SNORKELING PREFERENCES FOSTER AN AMINO ACID COMPOSITION BIAS IN TRANSMEMBRANE HELICES
SCIE
SCOPUS
- Title
- SNORKELING PREFERENCES FOSTER AN AMINO ACID COMPOSITION BIAS IN TRANSMEMBRANE HELICES
- Authors
- Chamberlain, AK; Lee, Y; Kim, S; Bowie, JU
- Date Issued
- 2004-05-28
- Publisher
- ACADEMIC PRESS LTD ELSEVIER SCIENCE L
- Abstract
- By analyzing transmembrane (TM) helices in known structures, we find that some polar amino acids are more frequent at the N terminus than at the C terminus. We propose the asymmetry occurs because most polar amino acids are better able to snorkel their polar atoms away from the membrane core at the N terminus than at the C terminus. Two findings lead us to this proposition: (1) side-chain conformations are influenced strongly by the N or C-terminal position of the amino acid in the bilayer, and (2) the favored snorkeling direction of an amino acid correlates well with its N to C-terminal composition bias. Our results suggest that TM helix predictions should incorporate an N to C-terminal composition bias, that rotamer preferences of TM side-chains are position-dependent, and that the ability to snorkel influences the evolutionary selection of amino acids for the helix N and C termini. (C) 2004 Elsevier Ltd. All rights reserved.
- Keywords
- membrane; protein; side-chain; polarity; rotamer; MEMBRANE-PROTEIN TOPOLOGY; STATISTICAL-ANALYSIS; CHARGED RESIDUES; BACTERIORHODOPSIN LATTICE; SECONDARY STRUCTURE; AMPHIPATHIC HELIX; CRYSTAL-STRUCTURE; STRUCTURAL BASIS; SIDE-CHAINS; ASSOCIATION
- URI
- https://oasis.postech.ac.kr/handle/2014.oak/28840
- DOI
- 10.1016/J.JMB.2004.0
- ISSN
- 0022-2836
- Article Type
- Article
- Citation
- JOURNAL OF MOLECULAR BIOLOGY, vol. 339, no. 2, page. 471 - 479, 2004-05-28
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