using networks for modelling three-dimensional structures of proteins

somdatasina

INDIAN INSTITUTE OF SCIENCE EDUCATION RESEARCH (IISER) KOLKATA, INDIA

"using networks for modelling three-dimensional structures of proteins"

Proteins are macromolecules in the cell performing most of the metabolic processes. The protein is made up of a linear chain of amino-acids (primary structure) synthesized, through transcription and translation of the corresponding gene/DNA sequence inside the cell. The functional protein is a three-dimensional structure that is formed due to spontaneous or assisted folding of the linear chain decided by the physicochemical forces exerted due to the size, charge and chemical nature of the amino acids. The 3D structure essentially determines the function of the protein - known as the 'Structure-Function paradigm' in molecular biophysics. We have modelled the 3-dimensional structure of proteins using the network/graph theory, where the amino acids are the nodes, and links are the physicochemical forces that hold any two amino acids together. I will show how the network approach can clearly explain the large functional differences in proteins and their mutants, having insignificant structural variations, not easily identifiable using standard structural biology methods, and thereby questioning the universality of the 'Structure-Function paradigm'.
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