Local feature analysis: a statistical theory for reproducible essential dynamics of large macromolecules.
Multivariate statistical methods are widely used to extract functional collective motions from macromolecular molecular dynamics (MD) simulations. In principal component analysis (PCA), a covariance matrix of positional fluctuations is diagonalized to obtain orthogonal eigenvectors and corresponding eigenvalues. The first few eigenvectors usually correspond to collective modes that approximate the functional motions in the protein. However, PCA representations are globally coherent by definition and, for a large biomolecular system, do not converge on the time scales accessible to MD. Also, the forced orthogonalization of modes leads to complex dependencies that are not necessarily consistent with the symmetry of biological macromolecules and assemblies. Here, we describe for the first time the application of local feature analysis (LFA) to construct a topographic representation of functional dynamics in terms of local features. The LFA representations are low dimensional, and like PCA provide a reduced basis set for collective motions, but they are sparsely distributed and spatially localized. This yields a more reliable assignment of essential dynamics modes across different MD time windows. Also, the intrinsic dynamics of local domains is more extensively sampled than that of globally coherent PCA modes.
Zhang
Zhiyong
Z
Laboratories for Biocomputing & Imaging, School of Health Information Sciences & Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA.
Wriggers
Willy
W
D017122:Bacteriophage T4 / Q000378:metabolism; D001671:Biochemistry / Q000379:methods*; D003198:Computer Simulation; D046911:Macromolecular Substances / Q000737:chemistry*; D015233:Models, Statistical; D008962:Models, Theoretical; D009113:Muramidase / Q000737:chemistry; D025341:Principal Component Analysis; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results
D046911:Macromolecular Substances; D011506:Proteins; D009113:Muramidase