Quantifying Inter-Residue Contacts through Interaction Energies

• Published in: Journal of chemical information and modeling Vol. 59; no. 12; pp. 5034 - 5044
• Main Authors: Summers, Thomas J, Daniel, Baty P, Cheng, Qianyi, DeYonker, Nathan J
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 23.12.2019
• Subjects: Amino acids; Chains; Construction; Functional groups; Model accuracy; Network analysis; Networks; Organic chemistry; Perturbation theory; Proteins
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/acs.jcim.9b00804

The validity and accuracy of protein modeling is dependent on constructing models that account for the inter-residue interactions crucial for protein structure and function. Residue interaction networks derived from interatomic van der Waals contacts have previously demonstrated usefulness toward designing protein models, but there has not yet been evidence of a connection between network-predicted interaction strength and quantitative interaction energies. This work evaluates the intraprotein contact networks of five proteins against ab initio interaction energies computed using symmetry-adapted perturbation theory. To more appropriately capture the local chemistry of the protein, we deviate from traditional protein network analysis to redefine the interacting nodes in terms of main chain and side chain functional groups rather than complete amino acids. While there is no simple correspondence between the features of the contact network and actual interaction strength, random forest models constructed from minimal structural, network, and chemical descriptors are capable of accurately predicting interaction energy. The results of this work serve as a foundation for the development and improvement of functional group-based contact networks.