Gromiha MM. Structure based sequence dependent stiffness scale for trinucleotides: a direct method.
J Biol Phys 2013;
26:43-50. [PMID:
23345711 DOI:
10.1023/a:1005250718139]
[Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new set of stiffness parameters for all the 32trinucleotide units has been set up directly from thethree dimensional structures of DNA molecules. It wasobserved that GAC/GTC is the stiffest trinucleotideand ACC/GGT is the most flexible one. The averagestiffness values computed for a set of operatorsequences using the new parameters correlate very wellwith the protein-DNA binding specificity and bindingfree energy change of 434 repressor and Cro repressor,respectively. The new structure based stiffness scalecan explain the protein-DNA binding specificity to thelevel of 0.92.
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