Folding and binding cascades: Shifts in energy landscapes
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Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
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The conformational selection and population shift model provides a more realistic description of molecular mechanism considering ensemble nature.
“The ‘conformational selection and population shift’ model87–89,134 provides a more realistic description of the molecular mechanism considering the ensemble nature of protein molecules.”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [134]
During binding, higher energy (lower population) conformers most complementary to pre-existing ligand conformations can be selected, shifting equilibrium toward them.
“During binding, higher energy (lower population) conformers which are most complementary to some pre-existing ligand conformations can be selected and the equilibrium shifts toward these conformers.87–89,134”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [134]
Biomolecules are dynamical objects that are always interconverting between structures with varying energies, and this is the origin of allosteric mechanisms.
“biomolecules are dynamical objects that are always interconverting between a variety of structures with varying energies,166 and that this is the origin of allosteric mechanisms.”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [167]
The conformational selection mechanism theorizes that the energy surface hosts a very large number of conformations, the best-fitting one is selected, with subsequent minor induced fit optimization largely by side chains.
“In contrast, the conformational selection mechanism167−169,185 theorizes that the energy surface hosts a very large number of conformations, and the one that fits best is selected, with subsequent minor induced fit optimization, largely by side chains.”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [167]
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- Authors
- Tsai, C.-J., Ma, B., & Nussinov, R.
- Affiliations
- Leidos (United States) (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1999-08-31
- Volume
- 96
- Issue
- 18
- Pages
- 9970-9972
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC33715
- OpenAlex
- W2107238748
- Cited by
- 365
- References
- 21
- Citations by year
- 2026: 9 · 2025: 7 · 2024: 12 · 2023: 9 · 2022: 12 · 2021: 18 · 2020: 10 · 2019: 14 · 2018: 7 · 2017: 9 · 2016: 21 · 2015: 14 · 2014: 24 · 2013: 36 · 2012: 20
- FWCI
- 2.53
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Israel Science Foundation
- Tel Aviv University
- National Institutes of Health (n01co056000-057, NO1-CO-56000, CO-56000)
- National Cancer Institute (N01 CO 56000, NO1CO56000)
- 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 › Advanced biosensing and bioanalysis techniques
- Keywords
- protein folding, protein binding, energy landscape, protein conformational change
- MeSH terms
- Binding Sites, Ligands, Models, Molecular, Muramidase, Protein Binding, Protein Conformation, Proteins, Thermodynamics, Protein Folding
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