Lakshmi, B and Archunan, G and Srinivasan, N (2013) PROPENSITIES OF AMINO ACID RESIDUES IN PROTEINS FOR DIFFERENT REGIONS OF THE RAMACHANDRAN MAP. In: Conference on Biomolecular Forms and Functions - A Celebration of 50 Years of the Ramachandran Map, JAN, 2013, Indian Inst Sci, Bangalore, INDIA, pp. 128-135.
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Using a dataset of 1164 crystal structures of largely non-homologous proteins defined at a resolution of 1.5 angstrom or better, we have investigated the (phi,psi) preferences of 20 residue types by considering the residues which occur in loops. Propensities of residue types to occur in the loops with (phi,psi) values in the aa region of the Ramachandran map has a poor correlation coefficient of 0.48 to the Chou-Fasman propensities of the residue types to occur in the a-helical segments. However the correlation coefficient between propensities of residues in loops to adopt beta conformations and those in beta-sheet is much higher (0.95). These observations suggest that a-helix formation is well influenced by the local amino acid sequence while intrinsic preference of residue types for beta-sheet plays a major role in the formation of beta-sheet. The main chain polar groups of residues in loops, that can affect the (phi,psi) values, can be involved in intra-molecular hydrogen bonding. Therefore we investigated further by considering subset of residues in loops with low (0 to 2) number of intra-molecular hydrogen bonds per residue involving main chain polar atoms. For this subset, the correlation coefficients between propensities for alpha-helix and alpha(R) region and between beta-sheet and beta-region are 0.26 and 0.64 respectively. This reiterates higher intrinsic tendency of beta-region favouring residues to adopt beta-sheet than alpha(R) region favouring residues to adopt alpha-helical structure.
| Item Type: | Conference Proceedings |
|---|---|
| Publisher: | WORLD SCIENTIFIC PUBL CO PTE LTD |
| Additional Information: | Copyright for this article belongs to the WORLD SCIENTIFIC PUBL CO PTE LTD, PO BOX 128 FARRER RD, SINGAPORE 9128, SINGAPORE |
| Department/Centre: | Division of Biological Sciences > Molecular Biophysics Unit |
| Date Deposited: | 14 Jul 2014 08:45 |
| Last Modified: | 14 Jul 2014 08:45 |
| URI: | http://eprints.iisc.ac.in/id/eprint/49487 |
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