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Analysis of Rate-limiting Long-range Contacts in the Folding Rate of Three-state and Two-state Proteins

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Abstract:

In the past decade, when compared to models describing the folding rates of two-state proteins, models describing the folding mechanism of three-state proteins remain quite limited due to the complexity present in the folding mechanism and lack in their experimental data. In the present work, rate-limiting long-range contacts were classified into various bins based on sequence separation distance between the contacting residues and the role of these bins were analyzed for their importance in a data set of 35 three-state proteins. Predicting the folding rates of these proteins have been carried out by relating experimental folding rates and long-range contacts obtained from various sequence separation bins. For comparison, using the present model, prediction of the folding rates of 45 two-state proteins also resulted with good accuracy. Our method shows that long-range contacts observed in the final 3-D structure of proteins at various sequence separation bins are found to be an important descriptor in explaining the folding rates of three-state proteins and suggest that formation of contacts between residues present at these sequence separation distance may be a crucial factor in deciding structure formation and folding rates of these proteins. The aim of our present work is not to construct a new descriptor for the folding rates of three-state proteins, nor is to provide improved means of folding-rate prediction for these proteins. We tend to elucidate that how long-range contacts play a crucial role in the folding mechanism of three state proteins belonging to three major structural classes and implication of these observations due to rate-limiting long-range contacts has been discussed in the light of other experimental studies of protein folding.





Keywords: AABUF; Contact Order; Correlation coefficient; FORTRAN program; LRO; NMR study; TCD; Trp-cage; contact formation; folding rate prediction; hydrogen bonding pattern; jack-knife methods; long-range contacts; sequence separation distance; three-state proteins

Document Type: Research Article

Publication date: 2011-10-01

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  • Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.
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