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Understanding the folding mechanism of proteins: theory meets experiments
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Abstract
Globally the energy landscape of a folding protein resembles a partially rough funnel. An important idea that emerges from the energy landscape theory is that subtle features of the protein landscape can profoundly affect the mechanism of folding. Recent experimental results suggest that the native fold, or topology, plays a primary role in shaping the protein energy landscape.
To quantitatively investigate the extent of the topological control of the folding process, we study the folding of simplified models of a set of small globular proteins constructed using a energetically unfrustrated potential. Such a potential retains the information about the native structures but drastically reduces the energetic frustration and energetic heterogeneity. By comparing the results of our study with the available experimental data we show that these energetically unfrustrated models can reproduce the global features of the transition state ensembles and ``on--route" intermediates.
This result clearly indicates that, as long as the protein sequence is sufficiently minimally frustrated, topology plays a central role in determining the folding mechanism. Starting from this result, interesting applications and further developments of the model are presented.
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