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Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
Author(s) -
Abseher Roger,
Horstink Lennard,
Hilbers Cornelis W.,
Nilges Michael
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(19980601)31:4<370::aid-prot4>3.0.co;2-m
Subject(s) - molecular dynamics , principal component analysis , statistical physics , biological system , covariance , eigenvalues and eigenvectors , chemistry , protein dynamics , physics , computational chemistry , chemical physics , computer science , mathematics , biology , artificial intelligence , statistics , quantum mechanics
Large concerted motions of proteins which span its “essential space,” are an important component of protein dynamics. We investigate to what extent structure ensembles generated with standard structure calculation techniques such as simulated annealing can capture these motions by comparing them to long‐time molecular dynamics (MD) trajectories. The motions are analyzed by principal component analysis and compared using inner products of eigenvectors of the respective covariance matrices. Two very different systems are studied, the β‐spectrin PH domain and the single‐stranded DNA binding protein (ssDBP) from the filamentous phage Pf3. A comparison of the ensembles from NMR and MD shows significant overlap of the essential spaces, which in the case of ssDBP is extraordinarily high. The influence of variations in the specifications of distance restraints is investigated. We also study the influence of the selection criterion for the final structure ensemble on the definition of mobility. The results suggest a modified criterion that improves conformational sampling in terms of amplitudes of correlated motion. Proteins 31:370–382, 1998. © 1998 Wiley‐Liss, Inc.