Communication: Accurate determination of side-chain torsion angle χ1 in proteins: Phenylalanine residues

Abstract

Quantitative side-chain torsion angle χ1 determinations of phenylalanine residues in Desulfovibrio vulgaris flavodoxin are carried out using exclusively the correlation between the experimental vicinal coupling constants and theoretically determined Karplus equations. Karplus coefficients for nine vicinal coupling related with the torsion angle χ1 were calculated using the B3LYP functional and basis sets of different size. Optimized χ1 angles are in outstanding agreement with those previously reported by employing x ray and NMR measurements.

Computational NMR coupling constants: Shifting and scaling factors for evaluating 1JCH

“…Computations were performed using nine basis sets of contracted Gaussian functions, namely TZVP, EPR‐III, HIII‐su3, aug‐cc‐pVTZ‐J, ccJ‐pVDZ, ccJ‐pVTZ, ccJ‐pVQZ, pcJ‐2 and pcJ‐3. TZVP is a DFT‐optimized valence triple‐ ζ basis set with promising results for the prediction of hyperfine couplings and SSCCs in combination with the B3LYP functional. EPR‐III is larger and has been optimized for the computation of hyperfine coupling constants by DFT methods with the s‐part improved to describe better the nuclear regions; it is a triple‐ ζ basis including diffuse functions, doubled polarizations and a single set of f‐polarization functions.…”

Toward a Computational NMR Procedure for Modeling Dipeptide Side-Chain Conformation

“…They generally exhibit two minima due to the intrinsic degeneracy of the Karplus equation. 32 For the majority of residues, the χ 1 angles, as shown in column #2 of Table 1 , correspond to the absolute minima, that is, the first minimum, indicated by a superindex ( 1 ) together with the minimum rmsd J ,res in column #3. For three residues, Leu46, Leu74, and Leu124, the considered χ 1 angle corresponds to a second minimum (superindex 2 ).…”

“…This model usually predicts two different minima, if one is at χ 1 , the other will be around χ 1 + 180°. 32 This ambiguity is inherent in the degeneration of the Karplus equation that even with up to nine experimental couplings gives a multi-valued solution. 32 To avoid this ambiguity, we consider within this model the results that fulfill two conditions: (i) the determined χ 1 value corresponds to an staggered conformer within an uncertainty of ±30°, and (ii) the population for this unimodal conformer, calculated as suggested below [trimodal-static-staggered (TMSS)], is larger than 60%.…”

Computational Protocol to Evaluate Side-Chain Vicinal Spin–Spin Coupling Constants and Karplus Equation in Amino Acids: Alanine Dipeptide Model

“…The well-known classical Karplus (eq ) uses the terms up to P = 2 and Q = 0, neglecting the sine terms that are responsible for the asymmetry of vicinal couplings around θ = 180°. Moreover, although the coefficients C 3 and S 1 are usually small, the coefficient S 2 is not negligible and its accurate determination could improve to resolve ambiguities on the molecular conformation …”