Clustering and diversity of fluctuations for proteins

Background: Protein topology plays a key role in various types of interactions. Topological constraints of a protein are defined by a contact map. We studied the fluctuations of proteins with use of a new approach based on contact map. Methods: An annealing algorithm is used to generate a 3-dimensional protein structure from the contact map. First, we study the properties of structural elements based on fluctuations by adding individual structures (domains or subdomains). Thereafter, we focus on the building block of proteins in terms of fluctuations. Results: To verify our hypothesis, we analyzed the pattern of fluctuations for chymotrypsin inhibitor-2 (CI2) by unstructuring (melting) of subregions. The data show different patterns of fluctuations for the unstructured CI2 relative to that calculated for the intact protein. Conclusion: Our approach introduces a new concept for classifying building blocks of proteins based on thermal fluctuations.