Oligomeric interfaces under the lens: gemini.

Abstract

The assembly of subunits in protein oligomers is an important topic to study as a vast number of proteins exists as stable or transient oligomer and because it is a mechanism used by some protein oligomers for killing cells (e.g., perforin from the human immune system, pore-forming toxins from bacteria, phage, amoeba, protein misfolding diseases, etc.). Only a few of the amino acids that constitute a protein oligomer seem to regulate the capacity of the protein to assemble (to form interfaces), and some of these amino acids are localized at the interfaces that link the different chains. The identification of the residues of these interfaces is rather difficult. We have developed a series of programs, under the common name of Gemini, that can select the subset of the residues that is involved in the interfaces of a protein oligomer of known atomic structure, and generate a 2D interaction network (or graph) of the subset. The graphs generated for several oligomers demonstrate the accuracy of the selection of subsets that are involved in the geometrical and the chemical properties of interfaces. The results of the Gemini programs are in good agreement with those of similar programs with an advantage that Gemini programs can perform the residue selection much more rapidly. Moreover, Gemini programs can also perform on a single protein oligomer without the need of comparison partners. The graphs are extremely useful for comparative studies that would help in addressing questions not only on the sequence specificity of protein interfaces but also on the mechanism of the assembly of unrelated protein oligomers.