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Cited by 331Protein Structure and DynamicsRNA and protein synthesis mechanismsAdvanced Physical and Chemical Molecular Interactions

The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

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Das, Payel, Moll, Mark, Stamati, Hernán, Kavraki, Lydia E., Clementi, Cecilia·2006·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0603553103PMC PMC1502548
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Abstract

The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the “simple” case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding.

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Research works printed but not linked: 7

  1. A. Ma, A. Dinner J. Phys. B.. 109, 6769–6779 (2005).
  2. Y. Rhee, V. Pande J. Phys. B.. 109, 6780–6786 (2005).
  3. 10.1021/ja049510 · DOI
  4. Y. Levy, A. Caflisch J. Phys. B.. 107, 3068–3079 (2003).
  5. K. Q. Weinberger L. K. Saul (IEEE Washington DC) pp. 988–995 (2004).
  6. V. de Silva, J. Tenenbaum Sparse Multidimensional Scaling Using Landmark Points. (Stanford Univ., Stanford, CA, 2004).
  7. A. Ferrenberg, R. Swendsen Phys. Rev. Lett.. 63, 1185–1198 (1989).

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Metadata

Authors
Das, P., Moll, M., Stamati, H., Kavraki, L. E., & Clementi, C.
Affiliations
  • Departments of *Chemistry,
  • Computer Science, and
  • Baylor College of Medicine (US)
  • Rice University (US)
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2006-06-27
Volume
103
Issue
26
Pages
9885-9890
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.0603553103
PMC
PMC1502548
OpenAlex
W2077412035
Cited by
331
References
60
Citations by year
2026: 9 · 2025: 10 · 2024: 13 · 2023: 11 · 2022: 21 · 2021: 15 · 2020: 18 · 2019: 23 · 2018: 24 · 2017: 20 · 2016: 15 · 2015: 23 · 2014: 14 · 2013: 18 · 2012: 19
FWCI
6.93
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Science Foundation (0523908, 0454333, 0349303, 0205671, 0216467)
  • Alfred P. Sloan Foundation
  • Division of Chemistry
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
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords
protein folding, free energy landscape, reaction coordinate, nonlinear dimensionality reduction, collective coordinates, transition state ensemble, coarse-grained protein models, molecular dynamics sampling
MeSH terms
Algorithms, Models, Molecular, Protein Folding, src Homology Domains, Entropy

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