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PEDS Advance Access published online on April 22, 2005
Protein Engineering Design and Selection, doi:10.1093/protein/gzi022
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org
Received July 31, 2004
Revised December 3, 2004
Accepted March 9, 2005

Article

Understanding the relationship between the primary structure of proteins and their amyloidogenic propensity: clues from inclusion body formation

Susan Idicula-Thomas 1 and Petety V. Balaji 1*

1 School of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India

* To whom correspondence should be addressed.
Petety V. Balaji, E-mail: balaji{at}iitb.ac.in


  Abstract

Amyloid formation is dependent to a considerable extent on the amino acid sequence of the protein. The present study delineates certain sequence-dependent features that are correlated with amyloidogenic propensity. The analyses indicate that amyloid formation is favored by lower thermostability and increased half-life of the protein. There seems to be a certain degree of bias in the composition of order-promoting amino acids in the case of amyloidogenic proteins. Based on these parameters, a prediction function for the amyloidogenic propensity of proteins has been created. The prediction function has been found to rationalize the reported effect of certain mutations on amyloid formation. It seems that a higher sheet propensity of residues that constitute the first seven residues of a helical structure in a protein might increase the propensity for a helix to sheet transition in that region under denaturing conditions.

Keywords: aliphatic index; discordant stretch; instability index; sheet propensity; thermostability.
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