A novel measure characterized by a polar energy surface approximation for recognition and classification of transmembrane protein structures
| Autor: | Henrik T. Yudate, Sigeki Mitaku, Makiko Suwa, Yasuhiko Masuho |
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| Rok vydání: | 2000 |
| Předmět: |
Models
Molecular Rhodopsin Protein family Molecular Sequence Data Static Electricity Biochemistry Protein Structure Secondary Electron Transport Complex IV Structural Biology Animals Humans Amino Acid Sequence Molecular Biology Root-mean-square deviation biology Chemistry Membrane Proteins Proteins Bacteriorhodopsin Transmembrane protein Protein Structure Tertiary Crystallography Transmembrane domain Models Chemical Membrane protein Bacteriorhodopsins Helix biology.protein Thermodynamics Sequence Alignment Algorithms |
| Zdroj: | Proteins: Structure, Function, and Genetics. 41:504-517 |
| ISSN: | 1097-0134 0887-3585 |
| DOI: | 10.1002/1097-0134(20001201)41:4<504::aid-prot80>3.0.co;2-k |
| Popis: | A new theoretical method has been developed for recognition and classification of membrane proteins. The method is based on computation of a polar energy surface that can reveal characteristic interaction patterns for individual helices even if crystal or NMR structure coordinates are not available. A protein with N transmembrane helices is described as a set of N vectors that are derived from a Fourier analysis of this polar energy surface computed for each helix. We then derive a polarity difference score (PDS) for any two proteins computed as the root mean square deviation between the respective vector coordinate sets. The score was found to correlate with the degree of structural similarity between the following three protein families for which tertiary structures have been determined: bacteriorhodopsin, rhodopsin, and the cytochrome c oxidase III subunit. Proteins 2000;41:504–517. © 2000 Wiley-Liss, Inc. |
| Databáze: | OpenAIRE |
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