Journal ArticleDOI
Theory of protein folding.
José N. Onuchic,Peter G. Wolynes +1 more
TLDR
This work states that proteins have a rugged funnel-like landscape biased toward the native structure as a result of evolution, and connecting theory and simulations of minimalist models with experiments has completely revolutionized the understanding of the underlying mechanisms that control protein folding.About:
This article is published in Current Opinion in Structural Biology.The article was published on 2004-02-01. It has received 1242 citations till now. The article focuses on the topics: Folding funnel & Protein folding.read more
Citations
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Journal ArticleDOI
Converging concepts of protein folding in vitro and in vivo
TL;DR: Recent concepts emerging from studies of protein folding in vitro and in vivo are reviewed, with a focus on how proteins navigate the complex folding energy landscape inside cells with the aid of molecular chaperones.
Journal ArticleDOI
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins.
TL;DR: IUPred, a novel method for estimating the total pairwise interaction energy of proteins of known structure, based on a quadratic form in the amino acid composition of the protein, is presented and substantiates the concept of protein disorder.
Journal ArticleDOI
Water mediation in protein folding and molecular recognition
Yaakov Levy,José N. Onuchic +1 more
TL;DR: Focusing on water sheds light on the physics and function of biological machinery and self-assembly and may advance the understanding of the natural design of proteins and nucleic acids.
Journal ArticleDOI
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.
William G. Noid,Jhih-Wei Chu,Jhih-Wei Chu,Gary S. Ayton,Vinod Krishna,Sergei Izvekov,Gregory A. Voth,Avisek Das,Hans C. Andersen +8 more
TL;DR: The present work develops a formal statistical mechanical framework for the MS-CG method and demonstrates that the variational principle underlying the method may, in principle, be employed to determine the many-body potential of mean force (PMF) that governs the equilibrium distribution of positions of the CG sites for theMS-CG models.
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Proteome-wide Analysis of Chaperonin-Dependent Protein Folding in Escherichia coli
Michael J. Kerner,Dean J. Naylor,Yasushi Ishihama,Tobias Maier,Hung-Chun Chang,Anna P. Stines,Costa Georgopoulos,Dmitrij Frishman,Manajit Hayer-Hartl,Matthias Mann,F. Ulrich Hartl +10 more
TL;DR: It is suggested that the chaperonin system may have facilitated the evolution of this fold into a versatile platform for the implementation of numerous enzymatic functions.
References
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Journal ArticleDOI
THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
TL;DR: The energy landscape theory of protein folding suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure.
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Spin glasses and the statistical mechanics of protein folding
TL;DR: The theory of spin glasses was used to study a simple model of protein folding and the phase diagram was calculated, and the results of dynamics calculations are briefly reported.
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Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution
Yong Duan,Peter A. Kollman +1 more
TL;DR: An implementation of classical molecular dynamics on parallel computers of increased efficiency has enabled a simulation of protein folding with explicit representation of water for 1 microsecond, about two orders of magnitude longer than the longest simulation of a protein in water reported to date.
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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
TL;DR: In this article, the authors investigated the role of topology in the transition state ensembles of small globular proteins and showed that topology plays a central role in determining the folding mechanism.
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Computer simulation of protein folding
TL;DR: A new and very simple representation of protein conformations has been used together with energy minimisation and thermalisation to simulate protein folding and succeeds in ‘renaturing’ bovine pancreatic trypsin inhibitor from an open-chain conformation into a folded conformation close to that of the native molecule.