Determination of Dihedral Angles in Peptides through Experimental and Theoretical Studies of α-Carbon Chemical Shielding Tensors

Analyzing atomic scale structural details and nuclear spin dynamics of four macrolide antibiotics: erythromycin, clarithromycin, azithromycin, and roxithromycin

The current investigation centers on elucidating the intricate molecular architecture and dynamic behavior of four macrolide antibiotics, specifically erythromycin, clarithromycin, azithromycin, and roxithromycin, through the application of sophisticated solid-state nuclear magnetic resonance (SSNMR) methodologies. We have measured the principal components of chemical shift anisotropy (CSA) parameters, and the site-specific spin-lattice relaxation time at carbon nuclei sites. To extract the principal components of CSA parameters, we have employed 13C 2DPASS CP-MAS SSNMR experiments at two different values of magic angle spinning (MAS) frequencies, namely 2 kHz and 600 Hz. Additionally, the spatial correlation between 13C and 1H nuclei has been investigated using 1H-13C frequency switched Lee-Goldburg heteronuclear correlation (FSLGHETCOR) experiment at a MAS frequency of 24 kHz. Our findings demonstrate that the incorporation of diverse functional groups, such as the ketone group and oxime group with the lactone ring, exerts notable influences on the structure and dynamics of the macrolide antibiotic. In particular, we have observed a significant decrease in the spin-lattice relaxation time of carbon nuclei residing on the lactone ring, desosamine, and cladinose in roxithromycin, compared to erythromycin. Overall, our findings provide detailed insight into the relationship between the structure and dynamics of macrolide antibiotics, which is eventually correlated with their biological activity. This knowledge can be utilized to develop new and more effective drugs by providing a rational basis for drug discovery and design.

Determination of the chemical shift tensor anisotropy and asymmetry of strongly dipolar coupled protons under fast MAS

Orientationally-dependent interactions such as dipolar coupling, quadrupolar coupling, and chemical shift anisotropy (CSA) contain a wealth of spatial information that can be used to elucidate molecular conformations and dynamics. To determine the sign of the chemical shift tensor anisotropy parameter (δ_aniso), both the |m| ​= ​1 and |m| ​= ​2 components of the CSA need to be symmetry allowed, while the recoupling of the |m| ​= ​1 term is accompanied with the reintroduction of homonuclear dipolar coupling components. Therefore, previously suggested sequences which solely recouple the |m| ​= ​2 term cannot determine the sign a ¹H's δ_aniso in a densely-coupled network. In this study, we demonstrate the CSA recoupling of strongly dipolar coupled ¹H spins using the Cn_n¹(90₀360₁₈₀540₀360₁₈₀90₀) sequence. This pulse scheme recouples both the |m| ​= ​1 and |m| ​= ​2 CSA terms but the scaling factors for the homonuclear dipolar coupling terms are zeroed. Consequently, the sequence is sensitive to the sign of δ_aniso but is not influenced by homonuclear dipolar interactions.

Investigation of the internal structure and dynamics of cellulose by 13C-NMR relaxometry and 2DPASS-MAS-NMR measurements

Internal structure and dynamics of commercial and natural cellulose were studied by measuring chemical shift anisotropy (CSA) parameters, and spin-lattice relaxation rate (1/T₁) at each and every chemically different carbon nuclear site. CSA parameters were measured by ¹³C two-dimensional phase adjusted spinning sideband (2DPASS) cross-polarization magic angle spinning (CP-MAS) NMR experiment. Site specific spin-lattice relaxation time was measured by Torchia-CP method. Anisotropy parameters of C4 and C6 regions are higher than C1 and C235 regions and asymmetry of C4 line is lower than any other carbon site. The higher values of CSA parameters of C4 and C6 nuclei arise due to the rotation of O4-C4, C1-O4, O5-C5-C6-O6 and C4-C5-C6-O6 bonds at torsion angles ψ, Φ, χ and χ' respectively and the influence of interchain and intrachain hydrogen bondings. Two distinct peaks are also observed for C4 and C6 resonance line position-one peak arises primarily due to the nuclei in amorphous region and another one arises due to the same nuclei resides in paracrystalline region. The spin-lattice relaxation time and the CSA parameters are different at these two distinct peak positions of C4 and C6 line. Molecular correlation time of each and every chemically different carbon site was calculated with the help of CSA parameters and spin-lattice relaxation time. The molecular correlation time of the amorphous region is one order of magnitude less than the crystalline region. The distinction between amorphous and paracrystalline regions of cellulose is more vividly portrayed by determining spin-lattice relaxation time, CSA parameters, and molecular correlation time at each and every chemically different carbon site. This type of study correlating the structure and dynamics of cellulose will illuminate the path of inventing biomimetic materials.

Predicting anisotropic thermal displacements for hydrogens from solid-state NMR: a study on hydrogen bonding in polymorphs of palmitic acid

The hydrogen-bonding environments at the COOH moiety in eight polycrystalline polymorphs of palmitic acid are explored using solid-state NMR. Although most phases have no previously reported crystal structure, measured 13C chemical shift tensors for COOH moieties, combined with DFT modeling establish that all phases crystallize with a cyclic dimer (R22(8)) hydrogen bonding arrangement. Phases A2, Bm and Em have localized OH hydrogens while phase C has a dynamically disordered OH hydrogen. The phase designated As is a mix of five forms, including 27.4% of Bm and four novel phases not fully characterized here due to insufficient sample mass. For phases A2, Bm, Em, and C the anisotropic uncertainties in the COOH hydrogen atom positions are established using a Monte Carlo sampling scheme. Sampled points are retained or rejected at the ±1σ level based upon agreement of DFT computed 13COOH tensors with experimental values. The collection of retained hydrogen positions bear a remarkable resemblance to the anisotropic displacement parameters (i.e. thermal ellipsoids) from diffraction studies. We posit that this similarity is no mere coincidence and that the two are fundamentally related. The volumes of NMR-derived anisotropic displacement ellipsoids for phases with localized OH hydrogens are 4.1 times smaller than those derived from single crystal X-ray diffraction and 1.8 times smaller than the volume of benchmark single crystal neutron diffraction values.

Measuring (13)C/(15)N chemical shift anisotropy in [(13)C,(15)N] uniformly enriched proteins using CSA amplification

Extended chemical shift anisotropy amplification (xCSA) is applied for measuring (13)C/(15)N chemical shift anisotropy (CSA) of uniformly labeled proteins under magic-angle spinning (MAS). The amplification sequence consists of a sequence of π-pulses that repetitively interrupt MAS averaging of the CSA interaction. The timing of the pulses is designed to generate amplified spinning sideband manifolds which can be fitted to extract CSA parameters. The (13)C/(13)C homonuclear dipolar interactions are not affected by the π-pulses due to the bilinear nature of the spin operators and are averaged by MAS in the xCSA experiment. These features make the constant evolution-time experiment suitable for measuring CSA of uniformly labeled samples. The incorporation of xCSA with multi-dimensional (13)C/(15)N correlation is demonstrated with a GB1 protein sample as a model system for measuring (13)C/(15)N CSA of all backbone (15)NH, (13)CA and (13)CO sites.

Effects of structural differences on the NMR chemical shifts in isostructural dipeptides

Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

NMR, IR, Mössbauer and quantum chemical investigations of metalloporphyrins and metalloproteins

We review contributions made towards the elucidation of CO and O2binding geometries in respiratory proteins. Nuclear magnetic resonance, infrared spectroscopy, Mössbauer spectroscopy, X-ray crystallography and quantum chemistry have all been used to investigate the Fe –ligand interactions. Early experimental results showed linear correlations between17O chemical shifts and the infrared stretching frequency (νCO) of the CO ligand in carbonmonoxyheme proteins and between the17O chemical shift and the13CO shift. These correlations led to early theoretical investigations of the vibrational frequency of carbon monoxide and of the13C and17O NMR chemical shifts in the presence of uniform and non-uniform electric fields. Early success in modeling these spectroscopic observables then led to the use of computational methods, in conjunction with experiment, to evaluate ligand-binding geometries in heme proteins. Density functional theory results are described which predict57Fe chemical shifts and Mössbauer electric field gradient tensors,17O NMR isotropic chemical shifts, chemical shift tensors and nuclear quadrupole coupling constants (e2qQ/h) as well as13C isotropic chemical shifts and chemical shift tensors in organometallic clusters, heme model metalloporphyrins and in metalloproteins. A principal result is that CO in most heme proteins has an essentially linear and untilted geometry (τ = 4 °, β = 7 °) which is in extremely good agreement with a recently published X-ray synchrotron structure. CO / O2discrimination is thus attributable to polar interactions with the distal histidine residue, rather than major Fe–C–O geometric distortions.

Calculation of chemical shift anisotropy in proteins

Individual peptide groups in proteins must exhibit some variation in the chemical shift anisotropy (CSA) of their constituent atoms, but not much is known about the extent or origins of this dispersion. Direct spectroscopic measurement of CSA remains technically challenging, and theoretical methods can help to overcome these limitations by estimating shielding tensors for arbitrary structures. Here we use an automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach to compute (15)N, (13)C' and (1)H chemical shift tensors for human ubiquitin and the GB1 and GB3 fragments of staphylococcal protein G. The average and range of variation of the anisotropies is in good agreement with experimental estimates from solid-state NMR, and the variation among residues is somewhat smaller than that estimated from solution-state measurements. Hydrogen-bond effects account for much of the variation, both between helix and sheet regions, and within elements of secondary structure, but other effects (including variations in torsion angles) may play a role as well.

Protein structure refinement using 13C alpha chemical shift tensors

We have obtained the (13)C alpha chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints and were also more accurate. When combined with isotropic chemical shifts, distance, and vector angle restraints, the root-mean squared error with respect to existing X-ray structures was better than approximately 1.0 A. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination.

Multidimensional solid state NMR of anisotropic interactions in peptides and proteins

Accurate determinations of chemical shift anisotropy (CSA) tensors are valuable for NMR of biological systems. In this review we describe recent developments in CSA measurement techniques and applications, particularly in the context of peptides and proteins. These techniques include goniometeric measurements of single crystals, slow magic-angle spinning studies of powder samples, and CSA recoupling under moderate to fast MAS. Experimental CSA data can be analyzed by comparison with ab initio calculations for structure determination and refinement. This approach has particularly high potential for aliphatic (13)C analysis, especially Calpha tensors which are directly related to structure. Carbonyl and (15)N CSA tensors demonstrate a more complex dependence upon hydrogen bonding and electrostatics, in addition to conformational dependence. The improved understanding of these tensors and the ability to measure them quantitatively provide additional opportunities for structure determination, as well as insights into dynamics.

Theoretical 13C chemical shift, 14N, and 2H quadrupole coupling- constant studies of hydrogen bonding in L-alanylglycine dipeptide

(13)C chemical shieldings and (14)N and (2)H electric field gradient (EFG) tensors of L-alanylglycine (L-alagly) dipeptide were calculated at RHF/6-31 + + G** and B3LYP/6-31 + + G** levels of theory respectively. For these calculations a crystal structure of this dipeptide obtained from X-ray crystallography was used. Atomic coordinates of different clusters containing several L-alagly molecules were used as input files for calculations. These clusters consist of central and surrounding L-alagly molecules, the latter forming short, strong, hydrogen bonds with the central molecule. Since the calculations did not converge for these clusters, the surrounding L-alagly molecules were replaced by glycine molecules. In order to improve the accuracy of calculated chemical shifts and nuclear quadrupole coupling constants (NQCCs), different geometry-optimization strategies were applied for hydrogen nuclei. Agreement between calculated and experimental data confirms that our optimized coordinates for hydrogen nuclei are more accurate than those obtained by X-ray diffraction.

Structural characterization of an anhydrous polymorph of paclitaxel by solid-state NMR

The three-dimensional structure of a unique polymorph of the anticancer drug paclitaxel (Taxol) is established using solid state NMR (SSNMR) tensor ((13)C & (15)N) and heteronuclear correlation ((1)H-(13)C) data. The polymorph has two molecules per asymmetric unit (Z' = 2) and is thus the first conformational characterization with Z' > 1 established solely by SSNMR. Experimental data are correlated with structure through a series of computational models that extensively sample all conformations. For each computational model, corresponding tensor values are computed to supply comparisons with experimental information which, in turn, establishes paclitaxel's structure. Heteronuclear correlation data at thirteen key positions provide shift assignments to the asymmetric unit for each comparison. The two distinct molecules of the asymmetric unit possess nearly identical baccatin III moieties with matching conformations of the C10 acetyl moiety and, specifically, the torsion angle formed by C30-O-C10-C9. Additionally, both are found to exhibit an extended conformation of the phenylisoserine sidechain at C13 with notable differences in the dihedral angles centered around the rotation axes of O-C13, C2'-C1' and C3'-C2'.

A Concerted Approach for the Determination of Molecular Conformation in Ordered and Disordered Materials

We present the successful application of a concerted approach for the investigation of the local environment in ordered and disordered phases in the solid state. In this approach we combined isotope labeling with computational methods and different solid-state NMR techniques. We chose triphenylphosphite (TPP) as an interesting example of our investigations because TPP exhibits two crystalline modifications and two different amorphous phases one of which is highly correlated. In particular we analyzed the conformational distribution in three of these phases. A sample of triply labeled 1-[13C]TPP was prepared and 1D MAS as well as wide-line 13C NMR spectra were measured. Furthermore we acquired 2D 13C wide-line exchange spectra and used this method to derive highly detailed information about the phenyl orientation in the investigated TPP phases. For linkage with a structure model a DFT analysis of the TPP molecule and its immediate environment was carried out. The ab initio calculations of the 13C chemical shift tensor in three- and six-spin systems served as a base for the calculation of 1D and 2D spectra. By comparing these simulations to the experiment an explicit picture of all phases could be drawn on a molecular level. Our results therefore reveal the high potential of the presented approach for detailed studies of the mesoscopic environment even in the challenging case of amorphous materials.

A comparison of quantum chemical models for calculating NMR shielding parameters in peptides: mixed basis set and ONIOM methods combined with a complete basis set extrapolation

This article compares several quantum mechanical approaches to the computation of chemical shielding tensors in peptide fragments. First, we describe the effects of basis set quality up to the complete basis set (CBS) limit and level of theory (HF, MP2, and DFT) for four different atoms in trans N-methylacetamide. For both isotropic shielding and shielding anisotropy, the MP2 results in the CBS limit show the best agreement with experiment. The HF values show quite a different tendency to MP2, and even in the CBS limit they are far from experiment for not only the isotropic shielding of carbonyl carbon but also most shielding anisotropies. In most cases, the DFT values differ systematically from MP2, and small basis-set (double- or triple-zeta) results are often fortuitously in better agreement with the experiment than the CBS ones. Second, we compare the mixed basis set and ONIOM methods, combined with CBS extrapolation, for chemical shielding calculations at a DFT level using various model peptides. From the results, it is shown that the mixed basis set method provides better results than ONIOM, compared to CBS calculations using the nonpartitioned full systems. The information studied here will be useful in guiding the selection of proper quantum chemical models, which are in a tradeoff between accuracy and cost, for shielding studies of peptides and proteins.

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.

Order parameters based on (13)C(1)H, (13)C(1)H(2) and (13)C(1)H(3) heteronuclear dipolar powder patterns: a comparison of MAS-based solid-state NMR sequences

Order parameters describing conformational exchange processes on the nanosecond to microsecond timescale can be obtained from powder patterns in solid-state NMR (SSNMR) experiments. Extensions of these experiments to magic-angle spinning (MAS) based high-resolution experiments have been demonstrated, which show a great promise for site-specific probes of biopolymers. In this study, we present a detailed comparison of two pulse sequences, transverse Manfield-Rhim-Elleman-Vaughn (T-MREV) and Lee-Goldburg cross-polarization (LGCP), using experimental and simulation tools to explore their utility in the study of order parameters. We discuss systematic errors due to passively coupled (13)C or (1)H nuclei, as well as due to B(1) inhomogeneity. Both pulse sequences can provide quantitative measurements of the order parameter, but the LGCP experiment is capable of greater accuracy provided that the B(1) field is highly homogeneous. The T-MREV experiment is far better compensated for B(1) inhomogeneity, and it also performs better in situations with limited signal.

A DOQSY approach for the elucidation of torsion angle distributions in biopolymers: application to silk

Silk from the wild silkworm Samia cynthia ricini with a molecular mass of about 300kDa consists of alternating repeats of nano-crystalline poly-(Ala) and non-crystalline glycine-rich domains. The backbone torsion angles between pairs of these two amino acids is determined by DOQSY solid-state NMR spectroscopy: the alanine-rich domains are predominantly in a beta-sheet conformation, whereas the glycine-rich domains are found to be partially in an extended beta-sheet conformation and partially in an approximately 3(1)-helical conformation. In the cast film from liquid silk significantly different secondary structures were found: the alanine-rich domains are alpha-helical conformation, whereas the results for glycine-labelled sample are explained by a random-coil state. A detailed error analysis of the technique is presented.

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.

Quantum chemical studies of protein structure

Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions.

Investigation of Ligand-Receptor Systems by High-Resolution Solid-State NMR: Recent Progress and Perspectives

Solid-state Nuclear Magnetic Resonance (NMR) provides a general method to study molecular structure and dynamics in a non-crystalline and insoluble environment. We discuss the latest methodological progress to construct 3D molecular structures from solid-state NMR data obtained under magic-angle-spinning conditions. As shown for the neurotensin/NTS-1 system, these methods can be readily applied to the investigation of ligand-binding to G-protein coupled receptors.

The conformation of neurotensin bound to its G protein-coupled receptor

G protein-coupled receptors (GPCRs) mediate the perception of smell, light, taste, and pain. They are involved in signal recognition and cell communication and are some of the most important targets for drug development. Because currently no direct structural information on high-affinity ligands bound to GPCRs is available, rational drug design is limited to computational prediction combined with mutagenesis experiments. Here, we present the conformation of a high-affinity peptide agonist (neurotensin, NT) bound to its GPCR NTS-1, determined by direct structural methods. Functional receptors were expressed in Escherichia coli, purified in milligram amounts by using optimized procedures, and subsequently reconstituted into lipid vesicles. Solid-state NMR experiments were tailored to allow for the unequivocal detection of microgram quantities of 13C,15N-labeled NT(8-13) in complex with functional NTS-1. The NMR data are consistent with a disordered state of the ligand in the absence of receptor. Upon receptor binding, the peptide undergoes a linear rearrangement, adopting a beta-strand conformation. Our results provide a viable structural template for further pharmacological investigations.

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.

Homonuclear decoupled 13C chemical shift anisotropy in 13C doubly labeled peptides by selective-pulse solid-state NMR

We describe a new experiment for measuring homonuclear-decoupled anisotropic chemical shift patterns in doubly 13C-labeled compounds under magic-angle spinning. The experiment combines a pair of selective and non-selective 180 degrees pulses to suppress the 13C-13C scalar and dipolar interactions. This is combined with the recently developed SUPER technique to recouple the chemical shift anisotropy. Demonstrations on 13Calpha and 13CO-labeled amino acids and peptides show that accurate chemical shift powder patterns can be obtained. This permits the use of chemical shift anisotropy for conformational studies of suitably extensively 13C-labeled peptides and proteins.

Application of REDOR subtraction for filtered MAS observation of labeled backbone carbons of membrane-bound fusion peptides

Clean MAS observation of 13C-labeled carbons in membrane-bound HIV-1 and influenza fusion peptides was made by using a rotational-echo double-resonance spectroscopy (REDOR) filter of directly bonded 13C-15N pairs. The clean filtering achieved with the REDOR approach is superior to filtering done with sample difference spectroscopy. In one labeling approach, the peptide had labels at a single 13C carbonyl and its directly bonded 15N. The resulting chemical shift distribution of the filtered signal is used to assess the distribution of local secondary structures at the labeled carbonyl. For the influenza peptide, the Leu-2 carbonyl chemical shift distribution is shown to vary markedly with lipid and detergent composition, as well as peptide:lipid ratio, suggesting that the local peptide structure also has a strong dependence on these factors. Because most carboxylic- and amino-labeled amino acids are commercially available, this REDOR approach should have broad applicability to chemically synthesized peptides as well as bacterially synthesized proteins. In a second labeling approach, the HIV-1 fusion peptide had U-13C, 15N labeling over three sequential residues. When a 1.6 ms REDOR dephasing time is used, only backbone 13C signals are observed. The resulting spectra are used to determine spectral linewidths and to assess feasibility of assignment of uniformly labeled peptide.

Solid-state NMR spectroscopic methods in chemistry

Over the last decades, NMR spectroscopy has grown into an indispensable tool for chemical analysis, structure determination, and the study of dynamics in organic, inorganic, and biological systems. It is commonly used for a wide range of applications from the characterization of synthetic products to the study of molecular structures of systems such as catalysts, polymers, and proteins. Although most NMR experiments are performed on liquid-state samples, solid-state NMR is rapidly emerging as a powerful method for the study of solid samples and materials. This Review outlines some of the developments of solid-state NMR spectroscopy, including techniques such as cross-polarization, magic-angle spinning, multiple-pulse sequences, homo- and heteronuclear decoupling and recoupling techniques, multiple-quantum spectroscopy, and dynamic angle spinning, as well as their applications to structure determination. Modern solid-state NMR spectroscopic techniques not only produce spectra with a resolution close to that of liquid-state spectra, but also capitalize on anisotropic interactions, which are often unavailable for liquid samples. With this background, the future of solid-state NMR spectroscopy in chemistry appears to be promising, indeed.

Chemical shifts in amino acids, peptides, and proteins: from quantum chemistry to drug design

This chapter discusses recent progress in the investigation and use of (13)C, (15)N, and (19)F nuclear magnetic resonance (NMR) chemical shifts and chemical shift tensors in proteins and model systems primarily using quantum chemical (ab initio Hartree-Fock and density functional theory) techniques. Correlations between spectra and structure are made and the techniques applied to other spectroscopic and electrostatic properties as well, including hydrogen bonding, ligand binding to heme proteins, J-couplings, electric field gradients, and atoms-in-molecules theory, together with a brief review of the use of NMR chemical shifts in drug design.

Obtaining molecular and structural information from 13C-14N systems with 13C FIREMAT experiments

The effect of dipolar coupling to 14N on 13C FIREMAT (five pi replicated magic angle turning) experiments is investigated. A method is developed for fitting the 13C FIREMAT FID employing the full theory to extract the 13C-14N dipolar and 13C chemical shift tensor information. The analysis requires prior knowledge of the electric field gradient (EFG) tensor at the 14N nucleus. In order to validate the method the analysis is done for the amino acids alpha-glycine, gamma-glycine, l-alanine, l-asparagine, and l-histidine on FIREMAT FIDs recorded at 13C frequencies of 50 and 100 MHz. The dipolar and chemical shift data obtained with this analysis are in very good agreement with the previous single-crystal 13C NMR results and neutron diffraction data on alpha-glycine, l-alanine, and l-asparagine. The values for gamma-glycine and l-histidine obtained with this new method are reported for the first time. The uncertainties in the EFG tensor on the resultant 13C chemical shift and dipolar tensor values are assessed.

A robust technique for two-dimensional separation of undistorted chemical-shift anisotropy powder patterns in magic-angle-spinning NMR

A robust magic-angle-spinning experiment for separating undistorted, quasi-static chemical-shift powder patterns is presented. It is derived from the technique of R. Tycko, G. Dabbagh, and P. Mirau (1989, J. Magn. Reson. 85, 265), but uses 360 degrees instead of 180 degrees pulses. In combination with a suitable phase sequence, this makes the spectral patterns very insensitive to pulse-length errors and other imperfections, as demonstrated both experimentally and theoretically. This method, termed separation of undistorted powder patterns by effortless recoupling (SUPER), can be used at standard spinning speeds, between 2.5 and 5 kHz, and with standard radiofrequency power levels (in particular, for protons, a decoupling field strength gammaB(1)/2pi of less than 80 kHz). No significant artifacts are observed even for samples extending to the ends of the radiofrequency coil. The method has been applied to samples containing various sp(2)- and sp(3)-hybridized carbon sites. Even for the methylene groups in polyethylene, a system with very strong C-H and H-H dipolar couplings and only moderate chemical-shift anisotropy (CSA), a useful CSA powder pattern has been obtained. With a CSA scaling factor of 0.155, accuracies of +/-5, +/-3, and +/-1 ppm of the principal values can be achieved for protonated aromatic carbons, unprotonated sp(2)-hybridized groups, and aliphatic sites, respectively. Examples of CSA-based assignment of COOC vs other COO or CON groups, and of aromatic vs olefinic C=C carbons are shown, for both small molecules and polymers.

Toward direct determination of conformations of protein building units from multidimensional NMR experiments part II: a theoretical case study of formyl-L-valine amide

Chemical shielding anisotropy tensors have been determined for all twenty-seven characteristic conformers of For-L-Val-NH2 using the GIAO-RHF formalism with the 6-31 + G* and TZ2P basis sets. The individual chemical shifts and their conformational averages have been compared to their experimental counterparts taken from the BioMagnetic Resonance Bank (BMRB). At the highest level of theory applied, for all nuclei but the amide proton, deviations between statistically averaged theoretical and experimental chemical shifts are as low as 1-3%. Correlated chemical shift plots of selected nuclei, as function of the respective phi, psi, chi1, and chi2 torsional angles, have been generated. On two-dimensional chemical shift-chemical shift plots, for example, 1H(NH)-15N(NH) and 15N(NH)-13Calpha, regions corresponding to major conformational clusters have been identified, providing a basis for the quantitative identification of conformers from NMR shift data. Experimental NMR resonances of nuclei of valine residues have been deduced from 18 selected proteins, resulting in 93 1Halpha-13Calpha chemical shift pairs. These experimental results have been compared to relevant ab initio values revealing remarkable correlation between the two sets of data. Correlations of 1Halpha and 13Calpha values with backbone conformational parameters (phi and psi) have also been found for all pairs (e.g. 1Halpha/phi and 13Calpha/phi) but 1Halpha/psi. Overall, the appealing idea of establishing backbone folding of proteins by employing chemical shift information alone, obtained from selected multiple-pulse NMR experiments (e.g. 2D-HSQC, 2D-HMQC, and 3D-HNCA), has received further support.

(13)C chemical shift and (13)C-(14)N dipolar coupling tensors determined by (13)C rotary resonance solid-state NMR

This work explores the utility of simple rotary resonance experiments for the determination of the magnitude and orientation of (13)C chemical shift tensors relative to one or more (13)C--(14)N internuclear axes from (13)C magic-angle-spinning NMR experiments. The experiment relies on simultaneous recoupling of the anisotropic (13)C chemical shift and (13)C--(14)N dipole--dipole coupling interactions using 2D rotary resonance NMR with RF irradiation on the (13)C spins only. The method is demonstrated by experiments and numerical simulations for the (13)C(alpha) spins in powder samples of L-alanine and glycine with (13)C in natural abundance. To investigate the potential of the experiment for determination of relative/absolute tensor orientations and backbone dihedral angles in peptides, the influence from long-range dipolar coupling to sequential (14)N spins in a peptide chain ((14)N(i)--(13)C(alpha)(i)--(14)N(i+1) and (14)N(i+1)--(13)C'(i)--(14)N(i) three-spin systems) as well as residual quadrupolar-dipolar coupling cross-terms is analyzed numerically.

Peptide torsion angle measurements: effects of nondilute spin pairs on carbon-observed, deuterium-dephased PM5-REDOR

Reintroducing dipolar coupling between spin-1/2 nuclei (e.g., (13)C, (15)N) and spin-1 (2)H, using phase-modulated deuterium dephasing pulses, provides a simple and efficient basis for obtaining peptide backbone torsion angles (phi, psi) in specific stable-isotope enriched samples. Multiple homonuclear spin-1/2 interactions due to isotopic enrichment can arise between neighboring molecules or within a multiply labeled protein after folding. The consequences of (13)C homonuclear interactions present during (13)C-observed, (2)H-dephased REDOR measurements are explored and the theoretical basis of the experimentally observed effects is investigated. Two tripeptides are taken to represent both the general case of (2)H(alpha)-alanine (in the tripeptide LAF) and the special case of (2)H(alpha)(2)-glycine (in the tripeptide LGF). The lyophilized tripeptides exhibit narrowed spectral linewidths over time due to reduced conformational dispersion. This is due to a hydration process whereby a small fraction of peptides is reorienting and the bulk peptide fraction undergoes a conformational change. The new molecular packing arrangement lacks homonuclear (13)C spin interactions, allowing determination of (phi, psi) backbone torsion angles.

Expression of doubly labeled Saccharomyces cerevisiae iso-1 ferricytochrome c and (1)H, (13)C and (15)N chemical shift assignments by multidimensional NMR

We have expressed [U-(13)C,(15)N]-labeled Saccharomyces cerevisiae iso-1 cytochrome c C102T;K72A in Escherichia coli with a yield of 11 mg/l of growth medium. Nuclear magnetic resonance (NMR) studies were conducted on the Fe(3+) form of the protein. We report herein chemical shift assignments for amide (1)H and (15)N, (13)C(omicron), (13)C(alpha), (13)C(beta), (1)H(alpha) and (1)H(beta) resonances based upon a series of three-dimensional NMR experiments: HNCA, HN(CO)CA, HNCO, HN(CA)CO, HNCACB, HCA(CO)N, HCCH-TOCSY and HBHA(CBCA)NH. An investigation of the chemical shifts of the threonine residues was also made by using density functional theory in order to help solve discrepancies between (15)N chemical shift assignments reported in this study and those reported previously.

Solid-state NMR determination of the secondary structure of Samia cynthia ricini silk

Silks are fibrous proteins that form heterogeneous, semi-crystalline solids. Silk proteins have a variety of physical properties reflecting their range of functions. Spider dragline silk, for example, has high tensile strength and elasticity, whereas other silks are better suited to making housing, egg sacs or the capture spiral of spiders' webs. The differing physical properties arise from variation in the protein's primary and secondary structure, and their packing in the solid phase. The high mechanical performance of spider dragline silk, for example, is probably due to a beta-sheet conformation of poly-alanine domains, embedded as small crystallites within the fibre. Only limited structural information can be obtained from diffraction of silks, so further characterization requires spectroscopic studies such as NMR. However, the classical approach to NMR structure determination fails because the high molecular weight, repetitive primary structure and structural heterogeneity of solid silk means that signals from individual amino-acid residues cannot be resolved. Here we adapt a recently developed solid-state NMR technique to determine torsion angle pairs (phi, psi) in the protein backbone, and we study the distribution of conformations in silk from the Eri silkworm, Samia cynthia ricini. Although the most probable conformation in native fibres is an anti-parallel beta-sheet, film produced from liquid directly extracted from the silk glands appears to be primarily alpha-helical.