Abstract
AbstractIntrinsic dynamics of proteins are known to play important roles in their function. In particular, collective dynamics of a protein, which are defined by the protein’s overall architecture, are important in promoting the active site conformation that favors substrate binding and effective catalysis. The primary sequence of a protein, which determines its three-dimensional structure, encodes unique dynamics. The intrinsic dynamics of a protein actually link protein structure to its function. In the present study, coarse-grained normal mode analysis was performed to examine the intrinsic dynamic patterns of 24 different enzymes involved in primary metabolic pathways. We observed that each metabolic enzyme exhibits unique patterns of motions, which are conserved across multiple species and functionally relevant. Dynamic cross-correlation matrices (DCCMs) are visibly identical for a given enzyme family but significantly different from DCCMs of other protein families, reinforcing that proteins with sim...
Highlights
Proteins play crucial roles in most biological processes
We examined the relationship among these three properties, as well as developed a catalog of dynamic cross-correlation matrices (DCCMs)
The normal mode analysis (NMA) study of 24 important enzymes has demonstrated that each enzyme has signature dynamic patterns and the intrinsic dynamics of proteins are conserved across species, from simple organisms like E. coli to the complex H. sapiens
Summary
Each protein has a primary amino acid sequence that dictates the tertiary structure of the protein, and determines the protein’s overall function. The amino acid sequence → structure → function relationship exists for proteins and enzymes. It has been suggested that the protein’s dynamics is the fundamental link between its structure and function (Hensen et al, 2012). The local dynamical character of an enzyme active site does not alone produce the functionally/catalytically competent state necessary to perform the protein’s biological function. The whole protein’s dynamism is essential for its overall function. It has been observed that the dynamics of residues that are not directly involved in catalysis are important for enzyme function (Roston, Kohen, Doron, & Major, 2014; Tousignant & Pelletier, 2004)
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