluded volume as a determinant of macromolecular structure and reactivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

On Interaction between Two Bodies Immersed in a Solution of Macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Interaction between particles suspended in solutions of macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Slow Conformational Dynamics and Unfolding of the Calmodulin C-Terminal Domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of salt

21 January 2018

1 reference

12 December 2020

Conformation and thermal denaturation of apocalmodulin: role of electrostatic mutations

1 reference

12 December 2020

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

1 reference

12 December 2020

Calculation of protein conformation from circular dichroism

1 reference

12 December 2020

Protein sliding along DNA: dynamics and structural characterization

1 reference

12 December 2020

The complete amino acid sequence of the Ca2 -dependent modulator protein (calmodulin) of bovine brain

1 reference

12 December 2020

Single-Molecule Resonance Energy Transfer and Fluorescence Correlation Spectroscopy of Calmodulin in Solution†

30

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

Understanding Molecular Simulation: From Algorithms to Applications

9 December 2024

67

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1002114

9 December 2024

Identifiers

1 reference

journals/ploscb/WangLCWC11

30 July 2017

1 reference

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

30 July 2017

1 reference