Proteins are dynamic entities in cellular solution which perform a remarkably large number of functions within cells and as such are the materials central to cellular function. The central dogma of structural biology is that a folded protein structure is essential for its biological function like enzyme mechanisms and regulation, transport across membranes, the building of large structures, biochemical transformations by enzymes as well as forming structural tissue such as muscles, hair, and the cytoskeleton. Protein structure is classified into four levels-
The primary structure is the simplest and consists of a sequence of amino acids in a polypeptide chain. Secondary structures such as the α helix and the β pleated sheet are formed within a polypeptide due to interactions between atoms of the backbone. Tertiary structure is the three-dimensional structure formed due to interactions between the R groups of the amino acids that make up the protein. When multiple polypeptide chains come together, it forms a quaternary structure. The biological function of a given protein is largely dependent on its 3D structure and especially the dynamical properties of it which requires prediction or experimental determination of their structures and it can be achieved by X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy thus providing a solid basis for structural and functional analyses of proteins. Recent advances in bio-structural sciences have resulted in enormous amounts of information of more than 45.000 known 3D structures of various proteins, stored at the Protein Data Bank for studying the dynamic behavior of proteins. Proteins and nucleic acids undergo significant conformational changes and dynamics can play a key role in their functionality. The internal motions and intrinsic dynamics of proteins including rearrangements, structural changes, and the conformational and allosteric mechanisms are crucial for its biological activity. The functional properties of proteins are determined by their dynamic personalities characterized by the thermodynamics and the kinetics of the protein under the free energy landscape. Molecular dynamics (MD) and normal mode analysis (NMA) are the two novel and emerging computational methods for characterizing protein dynamics and flexibility. MD simulations, first reported in the late 70s, have advanced into a mature technology that can be used effectively to characterize the interactions of chemicals with biomolecules such as proteins and nucleic acids. The study is used for analyzing the physical basis of the structure and function of biological macromolecules and further calculating the time-dependent behavior of a molecular system. MD simulations have become a fundamental part of structural biology as it plays a significant role in addressing a number of machining problems at the atomic scale. It uses simple approximations based on Newtonian physics for a system of interacting particles to simulate atomic motions, thus reducing the computational complexity. Bio3D-web, an online application that is open to all users and further provides an easy and quick analysis of protein sequence-structure-dynamic relationships. Recently, the concept of the conformational ensemble has been introduced to describe the structure of intrinsically unstructured proteins and derive its thermodynamic properties thus reconstructing the complex conformational transitions or even folding events.
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