FCCC LOGO Faculty Publications
Feng Jin-an , Crasto Chiquito J
Sequence codes for extended conformation: a neighbor-dependent sequence analysis of loops in proteins
Frontiers Science Series. 2000 ;30(Currents in Computational Molecular Biology) :115-117
PMID: AN 2000:417856   
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Abstract
An extensive anal. was conducted on the loop sequences in proteins using a loop databank that was derived from the Brookhaven Protein Data Bank. The databank was subdivided into different groups based on loop sizes, solvent accessibilities and connecting secondary structural elements. Amino acid loop propensities in different loop groups were calcd. in order to explore potential residue preferences in these loop groups. A neighbor-dependent sequence anal. of loops in proteins was carried out and the effect of neighboring amino acid type on the loop propensities of residues in loops were systematically analyzed to det. whether there is an inherent amino acid sequence preference for adopting loop conformations. The neighbor-dependent anal. of loop residues showed that the neighboring residues could have a profound effect on the preference of certain amino acids to adopt loop conformations. The most influential amino acids in loops are Pro and Gly. The dyad Pro-Val prefers loop conformation while the dyad Val-Pro has no preference for loop conformation. Some of the asym. dyads that have high propensity for loop conformation are listed. [on SciFinder (R)]
Notes
CAN 133:318667 6-3 General Biochemistry Fox Chase Cancer Center,Institute for Cancer Research,Philadelphia,PA,USA. Journal 0915-8502 written in English.