On the origin of residual dipolar couplings from denatured proteins

Effects of steric obstruction on random flight chains are examined. Spatial probability distributions are elaborated to calculate residual dipolar couplings and residual chemical shift anisotropy, parameters that are acquired by NMR spectroscopy from solutes dissolved in dilute liquid crystals. Calculations yield chain length and residue position-dependent values in good agreement with simulations to provide understanding of recently acquired data from denatured proteins.     

On the interpretation of residual dipolar couplings as reporters of molecular dynamics

The analysis of residual dipolar couplings from an ensemble of conformations to extract molecular dynamics is intricate. The very mechanism that is necessary to perturb overall molecular tumbling to generate nonvanishing residual dipolar couplings gives rise to convoluted data. The measured values are essentially weighted averages over conformations. However, the weights are not simply the populations of conformations. Consequently, the observed order parameter is not exactly the true measure of motion. In the case of paramagnetic alignment, the apparent order parameter is expected to depend on the number of torsions that separate the locus of interest from the paramagnetic site. In the case of alignment due to steric obstruction, the uneven selection of conformations by their differing Saupe order matrices leads to a bias in the residual dipolar couplings-probed molecular dynamics.     

Nuclear magnetic shielding and quadrupole coupling tensors in liquid water: a combined molecular dynamics simulation and quantum chemical study

Nuclear magnetic resonance (NMR) shielding tensors for the oxygen and hydrogen nuclei, as well as nuclear quadrupole coupling tensors for the oxygen and deuterium nuclei of water in the liquid and gaseous state, are calculated using Hartree-Fock and density functional theory methods, for snapshots sampled from Car-Parrinello molecular dynamics trajectories. Clusters representing local liquid structures and instantaneous configurations of a single molecule representing low-density gas are fed into a quantum chemical program for the calculation of the NMR tensors. The average isotropic and anisotropic tensorial properties of 400 samples in both states, averaged using a common Eckart coordinate frame, are calculated from the data. We report results for the gas-to-liquid chemical shifts of (17)O and (1)H nuclei, as well as the corresponding change in the nuclear quadrupole couplings of (17)O and (2)H. Full thermally averaged shielding and quadrupole coupling tensors are reported for the gaseous and liquid-state water, for the first time in the case of liquid. Electron correlation effects, the difference of classical vs quantum mechanical rovibrational averaging, and different methods of averaging anisotropic properties are discussed.     

Two Simple NMR Experiments for Measuring Dipolar Couplings in Asparagine and Glutamine Side Chains

Residual dipolar couplings are now widely used for structure determination of biological macromolecules. Until recently, the main focus has been on measurement of dipolar couplings in the protein main chain. However, with the aim of more complete protein structure, it is also essential to have information on the orientation of protein side chains. In addition, residual dipolar couplings can potentially be employed to study molecular dynamics. In this Communication, two simple NH(2) and spin-state edited experiments are presented for rapid and convenient determination of five residual dipolar couplings from (15)N, (1)H correlation spectrum in asparagine and glutamine side chains. The pulse sequences are demonstrated on two proteins, 30.4-kDa Cel6A in diluted liquid crystal phase and 18-kDa human cardiac troponin C in water.     

Determination of three-bond scalar coupling between 13C' and 1H(alpha) in proteins using an iHN(CA),CO(alpha/beta-J-COHA) experiment

Triple-resonance NMR experiments for measuring three-bond scalar coupling constant between 13C' (i-1) and 1H(alpha)(i) spins, defining the dihedral angle phi, are presented. The novel experiments enable the measurement of 3JC'H(alpha)) from simple two (or three)-dimensional 13C', (15N/13C(alpha)), 1H(N) correlation spectra with minimal resonance overlap, thanks to solely intraresidual coherence transfer pathway and spin-state-selection. The 3J(C'H(alpha)) values measured in human ubiquitin using the proposed intraresidual iHN(CA),CO(alpha/beta-J-COHA) TROSY method were compared with those determined previously utilizing the HCAN[C'] experiment.     

J-multiplied HSQC (MJ-HSQC): a new method for measuring 3J(HNHalpha) couplings in 15N-labeled proteins

A new method for the measurement of homonuclear 3J(HNHalpha) coupling constants in 15N-labeled small proteins is described. The method is based on a modified sensitivity enhanced HSQC experiment, where the 3J(HNHalpha) couplings are multiplied in the f1-dimension. The J-multiplication of homonuclear 3J(HNHalpha) couplings is based on simultaneous incrementation of 15N chemical shift and homonuclear coupling evolution periods. The time increment for the homonuclear coupling evolution period is chosen to be a suitable multiple (2N x t1) of the corresponding increment for 15N-shift evolution. This results in the splitting of the HSQC correlation in the f1-dimension by 2N x 3J(HNHalpha). Because the pulse sequence has good sensitivity and water suppression properties, it is particularly useful for natural abundance samples.     

Theoretical predictions of nuclear magnetic resonance parameters in a novel organo-xenon species: chemical shifts and nuclear quadrupole couplings in HXeCCH

We calibrate the methodology for the calculation of nuclear magnetic resonance (NMR) properties in novel organo-xenon compounds. The available state-of-the-art quantum-chemical approaches are combined and applied to the HXeCCH molecule as the model system. The studied properties are (129)Xe, (1)H, and (13)C chemical shifts and shielding anisotropies, as well as (131)Xe and (2)H nuclear quadrupole coupling constants. The aim is to obtain, as accurately as currently possible, converged results with respect to the basis set, electron correlation, and relativistic effects, including the coupling of relativity and correlation. This is done, on one hand, by nonrelativistic correlated ab initio calculations up to the CCSD(T) level and, on the other hand, for chemical shifts and shielding anisotropies by the leading-order relativistic Breit-Pauli perturbation theory (BPPT) with correlated ab initio and density-functional theory (DFT) reference states. BPPT at the uncorrelated Hartree-Fock level as well as the corresponding fully relativistic Dirac-Hartree-Fock method are found to be inapplicable due to a dramatic overestimation of relativistic effects, implying the influence of triplet instability in this multiply bonded system. In contrast, the fully relativistic second-order Moller-Plesset perturbation theory method can be applied for the quadrupole coupling, which is a ground-state electric property. The performance of DFT with various exchange-correlation functionals is found to be inadequate for the nonrelativistic shifts and shielding anisotropies as compared to the CCSD(T) results. The relativistic BPPT corrections to these quantities can, however, be reasonably predicted by DFT, due to the improved triplet excitation spectrum as compared to the Hartree-Fock method, as well as error cancellation within the five main BPPT contributions. We establish three computationally feasible models with characteristic error margins for future calculations of larger organo-xenon compounds to guide forthcoming experimental NMR efforts. The predicted (129)Xe chemical shift in HXeCCH is in a novel range for this nucleus, between weakly bonded or solvated atomic xenon and xenon in the hitherto characterized molecules.