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

Autor: Arroyuelo A; IMASL-CONICET, Universidad Nacional de San Luis , Ejército de Los Andes 950 , 5700 San Luis , Argentina., Martin OA; IMASL-CONICET, Universidad Nacional de San Luis , Ejército de Los Andes 950 , 5700 San Luis , Argentina., Scheraga HA; Baker Laboratory of Chemistry , Cornell University , Ithaca , New York 14850 , United States., Vila JA; IMASL-CONICET, Universidad Nacional de San Luis , Ejército de Los Andes 950 , 5700 San Luis , Argentina.; Baker Laboratory of Chemistry , Cornell University , Ithaca , New York 14850 , United States.
Jazyk: angličtina
Zdroj: The journal of physical chemistry. B [J Phys Chem B] 2020 Feb 06; Vol. 124 (5), pp. 735-741. Date of Electronic Publication: 2020 Jan 23.
DOI: 10.1021/acs.jpcb.9b10123
Abstrakt: In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) 1 J CαH 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 1 J CαH 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 1 J CαH 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.
Databáze: MEDLINE