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.


CONCLUSIONS
Our approach introduces a new concept for classifying building blocks of proteins based on thermal fluctuations.
Demirel
Melik C
MC
College of Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA. melikdemirel@psu.edu
Cherny
Dmitry
D
D016000:Cluster Analysis; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000648:ultrastructure*; D010455:Peptides / Q000737:chemistry*; D010940:Plant Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D011487:Protein Conformation; D017510:Protein Folding
D046912:Multiprotein Complexes; D010455:Peptides; D010940:Plant Proteins; C093336:chymotrypsin inhibitor 2