Specific interactions for ab initio folding of protein terminal regions with secondary structures
Abstract
Proteins fold into unique three-dimensional structures by specific, orientation-dependent interactions between amino acid residues. Here, we extract orientation-dependent interactions from protein structures by treating each polar atom as a dipole with a direction. The resulting statistical energy function successfully refolds 13 out of 16 fully unfolded secondary-structure terminal regions of 10-23 amino acid residues in 15 small proteins. Dissecting the orientation-dependent energy function reveals that the orientation preference between hydrogen-bonded atoms is not enough to account for the structural specificity of proteins. The result has significant implications on the theoretical and experimental searches for specific interactions involved in protein folding and molecular recognition between proteins and other biologically active molecules.
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The six benchmark datasets have been widely used to test the predictive power of PPI prediction methods.
“These datasets have been widely used to test the predictive power of the PPI prediction methods [12, 13, 27–29, 29–35].”
From Deep geometric representations for modeling effects of mutations on protein-protein binding affinity (2021) · cites this paper as [27]
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- Authors
- Yang, Y., & Zhou, Y.
- Affiliations
- Indiana University Indianapolis (US)
- Indiana University School of Medicine (US)
- Corresponding author
- Zhou, Yaoqi
- Venue
- Proteins Structure Function and Bioinformatics
- Publisher
- Wiley
- Published
- 2008-02-07
- Volume
- 72
- Issue
- 2
- Pages
- 793-803
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2008505479
- Cited by
- 245
- References
- 42
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 2 · 2023: 4 · 2022: 6 · 2021: 15 · 2020: 23 · 2019: 24 · 2018: 19 · 2017: 21 · 2016: 20 · 2015: 15 · 2014: 28 · 2013: 23 · 2012: 15
- FWCI
- 2.88
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Griffith Research Online (submittedVersion)
- Funders
- National Institute of General Medical Sciences (R0I GM 966049, R0I GM 068530)
- 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 › Chemical Synthesis and Analysis
- Keywords
- protein folding, orientation-dependent interactions, secondary structure, hydrogen bonding, molecular recognition
- MeSH terms
- Algorithms, Hydrogen Bonding, Proteins, Protein Structure, Secondary, Protein Folding, Databases, Protein
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