Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity (Q58747518)

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22 April 2020

title

Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity (English)

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22 April 2020

3

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22 April 2020

author name string

Jianlin Chen

series ordinal

1

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22 April 2020

Xiaorong Liu

series ordinal

2

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22 April 2020

language of work or name

English

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publication date

12 September 2018

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22 April 2020

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22 April 2020

volume

8

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22 April 2020

issue

1

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22 April 2020

page(s)

13668

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Force field development and simulations of intrinsically disordered proteins

22 April 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Accuracy of current all-atom force-fields in modeling protein disordered states

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Folding thermodynamics of β-hairpins studied by replica-exchange molecular dynamics simulations

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Modulation of the disordered conformational ensembles of the p53 transactivation domain by cancer-associated mutations

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Improved Generalized Born Solvent Model Parameters for Protein Simulations

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

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

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

How quickly can a β-hairpin fold from its transition state?

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Native contacts determine protein folding mechanisms in atomistic simulations

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

To milliseconds and beyond: challenges in the simulation of protein folding

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Biomolecular simulation: a computational microscope for molecular biology

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Atomistic molecular simulations of protein folding

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

How fast-folding proteins fold

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Microscopic events in β-hairpin folding from alternative unfolded ensembles

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

How robust are protein folding simulations with respect to force field parameterization?

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Improved side-chain torsion potentials for the Amber ff99SB protein force field

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

CHARMM: the biomolecular simulation program

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Intrinsically disordered p53 extreme C-terminus binds to S100B(betabeta) through "fly-casting".

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Recent advances in implicit solvent-based methods for biomolecular simulations

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Computational techniques for efficient conformational sampling of proteins

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Linking folding with aggregation in Alzheimer's beta-amyloid peptides

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Simulating replica exchange simulations of protein folding with a kinetic network model

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Ultrafast and downhill protein folding

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Exploring atomistic details of pH-dependent peptide folding

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

30 November 2018

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Folding mechanism of beta-hairpins studied by replica exchange molecular simulations

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Progress in modeling of protein structures and interactions

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

How well can simulation predict protein folding kinetics and thermodynamics?

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Empirical force fields for biological macromolecules: overview and issues.

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

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

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

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

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

The protein folding 'speed limit'.

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Generalized born model with a simple smoothing function

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Peptide folding simulations

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Designing a 20-residue protein

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

The free energy landscape for beta hairpin folding in explicit water

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Tryptophan zippers: Stable, monomeric -hairpins

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

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

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Generalized born models of macromolecular solvation effects

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Mechanisms and kinetics of beta-hairpin formation

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Understanding beta-hairpin formation

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Folding dynamics and mechanism of β-hairpin formation

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Theory of protein folding: the energy landscape perspective

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

From Levinthal to pathways to funnels

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Navigating the folding routes

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

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

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

Principles that govern the folding of protein chains

30 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6135771

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

30 November 2018

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Detailed microscopic unfolding pathways of an α-helix and a β-hairpin: direct observation and molecular dynamics

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Peptide folding in the presence of interacting protein crowders

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Replica-exchange molecular dynamics method for protein folding

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Numerical comparisons of three recently proposed algorithms in the protein folding problem

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Role of side-chains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Force Field Influence on the Observation of π-Helical Protein Structures in Molecular Dynamics Simulations

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Semianalytical treatment of solvation for molecular mechanics and dynamics

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Novel generalized Born methods

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

Accelerate Sampling in Atomistic Energy Landscapes Using Topology-Based Coarse-Grained Models

1 reference

https://api.crossref.org/works/10.1038/S41598-018-32028-7

7 January 2021

10.1038/S41598-018-32028-7

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30209295 AND SRC:MED&resulttype=core&format=json

22 April 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30209295 AND SRC:MED&resulttype=core&format=json

22 April 2020

PubMed publication ID

30209295

1 reference