A classification of disulfide patterns and its relationship to protein structure and function

Abstract

We report a detailed classification of disulfide patterns to further understand the role of disulfides in protein structure and function. The classification is applied to a unique searchable database of disulfide patterns derived from the SwissProt and Pfam databases. The disulfide database contains seven times the number of publicly available disulfide annotations. Each disulfide pattern in the database captures the topology and cysteine spacing of a protein domain. We have clustered the domains by their disulfide patterns and visualized the results using a novel representation termed the “classification wheel.” The classification is applied to 40,620 protein domains with 2–10 disulfides. The effectiveness of the classification is evaluated by determining the extent to which proteins of similar structure and function are grouped together through comparison with the SCOP and Pfam databases, respectively. In general, proteins with similar disulfide patterns have similar structure and function, even in cases of low sequence similarity, and we illustrate this with specific examples. Using a measure of disulfide topology complexity, we find that there is a predominance of less complex topologies. We also explored the importance of loss or addition of disulfides to protein structure and function by linking classification wheels through disulfide subpattern comparisons. This classification, when coupled with our disulfide database, will serve as a useful resource for searching and comparing disulfide patterns, and understanding their role in protein structure, folding, and stability. Proteins in the disulfide clusters that do not contain structural information are prime candidates for structural genomics initiatives, because they may correspond to novel structures.