Cited by 341Protein Structure and DynamicsRNA and protein synthesis mechanismsProtein purification and stability

Protein Folding Theory: From Lattice to All-Atom Models

Mirny, Leonid, Shakhnovich, Eugene·2001·Annual Review of Biophysics and Biomolecular Structure

Abstract

▪ Abstract This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, folding nucleus, and transition state ensemble and then discuss recent advances and challenges in theoretical understanding of several key aspects of protein folding kinetics. We cover recent topology-based approaches as well as evolutionary studies and molecular dynamics approaches to determine protein folding nucleus and analyze other aspects of folding kinetics. Finally, we briefly discuss successful all-atom Monte-Carlo simulations of protein folding and conclude with a brief outlook for the future.

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Crossref · 10.1146/annurev.biophys.30.1.361

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132 of 132 references verified0 citation errors · 0 not checkable

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  • AlphaFold does not resolve the protein folding problem and does not identify folding pathways.

    “AlphaFold does not resolve the decades-long protein folding challenge, nor does it identify the folding pathways.”

    From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [56]

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Authors
Mirny, L., & Shakhnovich, E.
Affiliations
Harvard University (US)
Venue
Annual Review of Biophysics and Biomolecular Structure
Published
2001-06
Volume
30
Issue
1
Pages
361-396
ISSN
  • 1056-8700 (ISSN-L)
  • 1545-4266
OpenAlex
W2130949317
Cited by
341
References
133
Citations by year
2026: 1 · 2025: 2 · 2024: 3 · 2023: 5 · 2022: 2 · 2021: 5 · 2020: 6 · 2019: 7 · 2018: 6 · 2017: 5 · 2016: 8 · 2015: 6 · 2014: 6 · 2013: 11 · 2012: 15
FWCI
2.36
Type
journal article
Language
en
Open access
closed
Locations
  • Annual Review of Biophysics and Biomolecular Structure (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein purification and stability
Keywords
protein folding kinetics, nucleation theory, folding nucleus, transition state ensemble, protein evolution, molecular dynamics, lattice model
MeSH terms
Cell Nucleus, Kinetics, Models, Molecular, Monte Carlo Method, Thermodynamics, Protein Folding, Evolution, Molecular

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