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Conformational studies of cyclic peptide structures in solution from 1 H‐Nmr data by distance geometry calculation and restrained energy minimization
Author(s) -
Senn Hans,
Loosli HansRudolf,
Sanner Michel,
Braun Werner
Publication year - 1990
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360291006
Subject(s) - energy minimization , chemistry , uniqueness , geometry , root mean square , crystallography , computational chemistry , mathematics , physics , mathematical analysis , quantum mechanics
The three‐dimensional structure of a cyclic bouvardin analogue, cyclo (‐Pro‐MeTyr‐Ala‐MeTyr‐MeTyr‐ D ‐Ala‐) has been determined by distance geomtry calculation and restrained energy minimization from nmr data. The preparation of the input for the distance geometry calculations, the modification of the amino acid library, and the analysis of the structures were done with the aid of a recently developed software package, GEOM. A great variety of different initial structures were explored to check the uniqueness of the determined solution structure. Calculations with 500 different initial structures and two different strategies led to a uniquely determined backbone conformation with a root mean square deviations value of 0.4 Å. The backbone structure consists of two β‐turns, a β‐II turn at Pro 1 ‐MeTyr 2 , and a β‐VI turn at MeTyr 4 ‐MeTyr 5 . The efficiency of the two calculation strategies were compared in order to propose an optimal means for performing distance geometry calculations with cyclic structures.