ProCS15: a DFT-based chemical shift predictor for backbone and C[beta] atoms in proteins

• Published in: PeerJ (San Francisco, CA) Vol. 3; p. e1344
• Main Authors: Larsen, Anders S, Bratholm, Lars A, Christensen, Anders S, Channir, Maher, Jensen, Jan H
• Format: Journal Article
• Language: English
• Published: PeerJ. Ltd 20-10-2015
• Subjects: Hydrogen; Hydrogen bonds; Nitrogen (Chemical element); Protein binding; Ubiquitin
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.1344

We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and C[beta] atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7-1.1, 0.2-0.4, and 1.8-2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.