title: Topography prediction of helical transmembrane proteins by a new modification of the sliding window method.
abstract: Protein functions are specified by its three-dimensional structure, which is usually obtained by X-ray crystallography. Due to difficulty of handling membrane proteins experimentally to date the structure has only been determined for a very limited part of membrane proteins (<4%). Nevertheless, investigation of structure and functions of membrane proteins is important for medicine and pharmacology and, therefore, is of significant interest. Methods of computer modeling based on the data on the primary protein structure or the symbolic amino acid sequence have become an actual alternative to the experimental method of X-ray crystallography for investigating the structure of membrane proteins. Here we presented the results of the study of 35 transmembrane proteins, mainly GPCRs, using the novel method of cascade averaging of hydrophobicity function within the limits of a sliding window. The proposed method allowed revealing 139 transmembrane domains out of 140 (or 99.3%) identified by other methods. Also 236 transmembrane domain boundary positions out of 280 (or 84%) were predicted correctly by the proposed method with deviation from the predictions made by other methods that does not exceed the detection error of this method.
authors.affiliation: A.F. Mozhaisky Military Space Academy, Yaroslavl 150001, Russia.
authors.forename: Maria N
authors.initials: MN
authors.lastname: Simakova
authors.affiliation: Yaroslavl State Technical University, Yaroslavl 150023, Russia.
authors.forename: Nikolai N
authors.initials: NN
authors.lastname: Simakov
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D008565:Membrane Proteins