2001 Fiscal Year Final Research Report Summary
Classification and analysis of local structure motifs in protein conformations
| Project/Area Number |
11680666
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Waseda University |
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Principal Investigator |
WAKO Hiroshi Waseda University, School of Social Sciences, Professor, 社会科学部, 教授 (60158607)
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| Project Period (FY) |
1999 – 2001
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| Keywords | protein conformation / structural motif / Delaunay tetrahedron / structural alignment / homologous protein / hydrophobic core / α-helix |
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| Research Abstract |
In order to reveal a principal of protein architectures we identified local structure motifs commonly found in different protein conformations and analyzed them. For this purpose we used the method developed by ourselves, in which Delaunay tessellation is applied to protein conformations and codes are assigned to Delaunay tetrahedrons to characterize the local structures containing them. In this research we carried out the following.
(1) The rules to assign the Delaunay codes were modified so that they could represent characteristics of the local structures more properly and be applied to the proteins constructed with more than one chain.
(2) A new algorithm was developed to detect a local structural motif consisting of more than one tetrahedron.
(3) Application 1 : We prepared to construct local-structure database.
(4) Application 2 : Making use of the local-structure codes site-dependent and environment-dependent frequencies of amino acid occurrences were examined for α-helix.
(5) Application 3 : We defined a hydrophobic core as the local structure containing a Delaunay tetrahedron with four vertices occupies by the hydrophobic amino acid residues. Then such structures were studied.
(6) Application 4 : Using local structure codes, the method was developed to classify proteins with the same amino acid sequence motif with each other in more detail.
(7) Application 5 : Using the algorithm described in (2) we analyzed the characteristics of the relatively larger local structures observed in homologous or non-homologous proteins.
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