ISSN (Online) : 2456 - 0774

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ISSN (Online) 2456 - 0774

Comparative Study on Structure Based Properties in Different Structural Classes of DNA Binding Proteins


Abstract:-During the process of protein folding, amino acid residues along theprimary sequence interact with each other in a cooperative manner to form thestable native structure. Knowledge about inter-residue interactions in proteinstructures is very helpful to understand the mechanism of protein folding andstability. Understanding the binding mechanism between DNA-binding domains andDNA will be useful for applications in industrial protein engineering. In thiscomparative study, we have systematically analyzed aminoacid composition andvarious structure based properties of molecular interactions in differentclasses of DNA binding proteins based on protein structure. Parameters used inthe study are aminoacid composition, long range order, surroundinghydrophobicity, long range interactions, medium range interactions, accessiblesurface area, ionic interactions, hydrophobic interactions and protein-DNAbinding interactions. Structural based properties of different types of DNAbinding proteins based on protein structure were statistically analyzed. Theresults obtained in this work highlight the low value of long range order ofall alpha proteins and high value of long range order of all beta proteins.Accessible surface area of polar residue was found to be greater than non-polarresidues. There is marked difference in structural based properties of bindingand non-binding residues. Ionic interacting residues have difference instructural based properties, compared to ionic non-interacting residues.Similarly difference in structural based properties of hydrophobic interactingresidues and hydrophobic non-interacting residues was noticed. Hence DNAbinding interactions, ionic interactions and hydrophobic interactions are influencedby the environment in which residues are present.

Keywords: Surrounding hydrophobicity, longrange order, ionic interaction, hydrophobic interactions, binding residue

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