| Recognition of α-helix transmembrane domains with an amphipathy scale generated by molecular dynamics using only the primary sequence of proteins F.M. Mazzé, C.A. Fuzo, P. Ciancaglini and L. Degrève Grupo de Simulação Molecular, Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil Corresponding author: F.M. Mazzé E-mail: femazze@usp.br Genet. Mol. Res. 6 (2): 422-433 (2007) Received February 08, 2007 Accepted May 25, 2007 Published June 30, 2007 ABSTRACT. We recently developed an amphipathy scale, elaborated from molecular dynamics data that can be used for the identification of hydrophobic or hydrophilic regions in proteins. This amphipathy scale reflects side chain/water molecule interaction energies. We have now used this amphipathy scale to find candidates for transmembrane segments, by examining a large sample of membrane proteins with α-helix segments. The candidates were selected based on an amphipathy coefficient value range and the minimum number of residues in a segment. We compared our results with the transmembrane segments previously identified in the PDB_TM database by the TMDET algorithm. We expected that the hydrophobic segments would be identified using only the primary structures of the proteins and the amphipathy scale. However, some of these hydrophobic segments may pertain to hydrophobic pockets not included in transmembrane regions. We found that our amphipathy scale could identify α-helix transmembrane regions with a probability of success of 76% when all segments were included and 90% when all membrane proteins were included. Key words: Membrane protein, Protein structure, Amphipathy scale, Primary structures, α-Helix transmembrane segments, Hydrophobic protein regions |
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