Assessing the One-Bond Cα-H Spin-Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches

J Phys Chem B. 2020 Feb 6;124(5):735-741. doi: 10.1021/acs.jpcb.9b10123. Epub 2020 Jan 23.

Abstract

In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) 1JCαH in proteins: density functional theory (DFT) calculations, a Karplus-like equation, and Gaussian process regression. The main motivation of this work is to select the best method for fast and accurate computation of the 1JCαH SSCC, for its use in everyday applications in protein structure validation, refinement, and/or determination. Our initial results showed a poor agreement between the DFT-computed and observed 1JCαH SSCC values. Further analysis leads us to the understanding that the model chosen for the DFT computations is inappropriate and that more complex models will require a higher, if not prohibitively, computational cost. Finally, we show that the Karplus-like equation and Gaussian Process regression provide faster and more accurate results than DFT-based calculations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbon / chemistry
  • Density Functional Theory
  • Hydrogen / chemistry
  • Models, Chemical
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Proteins / chemistry*
  • Regression Analysis

Substances

  • Proteins
  • Carbon
  • Hydrogen