DiffBond: A Method for Predicting Intermolecular Bond Formation

Abstract

Many tools that explore models of protein complexes are also able to analyze interactions between specific residues and atoms. A comprehensive exploration of these interactions can often uncover aspects of protein-protein recognition that are not obvious using other protein analysis techniques. This paper describes DiffBond, a novel method for searching for intermolecular interactions between protein complexes while differentiating between three different types of interaction: hydrogen bonds, ionic bonds, and salt bridges. DiffBond incorporates textbook definitions of these three interactions while contending with uncertainties that are inherent in computational models of interacting proteins. We used it to examine the barnase-barstar, Rap1a-raf, and Smad2-Smad4 complexes, as well as a subset of protein complexes formed between three-finger toxins and nAChRs. Based on electrostatic interactions established by previous experimental studies, DiffBond was able to identify ionic and hydrogen bonds with high precision and recall, and identify salt bridges with high precision. In combination with other electrostatic analysis methods, DiffBond can be a useful tool in helping predict influential amino acids in protein-protein interactions and characterizing the type of interaction.

Fig. 1.

Sidechain visualization of Arg59 on Barnase (green) and Glu76 on Barstar (teal). Arg59 and Glu76 are within 4Å and are oppositely charged amino acids, so they are predicted to form a salt bridge by DiffBond.

Fig. 2.. Intersection using CSG

a) Two proteins with oppositely charged electrostatic fields. b) When the proteins are in complex, the oppositely charged fields overlap forming an intersection region shown in orange. c) The intersection region represents the degree to which the field of one protein complements the field of the other.

Fig. 3.. Effect of Nullification on Barnase-barstar

a) Wildtype barnase electrostatic surface at isopotential of +1 kT/e. b) Barnase nullified at residue 59, electrostatic surface at isopotential of +1 kT/e. c) Overlap of wildtype (transparent yellow) and nullified barnase (green) surfaces. a,b,c) The red square encompasses the main difference in isopotential surface due to nullification. d) Wildtype barnase (blue) in complex with barstar (transparent yellow).

Fig. 4.

Volume difference between wildtype and mutant barnase-barstar complex when nullifying barnase amino acids at k= +/−1, +/−3, +/−5, and +/−7. Significant residue nullifications are those that surpass either the upper or lower threshold.