Coarse-grained normal mode analysis in structural biology.
The realization that experimentally observed functional motions of proteins can be predicted by coarse-grained normal mode analysis has renewed interest in applications to structural biology. Notable applications include the prediction of biologically relevant motions of proteins and supramolecular structures driven by their structure-encoded collective dynamics; the refinement of low-resolution structures, including those determined by cryo-electron microscopy; and the identification of conserved dynamic patterns and mechanically key regions within protein families. Additionally, hybrid methods that couple atomic simulations with deformations derived from coarse-grained normal mode analysis are able to sample collective motions beyond the range of conventional molecular dynamics simulations. Such applications have provided great insight into the underlying principles linking protein structures to their dynamics and their dynamics to their functions.
Bahar
Ivet
I
Department of Computational Biology, University of Pittsburgh, W1043 Biomedical Science Tower, 200 Lothrop Street, Pittsburgh, PA 15261, USA. bahar@ccbb.pitt.edu
Rader
A J
AJ
D001665:Binding Sites; D018835:Chaperonin 10 / Q000737:chemistry; D018834:Chaperonin 60 / Q000737:chemistry; D003198:Computer Simulation; D020285:Cryoelectron Microscopy; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation
D018835:Chaperonin 10; D018834:Chaperonin 60