Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies.
With advances in structure genomics, it is now recognized that knowledge of structure alone is insufficient to understand and control the mechanisms of biomolecular function. Additional information in the form of dynamics is needed. As demonstrated in a large number of studies, the machinery of proteins and their complexes can be understood to a good approximation by adopting Gaussian (or elastic) network models (GNM) for simplified normal mode analyses. While this approximation lacks chemical details, it provides us with a means for assessing the collective motions of large structures/assemblies and perform a comparative analysis of a series of proteins, thus providing insights into the mechanical aspects of biomolecular dynamics. In this paper, we discuss recent applications of GNM to a series of enzymes as well as large structures such as the HK97 bacteriophage viral capsids. Understanding the dynamics of large protein structures can be computationally challenging. To this end, we introduce a new approach for building a hierarchical, reduced rank representation of the protein topology and consequently the fluctuation dynamics.
Chennubhotla
Chakra
C
Department of Computational Biology, School of Medicine, University of Pittsburgh, W1040 BST 200 Lothrop Street, Pittsburgh, PA 15261, USA.
Rader
A J
AJ
Yang
Lee-Wei
LW
Bahar
Ivet
I
D001435:Bacteriophages / Q000378:metabolism; D001703:Biophysics / Q000379:methods*; D002213:Capsid / Q000737:chemistry*; D020134:Catalytic Domain; D003198:Computer Simulation; D004548:Elasticity; D046911:Macromolecular Substances / Q000737:chemistry; D008954:Models, Biological; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D016011:Normal Distribution; D009975:Orthomyxoviridae / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation
D046911:Macromolecular Substances