Average Distance Map Analysis of Amyloidogenic Protein Domains

S, Jeevotham and Patel, Basant Kumar (2018) Average Distance Map Analysis of Amyloidogenic Protein Domains. Masters thesis, Indian Institute of Technology Hyderabad.

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Abstract

Structural characterization of amyloidogenic peptides and prion domains has been a major area of interest in the �eld of Amyloid and Prion Biology. Over the past two decades, several new advanced techniques like ssNMR and cryo-electron microscopy have helped answer the challenging questions about the structure of proteins that constitute prions and amyloids. In this study, we use a technique called average distance map analysis (ADM) which employs inter-residue average distance statistics to predict structural domains in globular proteins based solely on their amino acid sequence to answer these questions. Five candidate proteins were analyzed: C-terminal domain of the fungal protein, Het-s, the amyloid � (1-42) peptide, N-terminal prion domain of the yeast Sup35 protein, N-terminal domain of the human prion protein and the low complexity domain of human TDP43 protein. ADMs were constructed for all, and the gross topology was predicted. The predictions made by this analysis coincided with a lot of structural information available about the proteins used. This study provides preliminary evidence on the utility of the ADM analysis in the �eld of amyloids and prions, warranting further investigation.

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