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Structural basis of hierarchical multiple substates of a protein. IV: Rearrangements in atom packing and local deformations
Author(s) -
Noguti Tosiyuki,
Gō Nobuhiro
Publication year - 1989
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340050206
Subject(s) - maxima and minima , cluster (spacecraft) , local structure , globular protein , atom (system on chip) , chemical physics , molecular dynamics , chain (unit) , molecule , crystallography , energy landscape , monte carlo method , basis (linear algebra) , molecular physics , space (punctuation) , statistical physics , chemistry , physics , computational chemistry , geometry , mathematics , thermodynamics , computer science , mathematical analysis , statistics , operating system , embedded system , programming language , organic chemistry , astronomy
Differences in atom packing are studied in the minimum energy conformations derived from the record of the Monte Carlo simulation of conformational fluctuation in the native state of a globular protein, bovine pancreatic trypsin inhibitor. It is found that local deformations observed among the minima which are found in the previous paper are accompanied by rearrangement of atom packing. Spatial locations of the local deformations in the three‐dimensional folded structure are also studied. It is foundthat the local deformations are distributed in space in several clusters inthe folded structure. The size and location of the clusters characterize the respective fluctuations of the first and the second levels observed in the simulation. In the fluctuations of the first level local deformations, each of which usually involves a few side chains and one main chain local segment, are thermally exited independently of each other near thesurface of the molecule. The observed fluctuation of the second level involves a cooperative deformation involving many side chains and local main chain segments all in one cluster, which goes though the core of the molecule. The collective local deformations observed both in the first and second levels are plastic in the sense that they are accompanied with rearrangement of atom packing.