Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity

Bridget E. Nolan, Emily Levenson, Brian Y. Chen
2017 Journal of Computational Biology  
This paper examines three techniques for rapidly assessing the electrostatic contribution of individual amino acids to the stability of protein-protein complexes. Whereas the energetic minimization of modeled oligomers may yield more accurate complexes, we examined the possibility that simple modeling may be sufficient to identify amino acids that add to or detract from electrostatic complementarity. The three methods evaluated were (a) the elimination of entire sidechains (e.g. glycine
more » ... ), (b) the elimination of the electrostatic contribution from the atoms of a sidechain, called nullification, and (c) sidechain structure prediction using SCWRL4. These techniques generate models in seconds, enabling large-scale mutational scanning. We evaluated these techniques on the SMAD2/SMAD4 heterotrimer, whose formation plays a crucial role in antitumor pathways. Many studies have documented the clinical and structural effect of specific mutations on trimer formation. Our results describe how glycine scanning yields more specific predictions, though nullification may be more sensitive, and how sidechain structure prediction enables the identification of uncharged-to-charge mutations.
doi:10.1089/cmb.2016.0162 pmid:28051901 fatcat:swcrtye5kfc3xozpg4x7soat7u