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Anatomy of hot spots in protein interfaces
Abstract
Binding of one protein to another is involved in nearly all biological functions, yet the principles governing the interaction of proteins are not fully understood. To analyze the contributions of individual amino acid residues in protein-protein binding we have compiled a database of 2325 alanine mutants for which the change in free energy of binding upon mutation to alanine has been measured (available at http://motorhead. ucsf.edu/thorn/hotspot). Our analysis shows that at the level of side-chains there is little correlation between buried surface area and free energy of binding. We find that the free energy of binding is not evenly distributed across interfaces; instead, there are hot spots of binding energy made up of a small subset of residues in the dimer interface. These hot spots are enriched in tryptophan, tyrosine and arginine, and are surrounded by energetically less important residues that most likely serve to occlude bulk solvent from the hot spot. Occlusion of solvent is found to be a necessary condition for highly energetic interactions.
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“Protein-protein interfaces are characterized by the existence of hot spots or ‘hot regions’ in interacting regions instead of an even contribution across all contact areas.371,476,487,492–495”
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 [495]
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“The latter two are experimental hot‐spots41 (Supporting Information Tables S2 and S8) and the third one is a candidate for experimental verification.”
From iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations (2019) · cites this paper as [41]
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Metadata
- Authors
- Bogan, A. A., & Thorn, K. S.
- Affiliations
- University of California, San Francisco (US)
- Corresponding author
- Bogan, Andrew A
- ORCID
- Thorn, Kurt S
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1998-07
- Volume
- 280
- Issue
- 1
- Pages
- 1-9
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W2051710717
- Cited by
- 1,988
- References
- 71
- Citations by year
- 2026: 62 · 2025: 52 · 2024: 68 · 2023: 40 · 2022: 51 · 2021: 75 · 2020: 69 · 2019: 65 · 2018: 77 · 2017: 75 · 2016: 94 · 2015: 105 · 2014: 88 · 2013: 110 · 2012: 112
- FWCI
- 11.85
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › thermodynamics and calorimetric analyses
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- protein-protein binding, binding hot spots, alanine scanning, binding free energy, protein interfaces, buried surface area, tryptophan, tyrosine, L-arginine, dimer interface, binding energy distribution
- MeSH terms
- Alanine, Amino Acids, Binding Sites, Humans, Protein Binding, Proteins, Structure-Activity Relationship
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