Ab initio IGLO study of the .phi.- and .chi.-angle dependence of the carbon-13 chemical shifts in the model peptide N-acetyl-N'-methylglycinamide

The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations

Sequence dependence of (13) C and (15) N chemical shifts in the receiver domain of CKI1 protein from Arabidopsis thaliana, CKI1RD , and its complexed form, CKI1RD •Mg(2+), was studied by means of MD/DFT calculations. MD simulations of a 20-ns production run length were performed. Nine explicitly hydrated structures of increasing complexity were explored, up to a 40-amino-acid structure. The size of the model necessary depended on the type of nucleus, the type of amino acid and its sequence neighbors, other spatially close amino acids, and the orientation of amino acid NH groups and their surface/interior position. Using models covering a 10 and a 15 Å environment of Mg(2+), a semi-quantitative agreement has been obtained between experiment and theory for the V67-I73 sequence. The influence of Mg(2+) binding was described better by the 15 Å as compared to the 10 Å model. Thirteen chemical shifts were analyzed in terms of the effect of Mg(2+) insertion and geometry preparation. The effect of geometry was significant and opposite in sign to the effect of Mg(2+) binding. The strongest individual effects were found for (15) N of D70, S74, and V68, where the electrostatics dominated; for (13) Cβ of D69 and (15) N of K76, where the influences were equal, and for (13) Cα of F72 and (13) Cβ of K76, where the geometry adjustment dominated. A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed.

Multi-conformer molecules in solutions: an NMR-based DFT/MP2 conformational study of two glucopyranosides of a vitamin E model compound

Overall geometries of both glucosyl derivatives of PMC were found on the basis of their NMR spectra in CDCl₃and relatedδ_H,C/ⁿJ_HHIEF-PCM(UFF,CHCl₃)/DFT calculational results.

13C longitudinal relaxation time measurements and DFT-GIAO NMR computations for two ammonium ions of a tetraazamacrocyclic scorpiand system

Abstract

Spin–lattice relaxation times, T₁s, for ¹³C nuclei in two cations H_n1ⁿ⁺ (n = 1, 5) of N-(2-aminoethyl)-cyclam (1, scorpiand) were determined by means of ¹³C{¹H} NMR experiments in aqueous solution at pH 11.5 and 0.2. The theoretical study [modeling with OPLS-AA, B3LYP/6-31G(d) geometry optimizations, dispersion-corrected energies (DFT-D3), and DFT-GIAO predictions of the NMR chemical shifts (including an IEF-PCM simulation of hydration)] was also done for several conformers of the tautomer iso-H₄1⁴⁺ not investigated before. The binding directions in protonated polyamino receptors necessary for efficient complexation of the nitrate anion(s) were briefly outlined, as well. All these results were discussed in terms of ‘abnormal’ ¹³C chemical shift changes found previously for the side-chain carbons of amine 1 in strongly acidic solution (HNO₃). In conclusion, an earlier proposal of its association with NO₃⁻ at pH <1 was rejected. Instead, the participation of small amounts of a micro-species iso-H₄1⁴⁺D_hydr under such conditions can be proposed.

Graphical Abstract

A small contribution of iso-H₄1⁴⁺D_hydr (see figure) to an ionic mixture of pentamine 1 was proposed to explain the ‘abnormal’ ¹³C NMR shifts observed for atoms C11 and C12 in its side-chain arm, at pH <1.

Electronic supplementary material

The online version of this article (doi:10.1007/s10847-013-0298-x) contains supplementary material, which is available to authorized users.

The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment

Biomolecular NMR spectroscopy frequently employs estimates of protein secondary structure using secondary chemical shift (Deltadelta) values, measured as the difference between experimental and random coil chemical shifts (RCCS). Most published random coil data have been determined in aqueous conditions, reasonable for non-membrane proteins, but potentially less relevant for membrane proteins. Two new RCCS sets are presented here, determined in dimethyl sulfoxide (DMSO) and chloroform:methanol:water (4:4:1 by volume) at 298 K. A web-based program, CS-CHEMeleon, has been implemented to determine the accuracy of secondary structure assessment by calculating and comparing Deltadelta values for various RCCS datasets. Using CS-CHEMeleon, Deltadelta predicted versus experimentally determined secondary structures were compared for large datasets of membrane and non-membrane proteins as a function of RCCS dataset, Deltadelta threshold, nucleus, localized parameter averaging and secondary structure type. Optimized Deltadelta thresholds are presented both for published and for the DMSO and chloroform:methanol:water derived RCCS tables. Despite obvious RCCS variations between datasets, prediction of secondary structure was consistently similar. Strikingly, predictive accuracy seems to be most dependent upon the type of secondary structure, with helices being the most accurately predicted by Deltadelta values using five different RCCS tables. We suggest caution when using Deltadelta-based restraints in structure calculations as the underlying dataset may be biased. Comparative assessment of multiple RCCS datasets should be performed, and resulting Deltadelta-based restraints weighted appropriately relative to other experimental restraints.

Dependence of amino acid side chain 13C shifts on dihedral angle: application to conformational analysis

Chemical shift data from the BiomagResDataBank and conformational data derived from the protein data bank have been correlated in order to explore the conformational dependence of side chain (13)C resonance shifts. Consistent with predictions based on steric compression, upfield shifts for Cgamma resonances of Thr, Val, Ile, Leu, Met, Arg, Lys, Glu, and Gln residues correlate with both the number of heavy atom (nonproton) gamma-substituents and with gauche conformational orientations of gamma-substituents. The (13)C shift/conformation correlations are most apparent for Cgamma carbons but also can be observed at positions further from the backbone. Intraresidue steric conflict leads to a correlation between upfield-shifted side chain (13)C resonances and statistically lower probabilities in surveys of protein side chain conformation. Illustrative applications to the DNA pol lambda lyase domain and to dihydrofolate reductase are discussed. In the latter case, (13)C shift analysis indicates that the conformation of the remote residue V119 on the betaF-betaG loop is correlated with the redox state of the bound pyridine nucleotide cofactor, providing one basis for discrimination between substrate and product. It is anticipated that (13)C shift data for protein sidechains can provide a useful basis for the analysis of conformational changes even in large, deuterated proteins. Additionally, the large dependence of the leucine methyl shift difference, deltaCdelta1-deltaCdelta2, on both chi1 and chi2 is sufficient to allow this parameter to be used as a restraint in structure calculations if stereospecific assignment data are available.

Secondary Structures of Peptides and Proteins via NMR Chemical-Shielding Anisotropy (CSA) Parameters

Complete nuclear magnetic resonance (NMR) chemical-shielding tensors, sigma, have been computed at different levels of density-functional theory (DFT), within the gauge-including atomic orbital (GIAO) formalism, for the atoms of the peptide model For-L-Ala-NH2 as a function of the backbone dihedral angles phi and psi by employing a dense grid of 10 degrees. A complete set of rigorously orthogonal symmetric tensor invariants, {sigma iso, rho, tau}, is introduced, where sigma iso is the usual isotropic chemical shielding, while the newly introduced rho and tau parameters describe the magnitude and the orientation/shape of the chemical-shielding anisotropy (CSA), respectively. The set {sigma iso, rho, tau} is unaffected by unitary transformations of the symmetric part of the shielding tensor. The mathematically and physically motivated {rho, tau} anisotropy pair is easily connected to more traditional shielding anisotropy measures, like span (Omega) and skew (kappa). The effectiveness of the different partitions of the CSA information in predicting conformations of peptides and proteins has been tested throughout the Ramachandran space by generating theoretical NMR anisotropy surfaces for our For-L-Ala-NH2 model. The CSA surfaces, including Omega(phi, psi), kappa(phi, psi), rho(phi, psi), and tau(phi, psi) are highly structured. Individually, none of these surfaces is able to distinguish unequivocally between the alpha-helix and beta-strand secondary structural types of proteins. However, two- and three-dimensional correlated plots, including Omega versus kappa, rho versus tau, and sigma iso versus rho versus tau, especially for 13Calpha, have considerable promise in distinguishing among all four of the major secondary structural elements.

Toward direct determination of conformations of protein building units from multidimensional NMR experiments VI. Chemical shift analysis of his to gain 3D structure and protonation state information

NMR--chemical shift structure correlations were investigated by using GIAO-RB3LYP/6-311++G(2d,2p) formalism. Geometries and chemical shifts (CSI values) of 103 different conformers of N'-formyl-L-histidinamide were determined including both neutral and charged protonation forms. Correlations between amino acid torsional angle values and chemical shifts were investigated for the first time for an aromatic and polar amino acid residue whose side chain may carry different charges. Linear correlation coefficients of a significant level were determined between chemical shifts and dihedral angles for CSI[(1)H(alpha)]/phi, CSI[(13)C(alpha)]/phi, and CSI[(13)C(alpha)]/psi. Protonation of the imidazole ring induces the upfield shift of CSI[(13)C(alpha)] for positively charged histidines and an opposite effect for the negative residue. We investigated the correspondence of theoretical and experimental (13)C(alpha), (13)C(beta), and (1)H(alpha) chemical shifts and the nine basic conformational building units characteristic for proteins. These three chemical shift values allow the identification of conformational building units at 80% accuracy. These results enable the prediction of additional regular secondary structural elements (e.g., polyProlineII, inverse gamma-turns) and loops beyond the assignment of chemical shifts to alpha-helices and beta-pleated sheets. Moreover, the location of the His residue can be further specified in a beta-sheet. It is possible to determine whether the appropriate residue is located at the middle or in a first/last beta-strand within a beta-sheet based on calculated CSI values. Thus, the attractive idea of establishing local residue specific backbone folding parameters in peptides and proteins by employing chemical shift information (e.g., (1)H(alpha) and (13)C(alpha)) obtained from selected heteronuclear correlation NMR experiments (e.g., 2D-HSQC) is reinforced.

Fast and accurate computation of the 13C chemical shifts for an alanine-rich peptide

The purpose of this work is, first, to present a fast and accurate technique to compute Boltzmann-averaged values of the quantum-chemical 13C chemical shifts for each amino acid in oligopeptides, demonstrated here by an application to the peptide Ac-XXAAAAAAAOO-NH2 (where X denotes diaminobutyric acid, A is alanine, and O is ornithine) [XAO] and, second, to discuss the capability of the 13Calpha and 13Cbeta chemical shifts to distinguish the PP(II) conformation from the alpha-helix and statistical-coil conformations. Use is made of a combination of approaches, summarized as follows: (1) derivation of an ensemble of conformations by using a molecular mechanics technique; (2) use of a clustering procedure to form families and build a reduced set of conformations consisting of the lowest-energy conformations of each family, and (3) computation of the 13C chemical shifts for the lowest-energy conformations of each family, using a quantum-chemical approach that treats a selected residue, or group of residues, with a 6-311+G(2d,p) locally-dense basis set, while the remaining residues in the sequence are treated with a 3-21G basis set. The whole procedure is quite accurate and speeds up the computation of the Boltzmann-averaged values of the 13C-chemical shifts by several orders of magnitude. The present application sheds some light on the conformational preference for alanine and non-alanine residues to occupy the PP(II) helical region of the Ramachandran map.

Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide, a model for polar side-chain containing peptides

Knowledge of chemical shift-structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For-L-Ser-NH(2), was studied. Using the GIAO-RHF/6-31+G(d) and GIAO-RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen ((1)H(N), (1)H(alpha), (1)H(beta1), (1)H(beta2)), carbon ((13)C(alpha), (13)C(beta), (13)C') and nitrogen ((15)N) atoms have been computed for all 44 stable conformers of For-L-Ser-NH(2). An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (omega(0), phi, psi, omega(1), chi,(1) and chi(2)). At both levels of theory a linear correlation can be observed between (1)H(alpha)/phi, (13)C(alpha)/phi, and (13)C(alpha)/psi. These results indicate that the backbone and side-chain structures of For-L-Ser-NH(2) have a strong influence on its chemical shifts.

Biomolecular solid state NMR: advances in structural methodology and applications to peptide and protein fibrils

Solid state nuclear magnetic resonance (NMR) methods can provide atomic-level structural constraints on peptides and proteins in forms that are not amenable to characterization by other high-resolution structural techniques, owing to insolubility, high molecular weight, noncrystallinity, or other characteristics. Important examples include peptide and protein fibrils and membrane-bound peptides and proteins. Recent advances in solid state NMR methodology aimed at structural problems in biological systems are reviewed. The power of these methods is illustrated by experimental results on amyloid fibrils and other protein fibrils.

Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA

The basic leucine zipper domain of the yeast transcription factor GCN4 consists of a C-terminal leucine zipper and an N-terminal basic DNA-binding region that achieves a stable structure only after association with DNA. Backbone dynamics of a peptide encompassing the basic and leucine zipper bZip domain (residues 226-281) are described using NMR spectroscopy. The 15N longitudinal relaxation rates, 15N transverse relaxation rates, and {1H}-15N nuclear Overhauser effects were measured for the backbone amide nitrogen atoms at 290 K, 300 K, and 310 K. The relaxation data were interpreted using reduced spectral density mapping to determine values of the spectral density function, J(omega), at the frequencies 0, omegaN, and 0.87omegaH to characterize overall and intramolecular motions on picosecond-nanosecond timescales. To account for the temperature dependence of overall rotational diffusion, the J(0) values were normalized using Stoke's Law. At 310 K, the 13Calpha and 13CO chemical shifts in conjunction with the spectral density values indicate that the leucine zipper sequence forms a highly ordered alpha-helix, while the basic region populates an ensemble of highly dynamic transient structures with substantial helical character. The normalized values of J(0) and the values of J(0.87omegaH) for residues in the leucine zipper dimerization domain are independent of temperature. In contrast, residues in the basic region exhibit pronounced increases in the normalized J(0) and decreases in J(0.87omegaH) as temperature is decreased. A strong correlation exists between the temperature dependence of 13CO chemical shifts and of J(0.87omegaH). These results suggest that, for the basic region, lowering the temperature increases the population of transient helical conformations, and concomitantly reduces the amplitude or timescale of conformational fluctuations on picosecond-nanosecond timescales. Changes in the conformational dynamics of the peptide backbone of the basic region that accompany DNA binding contribute to the overall thermodynamics of complex formation. The change in backbone conformational entropy derived from NMR spin-relaxation data agrees well with the result calculated from calorimetric measurements. Restriction of the conformational space accessible to the basic region may significantly reduce the entropic cost associated with formation of the basic region helices consequent to DNA binding.

Prospects for resonance assignments in multidimensional solid-state NMR spectra of uniformly labeled proteins

The feasibility of assigning the backbone 15N and 13C NMR chemical shifts in multidimensional magic angle spinning NMR spectra of uniformly isotopically labeled proteins and peptides in unoriented solid samples is assessed by means of numerical simulations. The goal of these simulations is to examine how the upper limit on the size of a peptide for which unique assignments can be made depends on the spectral resolution, i.e., the NMR line widths. Sets of simulated three-dimensional chemical shift correlation spectra for artificial peptides of varying length are constructed from published liquid-state NMR chemical shift data for ubiquitin, a well-characterized soluble protein. Resonance assignments consistent with these spectra to within the assumed spectral resolution are found by a numerical search algorithm. The dependence of the number of consistent assignments on the assumed spectral resolution and on the length of the peptide is reported. If only three-dimensional chemical shift correlation data for backbone 15N and 13C nuclei are used, no residue-specific chemical shift information, information from amino acid side-chain signals, and proton chemical shift information are available, a spectral resolution of 1 ppm or less is generally required for a unique assignment of backbone chemical shifts for a peptide of 30 amino acid residues.

Recent progress in understanding chemical shifts

In the past three or four years computer hardware and software developments have reached the stage where the nuclear magnetic resonance (NMR) spectra of many molecular systems can now be accurately evaluated. Detailed analysis of chemical shifts may soon become a routine part of solid (and liquid) state NMR structure prediction in chemistry and biology, and this Article covers the development of the topic from its earliest beginnings.