Research Article
Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
Roger Abseher,
Lennard Horstink,
Cornelis W. Hilbers,
Michael Nilges,
Roger Abseher
European Molecular Biology Laboratory, Heidelberg, Germany
Search for more papers by this authorLennard Horstink
NSR Center, Laboratory of Biophysical Chemistry, University of Nijmegen, Nijmegen, The Netherlands
Search for more papers by this authorCornelis W. Hilbers
NSR Center, Laboratory of Biophysical Chemistry, University of Nijmegen, Nijmegen, The Netherlands
Search for more papers by this authorCorresponding Author
Michael Nilges
European Molecular Biology Laboratory, Heidelberg, Germany
Meyerhofstraße 1, D-69117 Heidelberg, Germany===Search for more papers by this authorRoger Abseher,
Lennard Horstink,
Cornelis W. Hilbers,
Michael Nilges,
Roger Abseher
European Molecular Biology Laboratory, Heidelberg, Germany
Search for more papers by this authorLennard Horstink
NSR Center, Laboratory of Biophysical Chemistry, University of Nijmegen, Nijmegen, The Netherlands
Search for more papers by this authorCornelis W. Hilbers
NSR Center, Laboratory of Biophysical Chemistry, University of Nijmegen, Nijmegen, The Netherlands
Search for more papers by this authorCorresponding Author
Michael Nilges
European Molecular Biology Laboratory, Heidelberg, Germany
Meyerhofstraße 1, D-69117 Heidelberg, Germany===Search for more papers by this authorFirst published: 07 December 1998
Citations: 56
Abstract
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.
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