A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO). (Q35962923)

11 August 2017

A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO). (English)

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11 August 2017

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Qian Wang

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11 August 2017

Margaret S Cheung

series ordinal

2

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11 August 2017

language of work or name

English

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publication date

15 May 2012

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11 August 2017

9

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inferred from page(s)

published in

Biophysical Journal

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11 August 2017

102

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11 August 2017

10

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11 August 2017

2353-2361

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Variable interactions between protein crowders and biomolecular solutes are important in understanding cellular crowding

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Capturing the essence of folding and functions of biomolecules using coarse-grained models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Protein stability and folding kinetics in the nucleus and endoplasmic reticulum of eucaryotic cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Protein self-diffusion in crowded solutions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Macromolecular Crowding Fails To Fold a Globular Protein in Cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Macromolecular crowding extended to a heptameric system: the Co-chaperonin protein 10.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Effects of macromolecular crowding on the inhibition of virus assembly and virus-cell receptor recognition.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Protein folding in the cell: challenges and progress

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Attractive protein-polymer interactions markedly alter the effect of macromolecular crowding on protein association equilibria.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Effects of macromolecular crowding on protein conformational changes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Tracking mutant huntingtin aggregation kinetics in cells reveals three major populations that include an invariant oligomer pool.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Generalized fundamental measure theory for atomistic modeling of macromolecular crowding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Protein folding stability and dynamics imaged in a living cell

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Protein folding requires crowd control in a simulated cell.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Hybridization kinetics is different inside cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Protein structure determination in living cells by in-cell NMR spectroscopy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Fundamental aspects of protein-protein association kinetics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Crowding effects on the mechanical stability and unfolding pathways of ubiquitin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Determining the architectures of macromolecular assemblies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

FlgM gains structure in living cells

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Quantitative protein stability measurement in vivo

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Effect of a concentrated "inert" macromolecular cosolute on the stability of a globular protein with respect to denaturation by heat and by chaotropes: a statistical-thermodynamic model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

THE INTERACTION BETWEEN POLYSACCHARIDES AND OTHER MACROMOLECULES. 4. THE OSMOTIC PRESSURE OF MIXTURES OF SERUM ALBUMIN AND HYALURONIC ACID

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Modulation of calmodulin plasticity by the effect of macromolecular crowding

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

High-resolution multi-dimensional NMR spectroscopy of proteins in human cells.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Effect of mixed macromolecular crowding agents on protein folding

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Effects of crowding and confinement on the structures of the transition state ensemble in proteins

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Macromolecular crowding increases structural content of folded proteins

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Correlation between Protein Stability Cores and Protein Folding Kinetics: A Case Study on Pseudomonas aeruginosa Apo-Azurin

5 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

The Geometry of the Ribosomal Polypeptide Exit Tunnel

5 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography

5 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353097

Effect of dextran on protein stability and conformation attributed to macromolecular crowding

5 December 2018

1 reference

12 December 2020

Macromolecular crowding effects on protein–protein binding affinity and specificity

1 reference

12 December 2020

1 reference

12 December 2020

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

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12 December 2020

Protein Crowding Tunes Protein Stability

1 reference

12 December 2020

Free-energy model for the inhomogeneous hard-sphere fluid mixture and density-functional theory of freezing

1 reference

12 December 2020

10.1016/J.BPJ.2012.04.010

Identifiers

DOI

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11 August 2017

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11 August 2017

PubMed publication ID

22677389

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