Solid-state NMR spectroscopy of human immunodeficiency virus fusion peptides associated with host-cell-like membranes: 2D correlation spectra and distance measurements support a fully extended conformation and models for specific antiparallel strand registries

The human immunodeficiency virus (HIV) is "enveloped" by a membrane, and infection of a host cell begins with fusion between viral and target cell membranes. Fusion is catalyzed by the HIV gp41 protein which contains a functionally critical approximately 20-residue apolar "fusion peptide" (HFP) that associates with target cell membranes. In this study, chemically synthesized HFPs were associated with host-cell-like membranes and had "scatter-uniform" labeling (SUL), that is, only one residue of each amino acid type was U-(13)C, (15)N labeled. For the first sixteen HFP residues, an unambiguous (13)C chemical shift assignment was derived from 2D (13)C/(13)C correlation spectra with short mixing times, and the shifts were consistent with continuous beta-strand conformation. (13)C-(13)C contacts between residues on adjacent strands were derived from correlation spectra with long mixing times and suggested close proximity of the following residues: Ala-6/Gly-10, Ala-6/Phe-11, and Ile-4/Gly-13. Specific antiparallel beta-strand registries were further tested using a set of HFPs that were (13)CO-labeled at Ala-14 and (15)N-labeled at either Val-2, Gly-3, Ile-4, or Gly-5. The solid-state NMR data were fit with 50-60% population of antiparallel HFP with either Ala-14/Gly-3 or Ala-14/Ile-4 registries and 40-50% population of structures not specified by the NMR experiments. The first two registries correlated with intermolecular hydrogen bonding of 15-16 apolar N-terminal residues and this hydrogen-bonding pattern would be consistent with a predominant location of these residues in the hydrophobic membrane interior. To our knowledge, these results provide the first residue-specific structural models for membrane-associated HFP in its beta-strand conformation.     

Temperature dependence and resonance assignment of 13C NMR spectra of selectively and uniformly labeled fusion peptides associated with membranes

HIV-1 and influenza viral fusion peptides are biologically relevant model fusion systems and, in this study, their membrane-associated structures were probed by solid-state NMR (13)C chemical shift measurements. The influenza peptide IFP-L2CF3N contained a (13)C carbonyl label at Leu-2 and a (15)N label at Phe-3 while the HIV-1 peptide HFP-UF8L9G10 was uniformly (13)C and (15)N labeled at Phe-8, Leu-9 and Gly-10. The membrane composition of the IFP-L2CF3N sample was POPC-POPG (4:1) and the membrane composition of the HFP-UF8L9G10 sample was a mixture of lipids and cholesterol which approximately reflects the lipid headgroup and cholesterol composition of host cells of the HIV-1 virus. In one-dimensional magic angle spinning spectra, labeled backbone (13)C were selectively observed using a REDOR filter of the (13)C-(15)N dipolar coupling. Backbone chemical shifts were very similar at -50 and 20 degrees C, which suggests that low temperature does not appreciably change the peptide structure. Relative to -50 degrees C, the 20 degrees C spectra had narrower signals with lower integrated intensity, which is consistent with greater motion at the higher temperature. The Leu-2 chemical shift in the IFP-L2CF3N sample correlates with a helical structure at this residue and is consistent with detection of helical structure by other biophysical techniques. Two-dimensional (13)C-(13)C correlation spectra were obtained for the HFP-UF8L9G10 sample and were used to assign the chemical shifts of all of the (13)C labels in the peptide. Secondary shift analysis was consistent with a beta-strand structure over these three residues. The high signal-to-noise ratio of the 2D spectra suggests that membrane-associated fusion peptides with longer sequences of labeled amino acids can also be assigned with 2D and 3D methods.     

Constraints on {\rm I}\beta cellulose twist from DFT calculations of ^{13}\hbox {C} NMR chemical shifts

We investigate theoretically the NMR response of twisted configurations of \({\rm I}\beta\) cellulose in the tg conformation. These finite helical angle structures were constructed by a mathematical deformation of zero-angle configurations obtained via the periodic density functional energy minimizations with dispersion corrections (DFT-D2). Subsequent calculations of the \({^{13}\hbox {C}}\) nuclear magnetic resonance chemical shifts \(({\delta}^{13} \hbox {C})\) were compared with experimental findings by Erata et al. (Cellul Commun 4:128–131, 1997) and Kono et al. (Macromolecules 36:5131–5138, 2003). We determine the sensitivity of the NMR chemical shifts to helical deformation of the microfibril and find that a substantial range of helical angle, ±2 degrees/nm, is consistent with current experimental observations, with a most probable angle of ～0.2 degree/nm. Through exhaustive combinatorial provisional assignments, we also demonstrate that there are different choices of the chemical shift \(({\delta}^{13} \hbox {C})\) assignments which are consistent with the experiments, including ones with lower deviations than existing identifications.     

Tailoring 13C labeling for triple-resonance solid-state NMR experiments on aligned samples of proteins

In order to develop triple-resonance solid-state NMR spectroscopy of membrane proteins, we have implemented several different (13)C labeling schemes with the purpose of overcoming the interfering effects of (13)C-(13)C dipole-dipole couplings in stationary samples. The membrane-bound form of the major coat protein of the filamentous bacteriophage Pf1 was used as an example of a well-characterized helical membrane protein. Aligned protein samples randomly enriched to 35% (13)C in all sites and metabolically labeled from bacterial growth on media containing [2-(13)C]-glycerol or [1,3-(13)C]-glycerol enables direct (13)C detection in solid-state NMR experiments without the need for homonuclear (13)C-(13)C dipole-dipole decoupling. The (13)C-detected NMR spectra of Pf1 coat protein show a substantial increase in sensitivity compared to the equivalent (15)N-detected spectra. The isotopic labeling pattern was analyzed for [2-(13)C]-glycerol and [1,3-(13)C]-glycerol as metabolic precursors by solution-state NMR of micelle samples. Polarization inversion spin exchange at the magic angle (PISEMA) and other solid-state NMR experiments work well on 35% random fractionally and metabolically tailored (13)C-labeled samples, in contrast to their failure with conventional 100% uniformly (13)C-labeled samples.     

A (13)C INADEQUATE and HF-GIAO study of C(60)H(2) and C(60)H(6) identification of ring currents in a 1,2-dihydrofullerene

The hydrofullerenes C(60)H(2) (1) and C(60)H(6) (2) have been prepared in (13)C-enriched form and 2D INADEQUATE NMR spectra were measured. These spectra have provided unambiguous (13)C assignments for 2, and nearly unambiguous assignments for 1. In both cases, the most downfield resonances are immediately adjacent to the sp(3) carbons, despite the fact that these carbons are the least pyramidalized carbons in the molecule. Typically, (13)C chemical shifts move downfield with increasing pyramidalization (THETA(p)), but in these systems there is no strong correlation between THETA(p) and delta. HF-GIAO calculations are able to predict the chemical shifts, but provide little chemical insight into the origin of these chemical shifts. London theory reveals a significant paramagnetic ring current in 1, a feature that helps explain the (1)H shifts in these compounds and may contribute to the (13)C chemical shifts as well.     

Performance of density functional models to reproduce observed (13)C(alpha) chemical shifts of proteins in solution

The purpose of this work is to test several density functional models (namely, OPBE, O3LYP, OPW91, BPW91, OB98, BPBE, B971, OLYP, PBE1PBE, and B3LYP) to determine their accuracy and speed for computing (13)C(alpha) chemical shifts in proteins. The test is applied to 10 NMR-derived conformations of the 76-residue alpha/beta protein ubiquitin (protein data bank id 1D3Z). With each functional, the (13)C(alpha) shielding was computed for 760 amino acid residues by using a combination of approaches that includes, but is not limited to, treating each amino acid X in the sequence as a terminally blocked tripeptide with the sequence Ac-GXG-NMe in the conformation of the regularized experimental protein structure. As computation of the (13)C(alpha) chemical shifts, not their shielding, is the main goal of this work, a computation of the (13)C(alpha) shielding of the reference, namely, tetramethylsilane, is investigated here and an effective and a computed tetramethylsilane shielding value for each of the functionals is provided. Despite observed small differences among all functionals tested, the results indicate that four of them, namely, OPBE, OPW91, OB98, and OLYP, provide the most accurate functionals with which to reproduce observed (13)C(alpha) chemical shifts of proteins in solution, and are among the faster ones. This study also provides evidence for the applicability of these functionals to proteins of any size or class, and for the validation of our previous results and conclusions, obtained from calculations with the slower B3LYP functional.     

Site-directed 13C solid-state NMR studies on membrane proteins: strategy and goals toward revealing conformation and dynamics as illustrated for bacteriorhodopsin labeled with [1-13C]amino acid residues

We have so far demonstrated that well-resolved and site-specifically assigned (13)C peaks as recorded by site-directed NMR study on (13)C-labeled membrane proteins can serve as a convenient probe to reveal their local conformation and dynamics. We attempted here to clarify the extent to which (13)C NMR spectra of (13)C-labeled fully hydrated bacteriorhodopsin (bR) as a typical membrane protein are visible or well resolved in the presence of inherent fluctuation motions with frequency of 10(2)-10(8) Hz, especially at the membrane surfaces. Accordingly, we estimated the relative proportion of (13)C NMR signals from the surface areas with and without peak suppression by the accelerated transverse relaxation effect by surface-bound Mn(2+) ions, which could be effective for residues within 8.7 angstroms of the membrane surface. It turned out that the experimental findings are consistent with the predicted amount of amino acid residues under consideration located within 8.7 angstroms of the surface for [1-(13)C]Val- and Ile-labeled bR and also [3-(13)C]Ala-bR. In contrast, (13)C NMR peaks from such surfaces area are almost completely or partially suppressed for [1-(13)C]Gly-, Ala-, Leu-, Phe- and Trp-labeled bR, as a result of plausible interference of the fluctuation frequency with frequency of magic angle spinning (10(4) Hz). We further assigned several (13)C NMR signals of [1-(13)C] Val-, Trp- and Ile-labeled bR on the basis of a variety of site-directed mutants with reference to those of the wild type. Further, we recorded the (13)C NMR of bR in lipid bilayers to search for the optimal conditions to be able to obtain signals with the highest peak intensities and spectral resolution. Backbone dynamics turn out to be essential for recording (13)C NMR spectra so as to escape from motional frequencies of the order of 10(4)-10(5) Hz, either in the direction of accelerated fluctuation or slowed motions in the direction of forming the 2D array.     

内氢键对芳环~(13)C化学位移的影响

本文讨论水杨醛、邻——基苯乙酮及2——基雌甾化合物的分子内氢键对芳环~13C化学位移的影响。采用量子化学CNDO/2方法,计算取代芳烃各原子的净电荷,从碳原子的净电荷与化学位移的对应关系进一步论证了此种影响.首次得到形成内氢键的甲甲基、乙乙基及及基对所在碳的取代基增量的校正值,经校正后化学位移的计算值与实测值很好符合。     

Carbanion substituent effects on 1-disubstituted 4-(4'-pyridyl)pyridinium methylide structures using 13C NMR spectroscopy and DFT method

The structure of 1-disubstituted 4-(4'-pyridyl)pyridinium methylides or 4,4'-bipyridinium monoylides (2-5) with a wide range of carbanion substituents, were determined using 13C NMR signals in dimethylsufoxide (DMSO-d(6)) solution. For the first time, we developed a systematic determination of 13C NMR chemical shifts of the ylidic carbon using a long-range correlated (1H-(13)C) HMBC experiments. The chemical shift values are discussed in terms of magnetic and/or electronic effects of the ylidic carbon substituents. From the extracted NMR parameters and the results of accompanying quantum chemical DFT calculations for a three-dimensional (3D)-structure representation, we found a long distance electronic effect where the aromatic heterocycle C2z.sbnd;C6 and C4 centers are perturbed according to the electron acceptor strengths of ylidic carbon substituents in all monoylides (2-5c) capable to stabilize in a planar conformation. No significant perturbation on C2z.sbnd;C6 and C4 centers are found in all other monoylides (2-5a, b) that adopted a non-planar conformation. Good similar linear dependences of the chemical shift variation Delta (calculated by the differences of analogous C2z.sbnd;C6 and C4 chemical shifts in non-planar and planar monoylides) with the ylidic carbon chemical shifts modulated by the strength of electron acceptor substituents pointed out the resonance interaction or the delocalization phenomena of the ylidic carbon charge on the heterocycle.     

Conformations and 13C NMR chemical shifts of some polyamides in the solid state as studied by high-resolution 13C NMR spectroscopy

High-resolution ¹³Carbon nuclear magnetic resonance (NMR) spectra of Nylons 4, 6, and 66 in the solid state were measured over a wide range of temperature. From the results, it was found that resonance lines of crystalline and noncrystalline components were separable and their chemical shifts were determined. The ¹³C chemical shift behavior is closely related to their conformation. The origin of the conformational effects on the chemical shifts is discussed.     

Complete 1H and 13C NMR assignments of clerodane diterpenoids of Salvia splendens

Unambiguous and complete assignments of 1H and 13C NMR chemical shifts for five clerodane diterpenes, four of them isolated from Salvia splendens (salviarin, splendidin and splenolides A and B) and one obtained by acetylation of splenolide A, are presented. The assignments are based on 2D shift-correlated [1H,1H-COSY, 1H,13C-gHSQC-1J(C,H) and 1H,13C-gHMBC-nJ(C,H) (n=2 and 3)] and nuclear Overhauser effect (NOE) experiments. The conformation of the rings of these compounds is supported by the 3J(H,H) values and NOE results.     

Detailed analysis of coupling constants and isotope effects in NMR spectra of isotopomers of (12)C(68) (13)C(2)

A preliminary study of the long-range (i.e. two-bond or longer) (13)C--(13)C coupling constants in natural abundance C(70) shows, consistent with recent theoretical calculations by Peralta et al. that the largest long-range J(CC) values for the polar and equatorial sites are clearly smaller than the largest long-range J(CC) values for the other three sites. The unusually large size of the (2)J(CC) couplings between inequivalent carbons in a nonpolar pentagon in C(70) has no analog among (2)J(CC) data reported for planar aromatic compounds. No long-range J(CC) values appear to have been reported for any curved aromatic compounds. In addition, much more precise (1)J(CC) values were obtained for C(70) than was possible about 15 years ago. Comparing the chemical shifts for each of the five isotopomers of C(70) containing only one (13)C nucleus and the frequencies of the satellites for each of the four isotopomers containing two adjacent and inequivalent (13)C nuclei indicates that replacing (12)C with (13)C shields the adjacent (13)C nucleus by 15 to 23 ppb, consistent with the limited (1)Delta(13)C((13/12)C) isotope effect data available on a few small aromatic molecules. Such measurements become possible with natural abundance C(70) only by using a (13)C cryoprobe and a high-field spectrometer (700 MHz). The additional information that could be obtained from a spectrum obtained under ultrahigh resolution conditions is discussed. Secure identification of the singlets arising from the four (12)C(68) (13)C(2) isotopomers with equivalent adjacent (13)C nuclei is necessary to allow the largest long-range J(CC) values to be precisely determined. The presence of numerous isotopomers containing two or more (13)C nuclei would present a great challenge in interpreting the various signals in a spectrum obtained under ultrahigh resolution conditions.     

(13)C NMR quantitative spectrometric data-activity relationship (QSDAR) models of steroids binding the aromatase enzyme

Five quantitative spectroscopic data-activity relationships (QSDAR) models for 50 steroidal inhibitors binding to aromatase enzyme have been developed based on simulated (13)C nuclear magnetic resonance (NMR) data. Three of the models were based on comparative spectral analysis (CoSA), and the two other models were based on comparative structurally assigned spectral analysis (CoSASA). A CoSA QSDAR model based on five principal components had an explained variance (r(2)) of 0.78 and a leave-one-out (LOO) cross-validated variance (q(2)) of 0.71. A CoSASA model that used the assigned (13)C NMR chemical shifts from a steroidal backbone at five selected positions gave an r(2) of 0.75 and a q(2) of 0.66. The (13)C NMR chemical shifts from atoms in the steroid template position 9, 6, 3, and 7 each had correlations greater than 0.6 with the relative binding activity to the aromatase enzyme. All five QSDAR models had explained and cross-validated variances that were better than the explained and cross-validated variances from a five structural parameter quantitative structure-activity relationship (QSAR) model of the same compounds. QSAR modeling suffers from errors introduced by the assumptions and approximations used in partial charges, dielectric constants, and the molecular alignment process of one structural conformation. One postulated reason that the variances of QSDAR models are better than the QSAR models is that (13)C NMR spectral data, based on quantum mechanical principles, are more reflective of binding than the QSAR model's calculated electrostatic potentials and molecular alignment process. The QSDAR models provide a rapid, simple way to model the steroid inhibitor activity in relation to the aromatase enzyme.     

NMR “Crystallography” for Uniformly (13C, 15N)‐Labeled Oriented Membrane Proteins

In oriented‐sample (OS) solid‐state NMR of membrane proteins, the angular‐dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only ¹H–¹⁵N dipolar couplings and ¹⁵N chemical shifts have been routinely assessed in oriented ¹⁵N‐labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple‐resonance NMR technique, which was applied to uniformly doubly (¹⁵N, ¹³C)‐labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible ¹H_α–¹³C_α dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α‐helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α‐helical transmembrane structure for Pf1 protein.     

Complete assignments of the 1H and 13C resonances of 40-epi-(N1-tetrazolyl)-rapamycin and revised 13C assignments for rapamycin

Complete 1H and 13C assignments of 40-epi-(N1-tetrazolyl)-rapamycin (ABT-578) in DMSO-d6 were made using 1H, 13C, DQCOSY, ROESY, TOCSY, HSQC and HMBC spectra. Comparing the assignments with those of rapamycin showed that in the published 13C assignments of rapamycin in DMSO-d6 the shifts for C-12 and C-42 have been interchanged, as well as the shifts for C-1 and C-8.     

Probing adsorption sites of silica-supported platinum with (13)C(16)O + (12)C(16)O and (13)C(18)O + (12)C(16)O mixtures: a comparative fourier transform infrared investigation

A comparative investigation of the adsorption of (13)C(18)O + (12)C(16)O and (13)C(16)O + (12)C(16)O mixtures on silica-supported Pt has been conducted. It is advantageous to use (13)C(18)O + (12)C(16)O mixtures rather than (13)C(16)O + (12)C(16)O to probe the adsorption sites and electronic state of supported Group VIII metals because the vibrational bands of the adsorbed (13)C(18)O and (12)C(16)O isotopic molecules do not overlap. In addition, while an intensity redistribution suppresses the lower-frequency band with adsorbed (13)C(16)O and (12)C(16)O with vibrational frequencies differing by 50 cm(-1), the intensity redistribution is less pronounced with the adsorbed (13)C(18)O and (12)C(16)O in which the frequency difference is 100 cm(-1). Moreover, the small intensity redistribution that does occur between the bands of adsorbed (13)C(18)O and (12)C(16)O still allows the detection of the vibrational band of adsorbed (13)C(18)O at (13)C(18)O gas-phase concentrations as low as 3%. At such low concentrations, the dipole-dipole interaction between adsorbed (13)C(18)O molecules is negligible, and, hence, both the singleton frequency and the dipole-dipole shift for adsorbed CO may be obtained in a single experiment. Two types of strongly bound and one type of weakly bound linear CO-Pt adsorption complexes have been identified and characterized by their singleton frequencies and dipole-dipole coupling shifts. The origin of these CO adsorption modes is discussed.     

Conformation and configuration of tertiary amines via GIAO-derived (13)C NMR chemical shifts and a multiple independent variable regression analysis.

The (13)C chemical shifts of six tertiary amines of unambiguous conformational structure are compared to predicted (13)C NMR chemical shifts obtained via empirically scaled GIAO shieldings for geometries from MM3 molecular mechanics calculations. An average deviation, absolute value of Deltadelta(av), of 0.8 ppm and a maximum deviation, absolute value of Deltadelta(max), of 2.8 ppm between predicted and experimental (13)C shifts of the six tertiary amines of unambiguous structure are found. In several cases of tertiary amines subject to rapid exchange, where experimental (13)C shifts at room temperature are weighted averages of multiple conformers, a comparison of calculated (13)C shifts of all reasonable MM3 predicted conformers with experimental (13)C shifts via a multiple independent variable regression analysis provides an efficient method of determining the major and minor conformers. The examples presented are 2-methyl-2-azabicyclo[2.2.1]heptane and 1,6-diazabicyclo[4.3.1]decane, which each have two expected contributing structures, and 2-(diethylamino)propane and 1,8-diazabicyclo[6.3.1]dodecane, where ten and seven low-energy conformers, respectively, are predicted by MM3 calculations.     

Linear correlation between 1H and 13C chemical shifts of ferriheme proteins and model ferrihemes

The (1)H{(13)C} HMQC experiment at natural-abundance (13)C provides a very useful way of determining not only (1)H but also (13)C chemical shifts of most heme substituents, without isotopic labeling of the hemin. This is true both in model low-spin ferriheme complexes and in low-spin ferriheme proteins, even when the proton resonances are buried in the protein diamagnetic region, because the carbon shifts are much larger than the proton shifts. In addition, in many cases, the protohemin methyl cross peaks are fairly linearly related to each other, with the slope of the correlation, δ(C)/δ(H), being approximately -2.0 for most low-spin ferriheme proteins. The reasons why this should be the case, and when it is not, are discussed.     

Conformational studies of cyclo(L-Phe-L-Pro-Gly-L-Pro)2 by 13C nuclear magnetic resonance

The 13C-NMR spectrum (Fig. 2,1) of cyclooctapeptide cyclo(L-phe-L-Pro-Gly-L-Pro)2 (A) in CDC13 suggested that its conformation involved the coexistence of two kinds of C2-symmetric conformation with trans-trans-trans-trans and cis-trans-trans-trans forms. Adding 0.5 equivalent of CsSCN or one equivalent of DL-Phe-OMe.HCl to the solution of cyclopeptide (A) in CDC13 yielded 13C-NMR spectra (Fig. 2,2 and Table I) which suggested a single C2-symmetric conformation with trans-trans-trans-trans form, resulting from the formation of complexes with CsSCN or DL-Phe-OMe.HCl. The 13C-NMR spectrum of complexes of A with DL-Phe-OMe.HCl displayed separate resonances for C(gamma), C(o), C(m), C(alpha), and C(beta) of D-Phe-OMe.HCl and L-Phe-OMe.HCl (Table I).     

13C and proton NMR spectra of 2(1H)pyrazinones

¹³C and proton NMR spectra data are given for eleven 2(1H)pyraziones. Assignments of chemical shifts were made by methods which included: deuterium exchange with certain protons of 3-alkyl substituents; change of chemical shifts of certain carbon atoms with change in pH; the use of long-range coupling constants for ¹³C to protons; and various correlations among assigned spectra.