Theoretical DFT karplus equations: Amino acid side-chain torsion angle χ1

J. M. García De La Vega*, J. San Fabián, R. Crespo-Otero, R. Suardíaz, C. Pérez

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)

4 Citations (Scopus)

Abstract

Theoretical Karplus equations for determining the conformation in proteins is applied to phenylalanine and tyrosine residues of Desulfovibrio vulgaris flavodoxin using density functional theory (DFT) calculations. The accuracy of different Karplus equations is evaluated showing that S2 Fourier coefficient is not negligible and C1 adopts positive values for some couplings. These two points should be considered in future empirical parameterizations. The dihedral angles χ1 calculated in this study using the full set of Fourier coefficients present a root mean square deviation of 6° against those obtained from X-ray structures.

Original languageEnglish
Pages (from-to)656-660
Number of pages5
JournalInternational Journal of Quantum Chemistry
Volume113
Issue number5
DOIs
Publication statusPublished - 5 Mar 2013

Keywords

  • coupling constants
  • DFT
  • Karplus equation
  • proteins

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    García De La Vega, J. M., San Fabián, J., Crespo-Otero, R., Suardíaz, R., & Pérez, C. (2013). Theoretical DFT karplus equations: Amino acid side-chain torsion angle χ1. International Journal of Quantum Chemistry, 113(5), 656-660. https://doi.org/10.1002/qua.24030