Filamentous phage studied by magic-angle spinning NMR: resonance assignment and secondary structure of the coat protein in Pf1

Assignments are presented for resonances in the magic-angle spinning solid-state NMR spectra of the major coat protein subunit of the filamentous bacteriophage Pf1. NMR spectra were collected on uniformly 13C and 15N isotopically enriched, polyethylene glycol precipitated samples of fully infectious and hydrated phage. Site-specific assignments were achieved for 231 of the 251 labeled atoms (92%) of the 46-residue-long coat protein, including 136 of the 138 backbone atoms, by means of two- and three-dimensional 15N and 13C correlation experiments. A single chemical shift was observed for the vast majority of atoms, suggesting a single conformation for the 7300 subunits in the 36 MDa virion in its high-temperature form. On the other hand, multiple chemical shifts were observed for the Calpha, Cbeta, and Cgamma atoms of T5 in the helix terminus and the Calpha and Cbeta atoms of M42 in the DNA interaction domain. The chemical shifts of the backbone atoms indicate that the coat protein conformation involves a 40-residue continuous alpha-helix extending from residue 6 to the C-terminus.     

13C, 14N, 15N and 17O NMR spectra of the charged species of nitropyrroles and nitroimidazoles

Changes in ¹³C and ¹⁴N chemical shifts of the nitro derivatives of nitrogen heterocycles upon ionization (anion or cation formation) are twofold—first a uniform paramagnetic or in the case of protonation, a uniform diamagnetic shift of all the ring resonances that parallels the changes in the respective ultraviolet spectra and must be caused by changes in the molecular excited states, and second—the influence of the conjugated nitro group. About one third of the total negative anion charge may be localized on the nitro group, which causes unusually large shifts of the ring ¹³C resonances in this case.     

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.     

B环对位取代异黄酮化合物的核磁共振研究

对14个合成的B环对位取代异黄酮化合物核磁共振氢谱进行了研究.利用超导核磁共振归属了B环无取代异黄酮质子的化学位移,根据取代基化学位移的变化影响规律考察了取代基对分子的影响方式.研究结果表明,2'(6'),3'(5')位质子共振迁移分别与取代基参数σ_p和S_o线性相关,说明4'位取代基主要通过电子效应影响其间位质子,其磁各向异性仅影响邻位质子,该取代基对A环质子影响不大,而对C环尤其是对2-H影响较明显.     

Multinuclear magnetic resonance and theoretical calculations in the study of structure and tautomerism of some 2-amino-N'-(aryl)-benzamidines

1H, 13C and 15N NMR spectra of eight 2-amino-N'-(aryl)-benzamidines and of the parent compound were recorded, and unequivocal chemical shift assignments through the use of COSY, 1H-J resolved, HETCOR and COLOC sequences were performed. 1H and 13C chemical shifts for the nuclei of the benzamidine aromatic ring were not affected by the substituents present at N'-phenyl group, while the substituent effects in the chemical shifts of the same nuclei of N'-phenyl ring were very similar to the ones reported for the corresponding monosubstituted benzenes, indicating that there is no interaction between the two aromatic rings. 15N NMR spectra (DEPT sequence) show just two hydrogenated nitrogen atoms, which confirm that the amino form is the most stable tautomer, but the observation of a sharp signal and two broad signals (15N decoupled spectra), and the corresponding broad signal for the =C-NH(2) protons (in the 1H spectra), indicates the occurrence of tautomerism between the amino and imino forms, observable for some of the studied benzamidines. Theoretical calculations lead to the conclusion that these compounds occur mostly as the amino tautomer with Z configuration, which is stabilized by hydrogen bonding.     

Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p

Sup35p is a prion protein found in yeast that contains a prion-forming domain characterized by a repetitive sequence rich in Gln, Asn, Tyr, and Gly amino acid residues. The peptide GNNQQNY7-13 is one of the shortest segments of this domain found to form amyloid fibrils, in a fashion similar to the protein itself. Upon dissolution in water, GNNQQNY displays a concentration-dependent polymorphism, forming monoclinic and orthorhombic crystals at low concentrations and amyloid fibrils at higher concentrations. We prepared nanocrystals of both space groups as well as fibril samples that reproducibly contain three (coexisting) structural forms and examined the specimens with magic angle spinning (MAS) solid-state nuclear magnetic resonance. 13C and 15N MAS spectra of both nanocrystals and fibrils reveal narrow resonances indicative of a high level of microscopic sample homogeneity that permitted resonance assignments of all five species. We observed variations in chemical shift among the three dominant forms of the fibrils which were indicated by the presence of three distinct, self-consistent sets of correlated NMR signals. Similarly, the monoclinic and orthorhombic crystals exhibit chemical shifts that differ from one another and from the fibrils. Collectively, the chemical shift data suggest that the peptide assumes five conformations in the crystals and fibrils that differ from one another in subtle but distinct ways. This includes variations in the mobility of the aromatic Tyr ring. The data also suggest that various structures assumed by the peptide may be correlated to the "steric zipper" observed in the monoclinic crystals.     

Structural determination of 5'-OH alpha-ribofuranoside modified cobalamins via 13C and DEPT NMR

A protocol for the rapid NMR characterization of cobalamin (vitamin B(12)) analogues with 5'-hydroxy-alpha-ribofuranoside modification is reported. The structure of cyanocobalamin in DMSO-d(6) has been assigned using COSY, NOESY, HSQC, and HMBC NMR methods. The robust precision of (13)C NMR assignments in DMSO-d(6) allows for the rapid structural determination of 5'-hydroxy-alpha-ribofuranosyl cyanocobalamin derivatives with solely 1-D (13)C and DEPT NMR spectra and only 10 mg of derivatized cobalamin. Using this method, the (13)C NMR resonances of four cobalamin analogues were determined with the most significant variance of (13)C chemical shifts occurring in the alpha-ribofuranoside ring. In DMSO-d(6), cobalamin concentrations greater than 30 mM can be achieved for an improved signal-to-noise ratio.     

Comprehensive conformational analysis of the nucleoside analogue 2'-beta-deoxy-6-azacytidine by DFT and MP2 calculations

A comprehensive conformational analysis of isolated 2'-beta-deoxy-6-azacytidine (d6AC), an analogue of therapeutically active 6-azacytidine (6AC), has been performed by means of ab initio calculations at the MP2/6-311++G(2df,pd)//DFT B3LYP/6-31G(d,p) level of theory. Among the 81 conformers located within a 7.83 kcal/mol Gibbs energy range at T = 298.15 K, 38 contain syn-oriented bases with respect to 2'-deoxyribose; the other conformers include anti-oriented bases. Energetic analysis of these conformers shows that conformational equilibrium of isolated d6AC at T = 298.15 K is shifted to syn conformation with a syn/anti ratio estimated as 61.4%:38.6%. As far as the sugar conformation is concerned, 40 conformers contain north (N) (with 0.3 degrees < or = P < or = 40.1 degrees), and the rest possess south (S) (with 157.1 degrees < or = P < or = 207.0 degrees) puckers, where P is the pseudorotational angle of the furanose ring. The S/N occupancy ratio is estimated as 80.2%:19.8% (T = 298.15 K). The two most stable conformers are energetically quasidegenerate and correspond to both C2'-endo/syn conformers differing only by orientation of the O3'H hydroxyl group. They are both stabilized by means of similar intramolecular H-bonds, i.e., O5'H...O2, C2'H2...O2, and C2'H2...O5'. As examined by AIM criteria, from 1 to 3 H-bonds per conformer were identified among 13 possible interactions: O5'H...O2, O5'H...N6, O3'H...O5', O5'H...O3', C1'H...O2, C2'H2...O2, C2'H2...O5', C3'H...O2, C3'H...N6, C5'H1...O2, C5'H2...O2, C5'H1...N6, and C5'H2...N6. The biological effect of d6AC is conceived as an inhibition of replicative DNA polymerase caused by an unusual orientation of the sugar residue against the base in the only A form DNA-like conformer.     

The role of cation-pi interactions in biomolecular association. Design of peptides favoring interactions between cationic and aromatic amino acid side chains.

Cation-pi interactions between amino acid side chains are increasingly being recognized as important structural and functional features of proteins and other biomolecules. Although these interactions have been found in static protein structures, they have not yet been detected in dynamic biomolecular systems. We determined, by (1)H NMR spectroscopic titrations, the energies of cation-pi interactions of the amino acid derivative AcLysOMe (1) with AcPheOEt (2) and with AcTyrOEt (3) in aqueous and three organic solvents. The interaction energy is substantial; it ranges from -2.1 to -3.4 kcal/mol and depends only slightly on the dielectric constant of the solvent. To assess the effects of auxiliary interactions and structural preorganization on formation of cation-pi interactions, we studied these interactions in the association of pentapeptides. Upon binding of the positively-charged peptide AcLysLysLysLysLysNH(2) (5) to the negatively-charged partner AcAspAspXAspAspNH(2) (6), in which X is Leu (6a), Tyr (6b), and Phe (6c), multiple interactions occur. Association of the two pentapeptides is dynamic. Free peptides and their complex are in fast exchange on the NMR time-scale, and 2D (1)H ROESY spectra of the complex of the two pentapeptides do not show intermolecular ROESY peaks. Perturbations of the chemical shifts indicated that the aromatic groups in peptides 6b and 6c were affected by the association with 5. The association constants K(A) for 5 with 6a and with 6b are nearly equal, (4.0 +/- 0.7) x 10(3) and (5.0 +/- 1.0) x 10(3) M(-)(1), respectively, while K(A) for 5 with 6c is larger, (8.3 +/- 1.3) x 10(3) M(-)(1). Molecular-dynamics (MD) simulations of the pentapeptide pairs confirmed that their association is dynamic and showed that cation-pi contacts between the two peptides are stereochemically possible. A transient complex between 5 and 6 with a prominent cation-pi interaction, obtained from MD simulations, was used as a template to design cyclic peptides C(X) featuring persistent cation-pi interactions. The cyclic peptide C(X) had a sequence in which X is Tyr, Phe, and Leu. The first two peptides do, but the third does not, contain the aromatic residue capable of interacting with a cationic Lys residue. This covalent construct offered conformational stability over the noncovalent complexes and allowed thorough studies by 2D NMR spectroscopy. Multiple conformations of the cyclic peptides C(Tyr) and C(Phe) are in slow exchange on the NMR time-scale. In one of these conformations, cation-pi interaction between Lys3 and Tyr9/Phe9 is clearly evident. Multiple NOEs between the side chains of residues 3 and 9 are observed; chemical-shift changes are consistent with the placement of the side chain of Lys3 over the aromatic ring. In contrast, the cyclic peptide C(Leu) showed no evidence for close approach of the side chains of Lys3 and Leu9. The cation-pi interaction persists in both DMSO and aqueous solvents. When the disulfide bond in the cyclic peptide C(Phe) was removed, the cation-pi interaction in the acyclic peptide AC(Phe) remained. To test the reliability of the pK(a) criterion for the existence of cation-pi interactions, we determined residue-specific pK(a) values of all four Lys side chains in all three cyclic peptides C(X). While NOE cross-peaks and perturbations of the chemical shifts clearly show the existence of the cation-pi interaction, pK(a) values of Lys3 in C(Tyr) and in C(Phe) differ only marginally from those values of other lysines in these dynamic peptides. Our experimental results with dynamic peptide systems highlight the role of cation-pi interactions in both intermolecular recognition at the protein-protein interface and intramolecular processes such as protein folding.     

Magic-angle-spinning NMR of the drug resistant S31N M2 proton transporter from influenza A

We report chemical shift assignments of the drug-resistant S31N mutant of M2(18-60) determined using 3D magic-angle-spinning (MAS) NMR spectra acquired with a (15)N-(13)C ZF-TEDOR transfer followed by (13)C-(13)C mixing by RFDR. The MAS spectra reveal two sets of resonances, indicating that the tetramer assembles as a dimer of dimers, similar to the wild-type channel. Helicies from the two sets of chemical shifts are shown to be in close proximity at residue H37, and the assignments reveal a difference in the helix torsion angles, as predicted by TALOS+, for the key resistance residue N31. In contrast to wild-type M2(18-60), chemical shift changes are minimal upon addition of the inhibitor rimantadine, suggesting that the drug does not bind to S31N M2.     

5-amino-2-methylpyridinium hydrogen fumarate: An XRD and NMR crystallography analysis

Single-crystal X-ray diffraction structures of the 5-amino-2-methylpyridinium hydrogen fumarate salt have been solved at 150 and 300 K (CCDC 1952142 and 1952143). A base–acid–base–acid ring is formed through pyridinium-carboxylate and amine-carboxylate hydrogen bonds that hold together chains formed from hydrogen-bonded hydrogen fumarate ions. ¹H and ¹³C chemical shifts as well as ¹⁴N shifts that additionally depend on the quadrupolar interaction are determined by experimental magic angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) and gauge-including projector-augmented wave (GIPAW) calculation. Two-dimensional homonuclear ¹H-¹H double-quantum (DQ) MAS and heteronuclear ¹H-¹³C and ¹⁴N-¹H spectra are presented. Only small differences of up to 0.1 and 0.6 ppm for ¹H and ¹³C are observed between GIPAW calculations starting with the two structures solved at 150 and 300 K (after geometry optimisation of atomic positions, but not unit cell parameters). A comparison of GIPAW-calculated ¹H chemical shifts for isolated molecules and the full crystal structures is indicative of hydrogen bonding strength.     

Long-range deuterium isotope effects on (13)C chemical shifts of intramolecularly hydrogen-bonded N-substituted 3-(cycloamine)thiopropionamides or amides: a case of electric field effects

A series of intramolecularly hydrogen-bonded N-substituted 3-(piperidine, morpholine, N-methylpiperazine)thiopropionamides and some corresponding amides have been studied with special emphasis on hydrogen bonding. The compounds have been selected in order to vary and to minimize the N...N distance. Geometries, charge distributions, and chemical shifts of these compounds are obtained from DFT-type BP3LYP calculations. 1H and 13C 1D and 2D NMR experiments were performed to obtain H,H coupling constants, 13C chemical shifts assignments, and deuterium isotope effects on13C chemical shifts. Variable-temperature NMR studies and 2D exchange NMR spectra have been used to describe the rather complicated conformational behavior mainly governed by the ring flipping of the piperidine (morpholine) rings and intramolecular hydrogen bonding. Unusual long-range deuterium isotope effects on 13C chemical shifts are observed over as far as eight bonds away from the site of deuteriation. The isotope effects are related to the N...N distances, thus being related to the hydrogen bonding and polarization of the N-H bond. Arguments are presented showing that the deuterium isotope effects on 13C chemical shifts originate in electric field effects.     

A predictive tool for assessing (13)C NMR chemical shifts of flavonoids

Herein are presented the (1)H and (13)C NMR data for seven monohydroxyflavones (3-, 5-, 6-, 7-, 2'-, 3'-, and 4'-hydroxyflavone), five dihydroxyflavones (3,2'-, 3,3'-, 3,4'-, 3,6-, 2',3'-dihydroxyflavone), a trihydroxyflavone (apigenin; 5,7,4'-trihydroxyflavone), a tetrahydroxyflavone (luteolin; 5,7,3',4'-tetrahydroxyflavone), and three glycosylated hydroxyflavones (orientin; luteolin-6C-beta-D-glucoside, homoorientin; luteolin-8C-beta-D-glucoside, vitexin; apigenin-8C-beta-D-glucoside). When these NMR spectra are compared, it is possible to assess the impact of flavone modification and to elucidate detailed structural and electronic information for these flavonoids. A simple predictive tool for assigning flavonoid (13)C chemical shifts, which is based on the cumulative differences between the monohydroxyflavones and flavone (13)C chemical shifts, is demonstrated. The tool can be used to accurately predict (13)C flavonoid chemical shifts and it is expected to be useful for rapid assessment of flavonoid (13)C NMR spectra and for assigning substitution patterns in newly isolated flavonoids.     

13C NMR spectra of some 1-, 3- and 4-monosubstituted and disubstituted isoquinolines

Chemical shifts and substituent chemical shift (SCS) effects are reported for 21 monosubstituted iso-quinolines, carrying a halogeno, amino, piperidino or ethoxy group in position 1, 3 or 4. In some cases, assignments of ¹³C resonances were based on the spectra of the corresponding 5-deutero derivatives. For the fluoroisoquinolines some ¹³CF coupling constants are given. The ¹³C NMR spectra of 15 disubstituted isoquinolines were measured; with a few exceptions, mainly the 3,4- and 1,4-disubstituted isoquinolines, the chemical shifts agreed well with those calculated by addition of the SCS effects.     

1H and13C NMR spectra of 2-substituted 5-nitrofurans and conformation of chemotherapeutic preparations of the 5-nitrofuran series

The¹H and¹³NMR spectra of t-nitrofuran and 17 2-substituted 5-nitrofurans were investigated. The Δ¹H and Δ¹³C substituent increments [Δ = δ(2-X-5-nitrofuran) δ(5-nitrofuran)] in the spectra of these compounds were analyzed by comparison with the analogous 5-methylfuran and furan derivatives, and the change in the sensitivity of the chemical shifts of the ring protons and the carbon atoms to the effects of substituents X as a function of the electronic character of substituent R was also analyzed. The chemical shifts and the spin-spin coupling constants were used to determine the preferred orientation of the substituents relative to the furan ring. It was found that medicinal preparations of the 5-nitrofuran series (5-nitrofurfurylidenehydrazones) exist in the form of s-trans conformers in solutions in dimethyl sulfoxide and water, whereas furagin has primarily the structure of the E s-trans form. Translated from Khimiya Geterotsiklichesklkh Soedinenii, No. 2, pp. 167–176, February, 1980. The authors thank N. O. Saldabol, M. A. Trushule, and K. K. Venter for providing us with samples of the compounds, the synthesis of which has been described in the literature.     

Synthesis and dynamic NMR studies of Pt(eta(5)-C(5)Me(5))(CO){C(O)NR(2)} complexes

The formation of Pt(eta(5)-C(5)Me(5))(CO){C(O)NR(2)} (R=Me, Et) complexes was established by spectroscopic analysis. The infrared spectra of these complexes showed a sharp absorption due to the presence of coordinated carbonyl group in the region 2017-2013cm(-1). The N,N-dialkylcarbamoyl ligands showed a characteristic CO stretching absorption in the range 1609-1616cm(-1). The proton NMR spectra of these complexes revealed the expected singlet arising from five equivalent methyl groups on the cyclopentadienyl ring with satellites due to coupling to (195)Pt. The N-methyl and N-ethyl protons exhibited very broad resonances due to restricted rotation about the N-C bond at room temperature. On cooling to -30 degrees C, the N,N-dimethyl protons for complex Pt(eta(5)-C(5)Me(5))(CO){C(O)NMe(2)} showed two sharp singlets at delta 2.86 and 3.09ppm as expected for the static structure. For the N,N-diethyl derivative, Pt(eta(5)-C(5)Me(5))(CO){C(O)NEt(2)}, the methyl protons exhibited only a single triplet at delta 1.06ppm at -10 degrees C due to coupling with the methylene protons. This single resonance arises through accidental overlap as the methylene protons of the ethyl groups are inequivalent at this temperature and each exhibited a quartet at delta 3.33 and 3.70ppm due to coupling with the methyl protons. The singlet resonances for the methyl and ring carbons of the eta(5)-C(5)Me(5) group found in (13)C{(1)H} NMR spectra are illustrative of the chemical equivalence of all the carbon atoms caused by free rotation of the ring in these complexes. The signals attributable to the carbonyl and carbamoyl carbon atom resonances are found downfield as two singlets each with a large coupling constant to platinum. The platinum coupling constants of the downfield resonances could not be identified for Pt(eta(5)-C(5)Me(5))(CO){C(O)NMe(2)} due to presence of impurities.     

5-H-芳基-1,2,3-连三唑[2,3-d]咪啶-4-酮及相关化合物的~(13)C NMR谱研究

三唑并米啶类稠杂环衍生物由于具有抗真菌,抗细菌,抗过敏,抗肿瘤等方面的生物活性而受到广泛关注,合成这类化合物颇具意义。作者近期报道5-H-1-芳基-1,2,3-连三唑(2,3-d)米啶-4-酮(1)的合成,并发现它们对枯草杆菌,大肠杆菌、产气肠杆菌、金黄色葡萄球菌的繁殖有明显的抑制。作为对有生物活性杂环化合     

Ring-substituted benzohydroxamic acids: 1H, 13C and 15N NMR spectra and NH-OH proton exchange

NMR spectra (1H, 13C, 15N) of para- and meta-substituted benzohydroxamic acids were studied in dry dimethyl sulfoxide solutions. The 13C chemical shifts were very close to those found by cross-polarization magic angle spinning in solids, the hydroxamic (not hydroximic) structure of which is unambiguous. The hydroxamic structure of these acids in DMSO solutions was proved independently by their 15N chemical shifts. The 15N and 1H chemical shifts of the NH-OH fragment showed excellent mutual dependences and dependences on the nature of the ring substituent. According to these dependences and ab initio energy calculations, all the acids assume the same Z conformation. Proton exchange between hydroxamic OH and NH groups in DMSO proceeded by both intra- and intermolecular exchange and the rates did not exhibit any simple relationship to the substituent constants.     

Assignment of the 13C chemical shifts of ethidium bromide and analogs in D2O solution

The ¹³C resonances of ethidum bromide (1), dimidium bromide (2) and 3,8-diamino-5-methylphenanthridinium chloride (3) in D₂O solution have been assigned. Assignments were made using fully coupled spectra, spectra obtained from a selected 180°-τ-90° pulse sequence in conjunction with gated irradiation to obtain NOE intensification, selective proton decoupling, chemical shift arguments and by noting the effect of pD on the ¹³C chemical shifts of 1 and 3.     

Carbon-13 nuclear magnetic resonance spectra of substituted-s-triazolyl tetrazoles

The natural abundance carbon-13 nuclear magnetic resonance spectra of various 5-aryltetrazoles, 1-(5-aryltetrazol-2-ylacetyl)-4-phenyl thiosemicarbazides and 5-(5-aryltetrazol-2-ylmethyl)-4-phenyl-s-triazole-3-thiols were recorded using Fourier transform techniques. The chemical shifts of various carbon resonances have been assigned on the basis of chemical shift theory, the signal multiplicity observed in the single-frequency off-resonance decoupled (SFORD) spectra and comparison with the chemical shifts of the model compounds.