Synthesis, conformation and vibrational dynamics of apolipoprotein B fragment, -Asn-Cys-Lys-Val-Glu-Leu-

Abstract

It is assumed that all biological processes are dynamical in nature and the low frequency collective modes, particularly the skeletal modes arising from the main chain and the side chain play an important role in such processes. To identify these a complete normal mode analysis of the hexapeptide -Asn-Cys-Lys-Yal-Glu-Leu-, a fragment of apolipoprotein B has been carried out. The assignment of modes is greatly assisted by similar studies on the tetra -Cys-Lys-Val-Glu- and tripeptides (-Asn-Cys-Lys-, -Yal-Glu-Leu-) fragments of the hexapeptide. All the four peptides have been synthesized by the solid phase peptide method using 9-flurrenyl methyloxycarbonyl (Fmoc) on 4-methyl benzhyldrylamine (MBHA) and Wang's resins. Their conformation is determined from the Ramachandran Maps which are based on the global energy minimization method. It is supported by the propensity parameters for the amino acids.