DOI: 10.1002/prot.20229. Novel scoring function for modeling structures of oligomers of transmembrane α‐helices

Novel scoring function for modeling structures of oligomers of transmembrane α‐helices

10.1002/prot.20229

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractSpecific non‐covalent interactions between transmembrane (TM) α‐helices are important in a variety of biological processes. Experimental and computational studies have shown that van der Waals interactions play an important role in the tight packing between TM α‐helices, although polar interactions can also be important in some instances. Based on the assumption that van der Waals interaction alone is sufficient for a meso‐scale (residue‐scale) description of the interaction between TM α‐helices, we have designed a novel residue‐scale scoring function for modeling structures of oligomers of TM α‐helices. We first calculated atomistic van der Waals interaction energies between two amino acids, X and Y, of a pair of parallel α‐helices, glycine‐X‐glycine and glycine‐Y‐glycine and compiled them according to three variables, the distance between the two Cα atoms and the rotational angles of X and Y about their helical axes. Upon averaging over the rotational angles, we obtained one‐dimensional interaction energy profiles that are functions of the distance between Cα atoms only. Each of the interaction energy profiles was fitted with a generic fitting function of the distance between Cα atoms, yielding analytical scoring functions for all possible amino acid pairs. For glycophorin A, neu/erbB‐2, and phospholamban, lowest‐energy conformations obtained through exhaustive scanning of the entire conformational space using the scoring functions were compatible with available experimental data. Proteins 2004. © 2004 Wiley‐Liss, Inc.

Bibliography

Park, Y., Elsner, M., Staritzbichler, R., & Helms, V. (2004). Novel scoring function for modeling structures of oligomers of transmembrane Î±âhelices. Proteins: Structure, Function, and Bioinformatics, 57(3), 577â585. Portico.

Authors 4

Yungki Park (first)
Markus Elsner (additional)
Rene Staritzbichler (additional)
Volkhard Helms (additional)

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Dates

Type	When
Created	21 years, 1 month ago (July 12, 2004, 5:04 p.m.)
Deposited	1 year, 10 months ago (Oct. 16, 2023, 3:52 a.m.)
Indexed	1 year, 1 month ago (July 10, 2024, 4:03 p.m.)
Issued	21 years, 1 month ago (July 12, 2004)
Published	21 years, 1 month ago (July 12, 2004)
Published Online	21 years, 1 month ago (July 12, 2004)
Published Print	20 years, 9 months ago (Nov. 15, 2004)

Funders 0

None

BibTeX

@article{Park_2004, title={Novel scoring function for modeling structures of oligomers of transmembrane α‐helices}, volume={57}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.20229}, DOI={10.1002/prot.20229}, number={3}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Park, Yungki and Elsner, Markus and Staritzbichler, Rene and Helms, Volkhard}, year={2004}, month=jul, pages={577–585} }

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