Some Investigation on protiein Structure, Function and Dynamics in Disordered states and Non-ideal conditions

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The proteins we observe in nature have evolved through selective pressure to do certain specific functions such as catalyzing and regulating biochemical reactions, transporting molecules that permit cells to grow and reproduce. The three dimensional structure of protein is fundamentally related and tied to its biological function. So understanding the structure of protein is important to obtain insights on its function. The details of ordered secondary structures like helices and sheets in proteins are extensively discussed in the literature, but there are few reports on the remaining secondary structures comprising of turns, bends, bulges and other irregular structures that are commonly grouped and referred to as loops. Loops are essentially regions of non-repetitive conformation connecting regular secondary structures. These regions are important parts of protein structures as they have been shown in some cases to be the nucleation sites for protein folding, the sites of catalytic activity in enzymes or interfacial regions in the interaction between other proteins, ligands and nucleic acids. Thus loops play an important role in protein function. The structural-genomics initiative is expected to boost the population of high resolution protein 3D structures. Consequently, it has been argued that manual analysis of protein structure must be replaced by automated approaches of protein structure analysis. Loops play a major role in determining protein fold, hence methods that can facilitate automated analysis of loops in proteins are desirable. We have devised a method to identify and investigate functionally active loops and unstructured regions in protein structures using the MSRP parameter. This method (a) provides a unique classification tool for loops and folds among proteins, (b) permits automated identification of functional loops in protein structures, (c) provides clues on the diversity of conformations sampled by a disordered region during a molecular dynamics simulation. Traditionally acknowledged concept of protein function was the structurefunction paradigm, represented as Amino acid sequence-> 3D structure->Function. The 3D structure of protein in the folded state is related to its function and thus the native protein structure is the ordered 3D structure. However, recently it has emerged that the actual functional state for many proteins and protein domains are intrinsically unstructured. These unstructured proteins are also called intrinsically disordered proteins or natively unfolded proteins. They comprise a large fraction of eukaryotic...
Supervisor: R. Swaminathan