Premium
Energy landscape of a native protein: Jumping‐among‐minima model
Author(s) -
Kitao Akio,
Hayward Steven,
Go Nobuhiro
Publication year - 1998
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/(sici)1097-0134(19981201)33:4<496::aid-prot4>3.0.co;2-1
Subject(s) - maxima and minima , principal component analysis , hierarchy , component (thermodynamics) , harmonic , subspace topology , energy landscape , statistical physics , physics , square (algebra) , chemistry , molecular physics , chemical physics , biological system , geometry , mathematics , quantum mechanics , mathematical analysis , statistics , thermodynamics , biology , economics , market economy
We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping‐among‐minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra‐substate and inter‐substate motions. By examining intra‐substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5% of all modes, dominate contributions to total mean‐square atomic fluctuation. Inter‐substate motions are observed only in a small‐dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter‐substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low‐level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation. Proteins 33:496–517, 1998. © 1998 Wiley‐Liss, Inc.