Development of Met-In -Prot server : Analysis and prediction of the metal binding pockets in Apoproteins & Exploring the influence of non-Watson and Crick base pairs on DNA Conformation via Molecular Dynamics techniques and Circular dichroism spectroscopy

Tomar, Kripi (2018) Development of Met-In -Prot server : Analysis and prediction of the metal binding pockets in Apoproteins & Exploring the influence of non-Watson and Crick base pairs on DNA Conformation via Molecular Dynamics techniques and Circular dichroism spectroscopy. Masters thesis, Indian Institute of Technology Hyderabad.

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Abstract

DNA can adopt myriad of secondary structures. These can be in the form of a left handed Z DNA, hairpin, parallel double helix, triplex, quadruplex , i-motifs etc. These conformations prevail in the cell and are stable due to their interactions with proteins and supercoiling of the DNA in various electrolyte and solvent conditions. These structures dictate DNA functions and hence play a significant role in pathology of diseases like cancer. Mismatch formation is often a cause of alteration in the DNA structure naturally present in the genome. Insight into the geometrical and stereo-electronic effects of mismatches on the dynamics of DNA can effectively improve our understanding of various cancer types and neurodegenerative diseases arising as a result of genome instability and mutagenesis .To analyze these atomic scale variations in DNA sequences, Molecular Dynamics techniques is employed based upon its ability to capture minuscule structural changes in DNA .CD spectroscopy is also an extensively used biophysical technique having many advantages like sensitivity, flexibility in experiment design, fast results etc., and can be used to determine secondary structures of nucleic acids. Metals also play a very important role in folding and functioning of protein structures. Exploring about the dynamics of metal and protein interaction has wide application in drug development, deciphering molecular mechanism of metallo-proteins and metallo-enzymes etc. Present study includes development of a fast robust metal binding site prediction algorithm which can augment research in the mentioned areas.

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