Abstract
Proteins are essential parts of living organisms and participate in virtually every process within cells. As the genomic sequences for increasing number of organisms are completed, research into how proteins can perform such a variety of functions has become much more intensive because the value of the genomic sequences relies on the accuracy of understanding the encoded gene products. Although the static three-dimensional structures of many proteins are known, the functions of proteins are ultimately governed by their dynamic characteristics, including the folding process, conformational fluctuations, molecular motions, and protein-ligand interactions. In this review, the physicochemical principles underlying these dynamic processes are discussed in depth based on the free energy landscape (FEL) theory. Questions of why and how proteins fold into their native conformational states, why proteins are inherently dynamic, and how their dynamic personalities govern protein functions are answered. This paper will contribute to the understanding of structure-function relationship of proteins in the post-genome era of life science research.
Highlights
Proteins are essential parts of living organisms and participate in virtually every process within cells
The static three-dimensional structures of many proteins are known, the functions of proteins are governed by their dynamic characteristics, including the folding process, conformational fluctuations, molecular motions, and protein-ligand interactions
The central dogma of protein structural biology is that the amino acid sequence contains all the information necessary for a protein to fold into its three-dimensional structure under the proper physiological/experimental environment, and that the structure is essential for protein function [1,2,3]
Summary
A protein-solvent system is a thermodynamic system composed of the solute (the protein molecules), liquid water, buffer ions, and other substances such as small molecular compounds, cofactors, and ligands. Very complex interactions and energy/heat exchange exist among these substances; the macroscopic conformational states of a protein and a change in system properties are a result of the average behavior of a very large number of the microscopic constituents. The relationship between these substances and how heat transfer is related to various energy changes within a system are dictated by the laws of thermodynamics [30]. These include all the dihedral angles of the protein chain, the eigenvector projections derived from essential dynamics analysis of an MD trajectory [6,35,36], the number of native contacts, end-to-end distance of the peptide chain, and an order parameter that describes the similarity of the protein structure to the native or other states [37], or any degree of freedom of the protein [34]
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