(Q37277214)

19 August 2017

Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin (English)

1 reference

Pernilla Wittung-Stafshede

19 August 2017

1 reference

series ordinal

3

1 reference

19 August 2017

Dirar Homouz

1

0 references

author name string

Loren Stagg

series ordinal

2

1 reference

PMCID

2716520

19 August 2017

Margaret S Cheung

series ordinal

4

1 reference

PMCID

2716520

19 August 2017

language of work or name

English

0 references

publication date

1 January 2009

1 reference

19 August 2017

1 reference

19 August 2017

96

1 reference

19 August 2017

2

1 reference

19 August 2017

671-680

1 reference

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

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Residue-level interrogation of macromolecular crowding effects on protein stability.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Multiple routes lead to the native state in the energy landscape of the beta-trefoil family

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Influence of macromolecular crowding upon the stability and state of association of proteins: predictions and observations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Ficoll and dextran vs. globular proteins as probes for testing glomerular permselectivity: effects of molecular size, shape, charge, and deformability

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Protein self-association in crowded protein solutions: a time-resolved fluorescence polarization study.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Atomic-level observation of macromolecular crowding effects: escape of a protein from the GroEL cage

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Simulations of beta-hairpin folding confined to spherical pores using distributed computing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Presence of the cofactor speeds up folding of Desulfovibrio desulfuricans flavodoxin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Direct observation of the enhancement of noncooperative protein self-assembly by macromolecular crowding: indefinite linear self-association of bacterial cell division protein FtsZ.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Investigation of routes and funnels in protein folding by free energy functional methods

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Effects of macromolecular crowding on protein folding and aggregation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Principles of protein folding in the cellular environment

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Folding funnels and frustration in off-lattice minimalist protein landscapes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Theory of protein folding: the energy landscape perspective

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Closure of a tyrosine/tryptophan aromatic gate leads to a compact fold in apo flavodoxin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Protein self-association induced by macromolecular crowding: a quantitative analysis by magnetic relaxation dispersion

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Macromolecular crowding: biochemical, biophysical, and physiological consequences

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

An analysis of the molecular origin of osmolyte-dependent protein stability

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Protein-protein association in polymer solutions: from dilute to semidilute to concentrated

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Molecular docking using surface complementarity.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

ART 2: self-organization of stable category recognition codes for analog input patterns.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Alternate pathways for folding in the flavodoxin fold family revealed by a nucleation-growth model.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Protein topology affects the appearance of intermediates during the folding of proteins with a flavodoxin-like fold.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Entropically driven helix formation.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: statics.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Macromolecular crowding increases structural content of folded proteins

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2716520

Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity

3 December 2018

1 reference

12 December 2020

Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L

1 reference

12 December 2020

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

1 reference

12 December 2020

1 reference

12 December 2020

15N NMR spin relaxation dispersion study of the molecular crowding effects on protein folding under native conditions

1 reference

12 December 2020

Do proteins with similar folds have similar transition state structures? A diffuse transition state of the 169 residue apoflavodoxin

1 reference

12 December 2020

The influence of macromolecular crowding on thermodynamic activity: solubility and dimerization constants for spherical and dumbbell-shaped molecules in a hard-sphere mixture

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Structural characterisation of apoflavodoxin shows that the location of the stable nucleus differs among proteins with a flavodoxin-like topology

1 reference

12 December 2020

Free polymer in a colloidal solution

1 reference

12 December 2020

10.1016/J.BPJ.2008.10.014

Identifiers

DOI

1 reference

19 August 2017

1 reference

1 reference

19 August 2017

1 reference

PMCID

2716520