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Protein Engineering vol. 9 no. 3 pp. 253-263, 1996
© 1996 Oxford University Press

RESEARCH-ARTICLE

Recognition of transmembrane {alpha}-helical segments with environmental profiles

Roman G. Efremov1,2,1 and Gérard Vergoten3

1Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences UI, Miklukho-Maklaya, 16/10, Moscow V-437, 117871 GSP, Russia 3Université des Sciences et Technologies de Lille, Centre de Recherches et d'Etudes en Simulations et Modélisation Moléculaires (CRESIMM) Bâtiment C8, 59655 Villeneuve d'Aseq Cedex, France

1To whom correspondence should be addressed

A method for assessing the environmental properties of membrane-spanning {alpha}-helical peptides in proteins has beenproposed. The algorithm employs a set of environmental preference parameters derived for amino acid residues based on the analysis of the 3-D structures of membrane domains in bacteriorhodopsin and photoreaction centers Rhodopseudomonasviridis and Rhodobacter sphaeroides. The resulting 3-D–1-D scores for transmembrane segments are significantly different from those derived for {alpha}-helices in globular proteins. The parameters obtained havebeen used to construct environmental profiles for membrane {alpha}-helices in bacteriorhodopsin and photoreaction centers. The profiles successfully recognize their own sequences in several specially designed large databases. The method hasbeen applied to several membrane proteins with unknown spatial structures. Most of their membrane-spanning peptides were efficiently recognized by the profiles. The predicted environment of the residues in the membrane segments fits the experimental data well. The approach is independent of any homology data and can be employed to delineate the membrane segments of a protein with environmental characteristics close to those of bacteriorhodopsin and photoreaction centers. The alignment of these segments with the reference profiles provides a considerable amount of data about their lipid and protein exposure.

Keywords: hydrophobic organization/integral membrane proteins/molecular modeling/structure prediction/3-D profile method

Received May 19, 1995; revised November 15, 1995; accepted November 22, 1995.


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