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Analytical Loop Closure: Application to Protein Loops and Cyclic Peptides

등록일
2005년 2월 23일 13시 46분 31초
접수번호
1082
발표코드
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발표시간
토 10시 : 30분
발표형식
심포지엄
발표분야
물리화학 - 물리Ⅲ: 이론과 실험의 상호작용 II
저자 및
공동저자
석차옥
서울대학교 화학부,
We consider the problem of loop closure, i.e., of finding the ensemble of possible backbone structures of a chain segment of a protein molecule that is geometrically consistent with preceding and following parts of the chain whose structures are given. We reduce this problem of determining the loop conformations of six torsions to finding the real roots of a 16th degree polynomial in one variable, based on the robotics literature. We provide a simple intuitive view and derivation of the polynomial for the case in which each of the three pairs of torsional axes has a common point. We present applications to two problems. First, we show that Monte Carlo Minimization is made several-fold more efficient by employing the local moves generated by the loop closure algorithm, when applied to the global minimization of an eight-residue protein loop. Second, we present an ongoing application of a Monte Carlo Simulation using the local move sets to cyclic peptides.

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