Structural Dependencies of Interresidue Scalar Coupling ^h3J_NC‘ and Donor ¹H Chemical Shifts in the Hydrogen Bonding Regions of Proteins

Abstract

A study is presented of the structural dependencies for scalar J-coupling and the amide donor (1)H chemical shifts in the hydrogen bonding regions of proteins. An analysis of the interactions between the donor hydrogen and acceptor oxygen orbitals in an N-H...O=C moiety suggests that there are three major structural factors for (15)N-(13)C coupling across hydrogen bonds: (1) the H...O' internuclear separation r(HO)('), (2) the H...O'=C' angle theta(2), and (3) indirect contributions involving the oxygen loan pair electrons should lead to a dependence on the H...O'=C'-N' dihedral angle rho. Density functional theory (DFT) and finite perturbation theory (FPT) were used to obtain the Fermi contact (FC) contributions to interresidue coupling in formamide dimers with systematic variation of these structural parameters. The computed (h3)J(NC)(') exhibit good correlations with cos(2) theta;(2) combined with an exponential dependence on r(HO)('). The correlation is further improved by including a dependence on the dihedral angle rho. For each of the 34 H-bonds having observable interresidue coupling in the immunoglobulin binding domain of streptococcal protein G, a formamide dimer was generated from the crystallographic structure with energy-optimized donor H-atom positions. The computed coupling constants are in reasonable agreement with the experimental, and there are excellent correlations with the simple equations involving theta;(2) and r(HO) if alpha-helix and beta-sheet regions are treated separately. This dichotomy is removed by introducing the dependence on the dihedral angle rho. Justification for the use of formamide dimers is provided by almost identical interresidue coupling constants for larger sequences extracted from the X-ray structure. The amide donor (1)H chemical shifts, which were based on DFT and GIAO (gauge including atomic orbital) methods, are in poorer agreement with the experimental data but exhibit excellent correlation with r(HO)('), theta(2), and rho.

Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings

“…HBCs represent time averages over a time-scale range similar to the one probed by RDCs (37). We have used an analytical description of h3 J NCЈ scalar coupling that was recently parameterized from density functional theory calculations (32) to predict couplings for each of 10,000 conformers derived from Monte Carlo sampling of the 3D GAF distributions of peptide planes containing the two hydrogenbonding partners (see Materials and Methods). Averages were taken over this ensemble for the 29 hydrogen bonds for which h3 J NCЈ scalar couplings have been measured previously (38) (excluding the most flexible loop region [14][15][16][17].…”

Review on DFT and ab initio Calculations of Scalar Coupling Constants

“…In cases were the proton is shared between A and B the distinction between 1 J AH and 1h J B···H disappears; finally, when the proton is completely transferred, the situation again becomes "classical", with The contribution of the Bartlett, Perera and Del Bene's group to this topic is so significant that we have decided to divide this section in three parts: a) Other groups [9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]; b) Bartlett-Perera-Del Bene [25][26][27][28][29][30][31][32][33][34][35][36]; c) Data analysis [37][38][39][40][41].…”

“…Barfield's contribution is important having published four papers between 1999 and 2002 [14][15][16][17][18].…”

The Effect of Substituents on Indirect Nuclear Spin-Spin Coupling Constants: Methan- and Ethanimine, Methanal- and Ethanaloxime

“…Often these molecules are too large for accurate calculations and many authors [2][3][4][5][6][7][8][9][10][11] make therefore use of model-systems which are supposed to include the relevant atoms, e.g. the atoms involved in peptide bonds.…”