Microscopic events in β-hairpin folding from alternative unfolded ensembles (Q35090961)

6 August 2017

title

Microscopic events in β-hairpin folding from alternative unfolded ensembles (English)

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6 August 2017

Robert B Best

1

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author name string

Jeetain Mittal

series ordinal

2

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6 August 2017

language of work or name

English

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publication date

20 June 2011

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Proceedings of the National Academy of Sciences of the United States of America

6 August 2017

published in

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6 August 2017

volume

108

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6 August 2017

issue

27

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6 August 2017

page(s)

11087-11092

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Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

6 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Extremely slow intramolecular diffusion in unfolded protein L

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Protein folded states are kinetic hubs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Unfolded-state dynamics and structure of protein L characterized by simulation and experiment

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Theoretical perspectives on protein folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Measuring internal friction of an ultrafast-folding protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

A test on peptide stability of AMBER force fields with implicit solvation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

An experimental survey of the transition between two-state and downhill protein folding scenarios

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Protein folding studied by single-molecule FRET.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Recent successes of the energy landscape theory of protein folding and function

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Atom-by-atom analysis of global downhill protein folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

The experimental survey of protein-folding energy landscapes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Understanding the mechanism of beta-hairpin folding via phi-value analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Hairpin folding rates reflect mutations within and remote from the turn region

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Reaction coordinates and rates from transition paths

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Protein folding pathways from replica exchange simulations and a kinetic network model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Understanding the key factors that control the rate of beta-hairpin folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Kinetic pathways of beta-hairpin (un)folding in explicit solvent

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Hidden complexity of free energy surfaces for peptide (protein) folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

The protein folding 'speed limit'.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Transition-path sampling of β-hairpin folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Analysis of the distributed computing approach applied to the folding of a small beta peptide

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation: a mechanistic study

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Absolute comparison of simulated and experimental protein-folding dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

On the simulation of protein folding by short time scale molecular dynamics and distributed computing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

The free energy landscape for beta hairpin folding in explicit water

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Mechanisms and kinetics of beta-hairpin formation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

A molecular dynamics study of the 41-56 beta-hairpin from B1 domain of protein G

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Understanding beta-hairpin formation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

A statistical mechanical model for beta-hairpin kinetics.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Folding dynamics and mechanism of β-hairpin formation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

From Levinthal to pathways to funnels

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Kinetics and thermodynamics of folding in model proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Mapping the transition state and pathway of protein folding by protein engineering

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3131341

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates

8 July 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

How do small single-domain proteins fold?

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Complex folding pathways in a simple beta-hairpin

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Folding of the GB1 hairpin peptide from discrete path sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Theoretical characterization of alpha-helix and beta-hairpin folding kinetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Peptide folding kinetics from replica exchange molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

From transition paths to transition states and rate coefficients

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Diffusive Model of Protein Folding Dynamics with Kramers Turnover in Rate

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Folding at the speed limit

21 January 2018

1 reference

https://api.crossref.org/works/10.1073/PNAS.1016685108

Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus

21 January 2018

1 reference

12 December 2020

Exploring the energy landscape of a beta hairpin in explicit solvent

1 reference

12 December 2020

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation

1 reference

12 December 2020

Force-Induced Change in Protein Unfolding Mechanism: Discrete or Continuous Switch?

1 reference

12 December 2020

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

1 reference

12 December 2020

Balance between α and β Structures in Ab Initio Protein Folding

1 reference

12 December 2020

Minimal model systems for beta sheet secondary structure in proteins

1 reference

12 December 2020

Evidence of turn and salt bridge contributions to beta-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein G

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1016685108

1 reference

6 August 2017

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6 August 2017

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