A periodicity analysis of transmembrane helices
Transmembrane helices and the helical bundles which they form are the major building blocks of membrane proteins. Since helices are characterized by a given periodicity, it is possible to search for patterns of traits which typify one side of the helix and not the other (e.g. amphipathic helices con...
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| Veröffentlicht in: | Bioinformatics 2005-06, Vol.21 (11), p.2604-2610 |
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| container_title | Bioinformatics |
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| creator | Leonov, Hadas Arkin, Isaiah T. |
| description | Transmembrane helices and the helical bundles which they form are the major building blocks of membrane proteins. Since helices are characterized by a given periodicity, it is possible to search for patterns of traits which typify one side of the helix and not the other (e.g. amphipathic helices contain a polar and apolar sides). Using Fourier transformation we have analyzed solved membrane protein structures as well as sequences of membrane proteins from the Swiss-Prot database. The traits searched included aromaticity, volume and ionization. While a number of motifs were already recognized in the literature, many were not. One particular example involved helix VII of lactose permease which contains seven aromatic residues on six helical turns. Similarly six glycine residues in four consecutive helical turns were identified as forming a motif in the chloride channel. A tabulation of all the findings is presented as well as a possible rationalization of the function of the motif. Contact: arkin@cc.huji.ac.il |
| doi_str_mv | 10.1093/bioinformatics/bti369 |
| format | Article |
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| source | MEDLINE; Oxford Journals Open Access Collection; EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection |
| subjects | Algorithms Amino Acid Sequence Biological and medical sciences Computer Simulation Fourier Analysis Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Membrane Proteins - analysis Membrane Proteins - chemistry Models, Chemical Models, Molecular Molecular Sequence Data Periodicity Protein Conformation Protein Structure, Secondary Sequence Alignment - methods Sequence Analysis, Protein - methods |
| title | A periodicity analysis of transmembrane helices |
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