Sequence Determines Folding Patterns in Proteins

Biswas, Arikta (2013) Sequence Determines Folding Patterns in Proteins. Masters thesis, Indian Institute of Science Education and Research Kolkata.

PDF (MS Dissertation of Arikta Biswas (11IP09)) Arikta_Biswas-_11IP09-MSThesis.pdf - Submitted Version Restricted to Repository staff only Download (6MB)

Abstract

The formation of proteins from linear to tertiary states should be exactly tractable because the tertiary states have unambiguous crystalline forms. Since the amino acids interact with water while folding, due consideration must be given to the hydrophobic / hydrophilic indices of the amino acids to understand the folding process. Experimental evidences show that the kinetics of folding of a number of cytosolic proteins starts from the N-termini and extends to the C-termini through a sequential interaction with the same set of nucleotides in the peptidyl transferase center (PTC) of the ribosome. Binding with the nucleotides effectively divides the polypeptide chain into segments having different hydrophobicity and those segments are then sequentially released from the nucleotides. Representing the amino acids by the hydrophobic indices and considering that folding happens in segments, a tool has been generated to show a regularity in amino acid sequence of cytosolic and membrane proteins. 250 cytosolic proteins and 100 membrane proteins of widely varying number of amino acids and structures were analyzed by this tool and regularity of amino acid sequence in the proteins could indeed be seen. This tool has been seen to be able to predict regions of unfoldedness in proteins too. Distribution of water molecules among the proteins has been analyzed and two different patterns have been visualized for cytosolic and membrane proteins. On the basis of these patterns and the regularity seen by the tool, an attempt has been made here to hypothesize the probable mechanisms of folding of cytosolic and membrane proteins.

Actions (login required)

View Item