Linking topography of its potential surface with the dynamics of folding of a protein model

被引:81
作者
Berry, RS
Elmaci, N
Rose, JP
Vekhter, B
机构
[1] Department of Chemistry, University of Chicago, Chicago, IL 60637
[2] Simulations Plus, Inc., Building 110, Palmdale, CA 93550
关键词
folding pathways; stable structures; beta-barrel;
D O I
10.1073/pnas.94.18.9520
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The ''3-color, 46-bead'' model of a folding polypeptide is the vehicle for adapting to proteins a mode of analysis used heretofore for atomic clusters, to relate the topography of the potential surface to the dynamics that lead to formation of selected structures, The analysis is based on sequences of stationary points-successive minima, joined by saddles-that rise monotonically in energy from basin bottoms. Like structure-seeking clusters, the potential surface of the model studied here is staircase-like, rather than sawtooth-like, with highly collective motions required for passage from one minimum to the next. The surface has several deep basins whose minima correspond to very similar structures, but which are separated by high energy barriers.
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页码:9520 / 9524
页数:5
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