Evaluation of Folding Code Intrinsic to Amino Acids

Nair, Jyothi V. (2012) Evaluation of Folding Code Intrinsic to Amino Acids. Masters thesis, Indian Institute of Science Education and Research Kolkata.

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Abstract

Hydrophilic amino acids play a major role in the interaction between 23S r RNA and nascent polypeptide during Ribosome mediated protein folding. In the native conformation of cytosolic proteins hydrophobicity decreases from core to exterior. The predominant amino acids from each part, especially outer shell, are the ones that interact with 23S r-RNA during protein folding. Combining these two observations we can conclude that the ability of the amino acids that interact with 23S r-RNA to do so is propelled by their predominance in the protein as well as their extreme hydrophilicity. These amino acids that are extremely hydrophilic and occupy the outer shell of the protein belong to the N-terminal of the nascent polypeptide. Three possible nucleation sites have been discovered in cytosolic proteins, none of which contain the amino acids interacting with 23S r-RNA but share their property of having at least one highly hydrophilic component (ASP) and occupancy of the outer shell. Interestingly attempts to expand the motif i.e including a third member to these potential nucleation sites have resulted in inclusion of Lysine and Leucine. Overall from our observations, the protein folding code intrinsic to amino acids seems to be biased towards the N-terminal of the polypeptide and the outer shell of the native cytosolic proteins.

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