The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A (Q58041737)

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English	The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A	article

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scholarly article

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The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A (English)

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protein folding

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author name string

Apichart Linhananta

1

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Yaoqi Zhou

2

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language of work or name

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publication date

15 November 2002

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Journal of Chemical Physics

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117

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19

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8983-8995

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

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Reversible peptide folding in solution by molecular dynamics simulation

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Folding simulations of a three-stranded antiparallel beta -sheet peptide

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Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

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Molecular dynamics simulations of hydrophobic collapse of ubiquitin

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Exploring the folding free energy surface of a three-helix bundle protein

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Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2

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"New view" of protein folding reconciled with the old through multiple unfolding simulations.

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Hierarchy of structure loss in MD simulations of src SH3 domain unfolding.

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Origins of structure in globular proteins

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Kinetics and thermodynamics of folding in model proteins

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21 January 2018

How does a protein fold?

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Is the molten globule a third phase of proteins?

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The nature of folded states of globular proteins

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Thermodynamics of protein folding: a statistical mechanical study of a small all-beta protein

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Folding funnels and frustration in off-lattice minimalist protein landscapes

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Discrete molecular dynamics studies of the folding of a protein-like model.

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Folding thermodynamics of a model three-helix-bundle protein.

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Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

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Interpreting the folding kinetics of helical proteins

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Thermodynamics of an All-Atom Off-Lattice Model of the Fragment B ofStaphylococcalProtein A: Implication for the Origin of the Cooperativity of Protein Folding

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Role of hydrophilic and hydrophobic contacts in folding of the second beta-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model

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Principles of protein folding--a perspective from simple exact models.

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Theory of protein folding: the energy landscape perspective

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Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

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The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved.

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21 January 2018

Experiment and theory highlight role of native state topology in SH3 folding

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Mapping the transition state of the WW domain beta-sheet.

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Ultrafast folding of WW domains without structured aromatic clusters in the denatured state

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Using flexible loop mimetics to extend -value analysis to secondary structure interactions

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Keeping it in the family: folding studies of related proteins

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Mechanisms of protein folding

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Critical role of beta-hairpin formation in protein G folding.

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A breakdown of symmetry in the folding transition state of protein L

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Computer-based redesign of a protein folding pathway

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Properties and crystal structure of a beta-barrel folding mutant

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Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9.

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The SH3-fold family: experimental evidence and prediction of variations in the folding pathways

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Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

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Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.

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

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Understanding beta-hairpin formation

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

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

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Understanding beta-hairpin formation by molecular dynamics simulations of unfolding

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The free energy landscape for beta hairpin folding in explicit water

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Preorganized secondary structure as an important determinant of fast protein folding

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Absence of a stable intermediate on the folding pathway of protein A.

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Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains

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Folding of a small helical protein using hydrogen bonds and hydrophobicity forces

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A structure-based method for derivation of all-atom potentials for protein folding

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Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state

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The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers

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Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model

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alpha-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model

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Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics

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Mechanisms and kinetics of beta-hairpin formation

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Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures

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

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Intermediates can accelerate protein folding

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Three key residues form a critical contact network in a protein folding transition state

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Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations

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Intermediates in the folding reactions of small proteins

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The speed limit for protein folding measured by triplet-triplet energy transfer.

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Contact order, transition state placement and the refolding rates of single domain proteins.

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Folding rate prediction using total contact distance

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The dual role of a loop with low loop contact distance in folding and domain swapping

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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

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An atomically detailed study of the folding pathways of protein A with the stochastic difference equation

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Protein-folding dynamics

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Nanosecond time scale folding dynamics of a pentapeptide in water

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

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Computer simulations of protein folding by targeted molecular dynamics

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First-principles calculation of the folding free energy of a three-helix bundle protein

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Calculations on folding of segment B1 of streptococcal protein G

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The folding mechanism of a beta-sheet: the WW domain

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Folding mechanism of three structurally similar beta-sheet proteins

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Beta-sheet proteins with nearly identical structures have different folding intermediates

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Native topology or specific interactions: what is more important for protein folding?

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Exploring the energy landscape of a beta hairpin in explicit solvent

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

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The stability and unfolding of an IgG binding protein based upon the B domain of protein A from Staphylococcus aureus probed by tryptophan substitution and fluorescence spectroscopy

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Coexistence of multiple phases in finite systems

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Simulation of activation free energies in molecular systems

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10.1063/1.1514574

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