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Protein folding

Alzheimer's disease, Creutzfeldt-Jakob disease, cystic fibrosis and p53-related cancer are all associated with incorrect protein folding, and are major causes of morbidity, mortality and healthcare costs. To ensure that proteins fold correctly, biological systems have evolved elaborate checkpoints that utilize chaperones and proteases. Despite such checkpoints, proteins can misfold and cause serious damage to the host organism. While it is widely accepted that protein misfolding leads to either a loss or gain of function, the mechanisms that promote these altered functions are not understood. A lack of understanding of these issues represents a major problem because it hinders the prevention of incorrect folding and impedes the development of tailor-made protein folding catalysts.

Our long-term goals are to identify mechanisms of protein misfolding and to design peptides that direct efficient protein folding. There is a strong conviction that proteins fold through fixed pathways and the discovery of folding intermediates is consistent with this conviction. Recent experiments have also established that unique amino acid sequences can acquire multiple active conformations while two non-homologous proteins can adopt similar folds. It is however our conviction that every folding problem does not have a unique solution. Ours interests are (a) to understand the significance of folding intermediates and the role of their environment on folding (b) to identify common structural determinants that initiate protein folding and (c) to design denovo peptide chaperones.

We have already established pro-subtilisin (a serine protease) as a model for analyzing protein-folding mechanisms. This system also serves as the model for prohormone convertases, which is a protein family responsible for activating hormone precursors. We have successfully isolated several of these structured intermediates. One such intermediate isolated in an oxidizing environment can acquire a novel, environment-dependent proteolytic activity. This finding may represent the paradigm that protein-folding intermediates can catalyze biological reactions and emphasizes our earlier discovery that subtilisin memorizes its folding environment to adopt multiple active conformers. These discoveries position us uniquely to assess the nature, significance and the mechanisms of activation of these protein-folding intermediates. We hope that a clearer understanding of the extent to which intermediates and their environment affect the folding, will make it possible to maneuver the folding pathway and to even prevent misfolding.
 

Recent Publications:

1. Subbian E, Yabuta Y, Shinde UP. Folding pathway mediated by an intramolecular chaperone: intrinsically unstructured propeptide modulates stochastic activation of subtilisin. J Mol Biol. 2005 Mar 25;347(2):367-83. Epub 2005 Jan 27.

2. Yabuta Y, Subbian E, Oiry C, Shinde U. Folding pathway mediated by an intramolecular chaperone. A functional peptide chaperone designed using sequence databases. J. Biol. Chem. 278(17):15246-51 (2003).

3. Subbian E, Yabuta Y, Shinde U. Abstract Positive selection dictates the choice between kinetic and thermodynamic protein folding and stability in subtilases. Biochemistry. 2004 Nov 16;43(45):14348-60.

4. Yabuta Y, Subbian E, Takagi H, Shinde U, Inouye M. Folding pathway mediated by an intramolecular chaperone: dissecting conformational changes coincident with autoprocessing and the role of Ca(2+) in subtilisin maturation. J Biochem (Tokyo) 131(1):31-7 (2002).

5. Yabuta Y., Subbian E., Takagi H., Shinde U., Inouye M. Folding pathway mediated by an intramolecular chaperone: dissecting conformational changes coincident with autoprocessing and the role of ca(2+) in subtilisin maturation. J Biochem (Tokyo) 131(1):31-7 (2002).