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

In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) 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 be...

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Vydáno v:The journal of physical chemistry. B Ročník 124; číslo 5; s. 735
Hlavní autoři: Arroyuelo, Agustina, Martin, Osvaldo A, Scheraga, Harold A, Vila, Jorge A
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 06.02.2020
Témata:
Carbon - chemistry
Density Functional Theory
Hydrogen - chemistry
Models, Chemical
Nuclear Magnetic Resonance, Biomolecular - methods
Proteins - chemistry
Regression Analysis
ISSN:1520-5207, 1520-5207
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Shrnutí:In the present work, we explore three different approaches for the computation of the one-bond spin-spin coupling constants (SSCC) 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 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 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.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1520-5207
1520-5207
DOI:10.1021/acs.jpcb.9b10123