DOI: 10.1002/prot.20482. A consistent set of statistical potentials for quantifying local side‐chain and backbone interactions

A consistent set of statistical potentials for quantifying local side‐chain and backbone interactions

10.1002/prot.20482

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractThe frequencies of occurrence of atom arrangements in high‐resolution protein structures provide some of the most accurate quantitative measures of interaction energies in proteins. In this report we extend our development of a consistent set of statistical potentials for quantifying local interactions between side‐chains and the polypeptide backbone, as well as nearby side‐chains. Starting with ϕ/ψ/χ1 propensities that select for optimal interactions of the 20 amino acid side‐chains with the 2 flanking peptide bonds, the following 3 new terms are added: (1) a distance‐dependent interaction between the side‐chain at i and the carbonyl oxygens and amide protons of the peptide units at i ± 2, i ± 3, and i ± 4; (2) a distance‐dependent interaction between the side‐chain at position i and side‐chains at positions i + 1 through i + 4; and (3) an orientation‐dependent interaction between the side‐chain at position i and side‐chains at i + 1 through i + 4. The relative strengths of these 4 pseudo free energy terms are estimated by the average information content of each scoring matrix and by assessing their performance in a simple fragment threading test. They vary from −0.4–−0.5 kcal/mole per residue for ϕ/ψ/χ1 propensities to a range of −0.15–−0.6 kcal/mole per residue for each of the other 3 terms. The combined energy function, containing no interactions between atoms more than 4 residues apart, identifies the correct structural fragment for randomly selected 15 mers over 40% of the time, after searching through 232,000 alternative conformations. For 14 out of 20 sets of all‐atom Rosetta decoys analyzed, the native structure has a combined score lower than any of the 1700–1900 decoy conformations. The ability of this energy function to detect energetically important details of local structure is demonstrated by its power to distinguish high‐resolution crystal structures from NMR solution structures. Proteins 2005. © 2005 Wiley‐Liss, Inc.

Bibliography

Fang, Q., & Shortle, D. (2005). A consistent set of statistical potentials for quantifying local sideâchain and backbone interactions. Proteins: Structure, Function, and Bioinformatics, 60(1), 90â96. Portico.

Authors 2

Qiaojun Fang (first)
David Shortle (additional)

References 31 Referenced 35

10.1016/0968-0004(94)90171-6
10.1016/S1359-0278(96)00005-3
10.1016/S0959-440X(96)80091-1
10.1126/science.1060438
10.1021/bi049879b
10.1021/bi020511t
10.1051/jcp/1968650044
10.1126/science.181.4096.223
10.1002/prot.10541
10.1038/newbio234277a0
10.1021/ma60054a013
10.1021/ma00145a039
10.1016/S0022-2836(05)80269-4
10.1006/jmbi.1994.1109
10.1016/S0959-440X(96)80075-3
10.1016/S0959-440X(97)80025-5
10.1016/0959-440X(95)80081-6
10.1021/bi00699a001
10.1110/ps.0306903
10.1110/ps.31002
10.1002/(SICI)1097-0134(19990101)34:1<82::AID-PROT7>3.0.CO;2-A
{'key': 'e_1_2_6_23_2', 'first-page': '410', 'volume-title': 'Introduction to protein structure', 'author': 'Branden C', 'year': '1999'} / Introduction to protein structure by Branden C (1999)
10.1002/prot.340160110
10.1093/bioinformatics/btg224
10.1002/prot.340120407
10.1023/A:1014971029663
10.1006/jmre.2000.2142
10.1073/pnas.2434121100
10.1080/07391102.1989.10508503
10.1093/nar/30.1.264
10.1002/prot.10454

Dates

Type	When
Created	20 years, 4 months ago (April 25, 2005, 2:16 p.m.)
Deposited	1 year, 10 months ago (Oct. 16, 2023, 12:30 a.m.)
Indexed	1 year, 3 months ago (May 10, 2024, 4:56 a.m.)
Issued	20 years, 4 months ago (April 25, 2005)
Published	20 years, 4 months ago (April 25, 2005)
Published Online	20 years, 4 months ago (April 25, 2005)
Published Print	20 years, 2 months ago (July 1, 2005)

Funders 0

None

BibTeX

@article{Fang_2005, title={A consistent set of statistical potentials for quantifying local side‐chain and backbone interactions}, volume={60}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.20482}, DOI={10.1002/prot.20482}, number={1}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Fang, Qiaojun and Shortle, David}, year={2005}, month=apr, pages={90–96} }

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