Identifying importance of amino acids for protein folding from crystal structures. (Q51727934)

10 April 2018

title

Identifying importance of amino acids for protein folding from crystal structures. (English)

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10 April 2018

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1

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10 April 2018

Feng Ding

4

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10 April 2018

Sergey V. Buldyrev

object named as

Sergey V Buldyrev

3

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H. Eugene Stanley

5

object named as

H Eugene Stanley

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10 April 2018

2

Jose M Borreguero

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10 April 2018

Eugene I. Shakhnovich

6

object named as

Eugene I Shakhnovich

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10 April 2018

language of work or name

English

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publication date

1 January 2003

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10 April 2018

published in

Methods in Enzymology

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10 April 2018

volume

374

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10 April 2018

page(s)

616-638

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10 April 2018

Principles that govern the folding of protein chains

cites work

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Theoretical Studies of Protein Folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Kinetic and equilibrium intermediates in protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Specific nucleus as the transition state for protein folding: evidence from the lattice model.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Conserved residues and the mechanism of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Criterion that determines the foldability of proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Nucleation mechanisms in protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Theoretical studies of protein-folding thermodynamics and kinetics

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Theory of protein folding: the energy landscape perspective

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Protein design: a perspective from simple tractable models

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Pathways for protein folding: is a new view needed?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Obligatory steps in protein folding and the conformational diversity of the transition state

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Folding protein models with a simple hydrophobic energy function: the fundamental importance of monomer inside/outside segregation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Mechanism of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Transition states and the meaning of Phi-values in protein folding kinetics

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Understanding conserved amino acids in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Local squaring functions for non-spherical templates

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Kinetics and thermodynamics of folding in model proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Nonrandomness in protein sequences: evidence for a physically driven stage of evolution?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Are protein folds atypical?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

A simple model for calculating the kinetics of protein folding from three-dimensional structures

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

A theoretical search for folding/unfolding nuclei in three-dimensional protein structures

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Identifying the protein folding nucleus using molecular dynamics.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Solution structure of the SH3 domain of Src and identification of its ligand-binding site

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Folding dynamics of the src SH3 domain

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Characterization of the interaction of natural proline-rich peptides with five different SH3 domains.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Different folding transition states may result in the same native structure

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Thermodynamic analysis of alpha-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Thermal unfolding of small proteins with SH3 domain folding pattern.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Hydrophobic core packing in the SH3 domain folding transition state

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Protein folding kinetics beyond the phi value: using multiple amino acid substitutions to investigate the structure of the SH3 domain folding transition state

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Role of native topology investigated by multiple unfolding simulations of four SH3 domains

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Prediction of folding mechanism for circular-permuted proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Direct molecular dynamics observation of protein folding transition state ensemble

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

A protein engineering analysis of the transition state for protein folding: simulation in the lattice model

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Are there pathways for protein folding?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

The energy landscape theory of protein folding: insights into folding mechanisms and scenarios

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Funnels, pathways, and the energy landscape of protein folding: a synthesis

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Improved design of stable and fast-folding model proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: a critical test of the protein engineering method of analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

On the transition coordinate for protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Intermediates in the folding reactions of small proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Protein folding dynamics: the diffusion-collision model and experimental data

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Nucleation, rapid folding, and globular intrachain regions in proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Nucleation in protein folding--confusion of structure and process

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

How molten is the molten globule?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Transient folding intermediates characterized by protein engineering

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Structure of the transition state for folding of a protein derived from experiment and simulation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Molecular picture of folding of a small alpha/beta protein

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozyme

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Synergy between simulation and experiment in describing the energy landscape of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints a aEdited by A. R. Fersht

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

A computer model to dynamically simulate protein folding: studies with crambin.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Simulations of the folding of a globular protein

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Cooperativity in protein-folding kinetics

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Can protein unfolding simulate protein folding?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

The Protein Data Bank

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Atomic resolution (0.83 A) crystal structure of the hydrophobic protein crambin at 130 K

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

The prediction of protein contacts from multiple sequence alignments

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Is protein unfolding the reverse of protein folding? A lattice simulation analysis

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Conformations of proteins in equilibrium.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Multiple protein folding nuclei and the transition state ensemble in two-state proteins

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Proteins with selected sequences fold into unique native conformation

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Impact of local and non-local interactions on thermodynamics and kinetics of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

On the origin of the cooperativity of protein folding: implications from model simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Folding funnels and frustration in off-lattice minimalist protein landscapes

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Conformation, energy, and folding ability of selected amino acid sequences

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Topological determinants of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Folding studies of immunoglobulin-like β-sandwich proteins suggest that they share a common folding pathway

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Native and non-native interactions along protein folding and unfolding pathways

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

How evolution makes proteins fold quickly

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Non-functional conserved residues in globins and their possible role as a folding nucleus

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Evolutionary conservation in protein folding kinetics.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Glassy behavior of a homopolymer from molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Studies in Molecular Dynamics. I. General Method

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

How do small single-domain proteins fold?

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

A discussion of the solution for the best rotation to relate two sets of vectors

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

The identification of conserved interactions within the SH3 domain by alignment of sequences and structures

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Structure-derived potentials and protein simulations

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Small-world view of the amino acids that play a key role in protein folding.

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

Non-native interactions, effective contact order, and protein folding: a mutational investigation with the energetically frustrated hydrophobic model

1 reference

https://api.crossref.org/works/10.1016%2FS0076-6879%2803%2974025-7

7 January 2021

10.1016/S0076-6879(03)74025-7

Identifiers

DOI

1 reference

10 April 2018

1 reference

10 April 2018