Intermolecular 31P−15N and 31P−1H Scalar Couplings Across Hydrogen Bonds Formed between a Protein and a Nucleotide

NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups

Hydrogen bonds between protein side-chain hydroxyl (OH) and phosphate groups are one of the most common types of intermolecular hydrogen bonds in protein-DNA/RNA complexes. Using NMR spectroscopy, we identified and characterized the hydrogen bonds between tyrosine side-chain OH and DNA phosphate groups in a protein-DNA complex. These OH groups exhibited relatively slow hydrogen-exchange rates and sizable scalar couplings between hydroxyl 1H and DNA phosphate 31P nuclei across the hydrogen bonds. Information about intermolecular hydrogen bonds facilitates investigations of the DNA/RNA recognition by the protein.

NMR Spectroscopy for Metabolomics Research

Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.

NMR experiments for the rapid identification of P=O···H-X type hydrogen bonds in nucleic acids

Hydrogen bonds involving the backbone phosphate groups occur with high frequency in functional RNA molecules. They are often found in well-characterized tertiary structural motifs presenting powerful probes for the rapid identification of these motifs for structure elucidation purposes. We have shown recently that stable hydrogen bonds to the phosphate backbone can in principle be detected by relatively simple NMR-experiments, providing the identity of both the donor hydrogen and the acceptor phosphorous within the same experiment (Duchardt-Ferner et al., Angew Chem Int Ed Engl 50:7927-7930, 2011). However, for imino and hydroxyl hydrogen bond donor groups rapidly exchanging with the solvent as well as amino groups broadened by conformational exchange experimental sensitivity is severely hampered by extensive line broadening. Here, we present improved methods for the rapid identification of hydrogen bonds to phosphate groups in nucleic acids by NMR. The introduction of the SOFAST technique into ¹H,³¹P-correlation experiments as well as a BEST-HNP experiment exploiting ^3hJ_N,P rather than ^2hJ_H,P coupling constants enables the rapid and sensitive identification of these hydrogen bonds in RNA. The experiments are applicable for larger RNAs (up to ~ 100-nt), for donor groups influenced by conformational exchange processes such as amino groups and for hydrogen bonds with rather labile hydrogens such as 2'-OH groups as well as for moderate sample concentrations. Interestingly, the size of the through-hydrogen bond scalar coupling constants depends not only on the type of the donor group but also on the structural context. The largest coupling constants were measured for hydrogen bonds involving the imino groups of protonated cytosine nucleotides as donors.

NMR Spectroscopic Characterization of Charge Assisted Strong Hydrogen Bonds in Brønsted Acid Catalysis

Hydrogen bonding plays a crucial role in Brønsted acid catalysis. However, the hydrogen bond properties responsible for the activation of the substrate are still under debate. Here, we report an in depth study of the properties and geometries of the hydrogen bonds in (R)-TRIP imine complexes (TRIP: 3,3'-Bis(2,4,6-triisopropylphenyl)-1,1'-binaphthyl-2,2'-diylhydrogen phosphate). From NMR spectroscopic investigations 1H and 15N chemical shifts, a Steiner-Limbach correlation, a deuterium isotope effect as well as quantitative values of 1JNH,2hJPH and 3hJPN were used to determine atomic distances (rOH, rNH, rNO) and geometry information. Calculations at SCS-MP2/CBS//TPSS-D3/def2-SVP-level of theory provided potential surfaces, atomic distances and angles. In addition, scalar coupling constants were computed at TPSS-D3/IGLO-III. The combined experimental and theoretical data reveal mainly ion pair complexes providing strong hydrogen bonds with an asymmetric single well potential. The geometries of the hydrogen bonds are not affected by varying the steric or electronic properties of the aromatic imines. Hence, the strong hydrogen bond reduces the degree of freedom of the substrate and acts as a structural anchor in the (R)-TRIP imine complex.

NMR Scalar Couplings across Intermolecular Hydrogen Bonds between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups

NMR scalar couplings across hydrogen bonds represent direct evidence for the partial covalent nature of hydrogen bonds and provide structural and dynamic information on hydrogen bonding. In this article, we report heteronuclear 15N-31P and 1H-31P scalar couplings across the intermolecular hydrogen bonds between protein histidine (His) imidazole and DNA phosphate groups. These hydrogen-bond scalar couplings were observed for the Egr-1 zinc-finger-DNA complex. Although His side-chain NH protons are typically undetectable in heteronuclear 1H-15N correlation spectra due to rapid hydrogen exchange, this complex exhibited two His side-chain NH signals around 1H 14.3 ppm and 15N 178 ppm at 35 °C. Through various heteronuclear multidimensional NMR experiments, these signals were assigned to two zinc-coordinating His side chains in contact with DNA phosphate groups. The data show that the Nδ1 atoms of these His side chains are protonated and exhibit the 1H-15N cross-peaks. Using heteronuclear 1H, 15N, and 31P NMR experiments, we observed the hydrogen-bond scalar couplings between the His 15Nδ1/1Hδ1 and DNA phosphate 31P nuclei. These results demonstrate the direct involvement of the zinc-coordinating His side chains in the recognition of DNA by the Cys2His2-class zinc fingers in solution.

Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-Bond Scalar Coupling

The residence times of molecular complexes in solution are important for understanding biomolecular functions and drug actions. We show that NMR data of intermolecular hydrogen-bond scalar couplings can yield information on the residence times of molecular complexes in solution. The molecular exchange of binding partners via the breakage and reformation of a complex causes self-decoupling of intermolecular hydrogen-bond scalar couplings, and this self-decoupling effect depends on the residence time of the complex. For protein-DNA complexes, we investigated the salt concentration dependence of intermolecular hydrogen-bond scalar couplings between the protein side-chain (15)N and DNA phosphate (31)P nuclei, from which the residence times were analyzed. The results were consistent with those obtained by (15)Nz-exchange spectroscopy. This self-decoupling-based kinetic analysis is unique in that it does not require any different signatures for the states involved in the exchange, whereas such conditions are crucial for kinetic analyses by typical NMR and other methods.

Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy

Ion pairing is one of the most fundamental chemical interactions and is essential for molecular recognition by biological macromolecules. From an experimental standpoint, very little is known to date about ion-pair dynamics in biological macromolecular systems. Absorption, infrared, and Raman spectroscopic methods were previously used to characterize dynamic properties of ion pairs, but these methods can be applied only to small compounds. Here, using NMR (15)N relaxation and hydrogen-bond scalar (15)N-(31)P J-couplings ((h3)J(NP)), we have investigated the dynamics of the ion pairs between lysine side-chain NH3(+) amino groups and DNA phosphate groups at the molecular interface of the HoxD9 homeodomain-DNA complex. We have determined the order parameters and the correlation times for C-N bond rotation and reorientation of the lysine NH3(+) groups. Our data indicate that the NH3(+) groups in the intermolecular ion pairs are highly dynamic at the protein-DNA interface, which should lower the entropic costs for protein-DNA association. Judging from the C-N bond-rotation correlation times along with experimental and quantum-chemically derived (h3)J(NP) hydrogen-bond scalar couplings, it seems that breakage of hydrogen bonds in the ion pairs occurs on a sub-nanosecond time scale. Interestingly, the oxygen-to-sulfur substitution in a DNA phosphate group was found to enhance the mobility of the NH3(+) group in the intermolecular ion pair. This can partially account for the affinity enhancement of the protein-DNA association by the oxygen-to-sulfur substitution, which is a previously observed but poorly understood phenomenon.

Structural dynamics of bacterial translation initiation factor IF2

Bacterial translation initiation factor IF2 promotes ribosomal subunit association, recruitment, and binding of fMet-tRNA to the ribosomal P-site and initiation dipeptide formation. Here, we present the solution structures of GDP-bound and apo-IF2-G2 of Bacillus stearothermophilus and provide evidence that this isolated domain binds the 50 S ribosomal subunit and hydrolyzes GTP. Differences between the free and GDP-bound structures of IF2-G2 suggest that domain reorganization within the G2-G3-C1 regions underlies the different structural requirements of IF2 during the initiation process. However, these structural signals are unlikely forwarded from IF2-G2 to the C-terminal fMet-tRNA binding domain (IF2-C2) because the connected IF2-C1 and IF2-C2 modules show completely independent mobility, indicating that the bacterial interdomain connector lacks the rigidity that was found in the archaeal IF2 homolog aIF5B.

Detection and assignment of phosphoserine and phosphothreonine residues by (13)C- (31)P spin-echo difference NMR spectroscopy

A simple NMR method is presented for the identification and assignment of phosphorylated serine and threonine residues in (13)C- or (13)C/(15)N-labeled proteins. By exploiting modest (~5 Hz) 2- and 3-bond (13)C-(31)P scalar couplings, the aliphatic (1)H-(13)C signals from phosphoserines and phosphothreonines can be detected selectively in a (31)P spin-echo difference constant time (1)H-(13)C HSQC spectrum. Inclusion of the same (31)P spin-echo element within the (13)C frequency editing period of an intraHNCA or HN(CO)CA experiment allows identification of the amide (1)H(N) and (15)N signals of residues (i) for which( 13)C(alpha)(i) or ( 13)C(alpha)(i - 1), respectively, are coupled to a phosphate. Furthermore, (31)P resonance assignments can be obtained by applying selective low power cw (31)P decoupling during the spin-echo period. The approach is demonstrated using a PNT domain containing fragment of the transcription factor Ets-1, phosphorylated in vitro at Thr38 and Ser41 with the MAP kinase ERK2.

A review with comprehensive data on experimental indirect scalar NMR spin-spin coupling constants across hydrogen bonds

Scalar NMR spin-spin coupling constants across hydrogen bonds are fundamental in structural studies and as test grounds for theoretical calculations. Since they are scattered among many articles of different kinds, it seems useful to collect them in the most comprehensive way.

Probing the proton-transfer coordinate of complexes with F--H...P hydrogen bonds using one- and two-bond spin-spin coupling constants

Scalar coupling constants have been computed using the EOM-CCSD method for equilibrium structures of complexes stabilized by F--H...P hydrogen bonds, as well as structures along the proton-transfer coordinates of these complexes. Variations in the signs and absolute values of (1)J(F--H), (1h)J(H--P) and (2h)J(F--P) have been analyzed and interpreted in terms of changing hydrogen bond type. Of the three phosphorus bases (phosphine, trimethylphosphine and phosphinine) investigated in this study, trimethylphosphine forms the strongest complex with FH, and has the largest two-bond F--P coupling constant. Among the relatively simple phosphorus bases, it would appear to be a leading candidate for experimental NMR study. Similarities and differences are noted between the corresponding coupling constants (J) and the reduced coupling constants (K) across F--H...P and F--H...N hydrogen bonds.

Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-watson-crick/sugar edge base pair family

The structure and function of RNA molecules are substantially affected by non-Watson-Crick base pairs actively utilizing the 2'-hydroxyl group of ribose. Here we correlate scalar coupling constants across the noncovalent contacts calculated for the cis- and trans-WC/SE (Watson-Crick/sugar edge) RNA base pairs with the geometry of base to base and sugar to base hydrogen bond(s). 23 RNA base pairs from the 32 investigated were found in RNA crystal structures, and the calculated scalar couplings are therefore experimentally relevant with regard to the binding patterns occurring in this class of RNA base pairs. The intermolecular scalar couplings 1hJ(N,H), 2hJ(N,N), 2hJ(C,H), and 3hJ(C,N) were calculated for the N-H...N and N-H...O=C base to base contacts and various noncovalent links between the sugar hydroxyl and RNA base. Also, the intramolecular 1J(N,H) and 2J(C,H) couplings were calculated for the amino or imino group of RNA base and the ribose 2'-hydroxyl group involved in the noncovalent interactions. The calculated scalar couplings have implications for validation of local geometry, show specificity for the amino and imino groups of RNA base involved in the linkage, and can be used for discrimination between the cis- and trans-WC/SE base pairs. The RNA base pairs within an isosteric subclass of the WC/SE binding patterns can be further sorted according to the scalar couplings calculated across different local noncovalent contacts. The effect of explicit water inserted in the RNA base pairs on the magnitude of the scalar couplings was calculated, and the data for discrimination between the water-inserted and direct RNA base pairs are presented. The calculated NMR data are significant for structural interpretation of the scalar couplings in the noncanonical RNA base pairs.

Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for structure determination of nucleic acids

Calculated indirect NMR spin-spin coupling constants (3)J(P,C) and (2)J(P,H) were correlated with the local structure of the P-O...H-C linkage between the nucleic acid (NA) backbone phosphate and the H-C group(s) of a nucleic acid base. The calculations were carried out for selected nucleotides from the large ribosomal subunit (Ban et al. Science 2000, 289, 905) with the aim of identifying NMR parameters suitable for detection of certain noncanonical RNA structures. As calculations in the model system, dimethyl-phosphate-guanine, suggest, the calculated indirect spin-spin couplings across the linkage are sensitive to the mutual orientation and distance between the phosphate and nucleic acid base. A short distance between the nucleic acid base and phosphate group and the angles C...P-O and P...C-H smaller than 50 degrees are prerequisites for a measurable spin-spin interaction of either coupling (|J| > 1 Hz). A less favorable arrangement of the P-O...H-C motif, e.g., in nucleotides of the canonical A-RNA, results in an effective dumping of both spin-spin interactions and insignificant values of the NMR coupling constants. The present work indicates that quantum chemical calculations of the indirect spin-spin couplings across the P-O...H-C motif can help detect some rare but important backbone topologies, as seen for example in the reverse kink-turn. Measuring of (3)J(P,C) and (2)J(P,H) couplings can therefore provide critical constraints on the NA base and phosphate geometry and help to determine the structure of NAs.

Characterizing the Cooperativity in H-Bonded Amino Structures

Density functional theory calculations were used to examine the effect of H-bond cooperativity on the magnitude of the NMR chemical shifts and spin-spin coupling constants in a C4h-symmetric G-quartet and in structures consisting of six cyanamide monomers. These included two ring structures (a planar C6h-symmetric structure and a nonplanar S6-symmetric structure) and two linear chain structures (a fully optimized planar Cs-symmetric chain and a planar chain structure where all intra- and intermolecular parameters were constrained to be identical). The NMR parameters were computed for the G-quartet and cyanamide structures, as well as for shorter fragments derived from these assemblies without reoptimization. In the ring structures and the chain with identical monomers, the intra- and intermolecular geometries of the cyanamides were identical, thereby allowing the study of cooperative effects in the absence of geometry changes. The magnitude of the |1JNH| coupling, 1H and 15N chemical shifts of the H-bonding amino N-H group, and the |h2JNN| H-bond coupling increased, whereas the size of the |1JNH| coupling of the non-H-bonded amino N-H bonds of the first amino group in the chain, which are roughly perpendicular to the H-bonding network, decreased in magnitude when H-bonding monomers were progressively added to extending ring or chain structures. These effects are attributed to electron redistribution induced by the presence of the nearby H-bonding guanine or cyanamide molecules.

Complexes with N-H(+)-P hydrogen bonds: structures, binding energies, and spin-spin coupling constants

Ab-initio MP2/aug'-cc-pVTZ calculations have been performed to determine the structures and binding energies of proton-bound complexes stabilized by N-H+-P hydrogen bonds and to investigate the nature of the proton-transfer coordinate in these systems. Double minima are found only when the difference between the protonation energies of the N and P bases is less than about 4 kcal/mol. The isomer in which the protonated nitrogen base is the donor lies lower on the potential surface and also has a greater binding energy relative to the corresponding isolated monomers. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculations have been employed to obtain one- and two-bond spin-spin coupling constants across these hydrogen bonds. Two-bond coupling constants (2h)J(N-P) correlate with N-P distances, irrespective of whether the donor ion is N-H+ or P-H+. One-bond coupling constants (1)J(N-H) and (1h)J(H-P) for complexes stabilized by N-H+...P hydrogen bonds correlate with corresponding distances, but similar correlations are not found for (1)J(P-H) and (1h)J(H-N) for complexes with P-H+...N hydrogen bonds. Negative values of (1h)K(H-N) and (1h)K(H-P) indicate that the hydrogen bonds in these complexes are traditional. Comparisons are made with complexes stabilized by N-H+-N and P-H+-P hydrogen bonds.

Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters

Conformational stability of G-quartets found in telomeric DNA quadruplex structures requires the coordination of monovalent ions. Here, an extensive Hartree-Fock and density functional theory analysis of the energetically favored position of Li+, Na+, and K+ ions is presented. The calculations show that at quartet-quartet distances observed in DNA quadruplex structures (3.3 A), the Li+ and Na+ ions favor positions of 0.55 and 0.95 A outside the plane of the G-quartet, respectively. The larger K+ ion prefers a central position between successive G-quartets. The energy barrier separating the minima in the quartet-ion-quartet model are much smaller for the Li+ and Na+ ions compared with the K+ ion; this suggests that K+ ions will not move as freely through the central channel of the DNA quadruplex. Spin-spin coupling constants and isotropic chemical shifts in G-quartets extracted from crystal structures of K+- and Na+-coordinated DNA quadruplexes were calculated with B3LYP/6-311G(d). The results show that the sizes of the trans-hydrogen-bond couplings are influenced primarily by the hydrogen bond geometry and only slightly by the presence of the ion. The calculations show that the R(N2N7) distance of the N2-H2...N7 hydrogen bond is characterized by strong correlations to both the chemical shifts of the donor group atoms and the (h2)J(N2N7) couplings. In contrast, weaker correlations between the (h3)J(N1C6') couplings and single geometric factors related to the N1-H1...O6=C6 hydrogen bond are observed. As such, deriving geometric information on the hydrogen bond through the use of trans-hydrogen-bond couplings and chemical shifts is more complex for the N1-H1...O6=C6 hydrogen bond than for the N2-H2...N7 moiety. The computed trans-hydrogen-bond couplings are shown to correlate with the experimentally determined couplings. However, the experimental values do not show such strong geometric dependencies.

Low-barrier hydrogen bond between phosphate and the amide group in phosphopeptide

As the conversion between the monoionic (1) and diionic (2) form of the phosphate occurs, the phosphorylated peptides or proteins can not only cause the formation of a hydrogen bond between the phosphate group and the amide group but also change the strength of the hydrogen bond to form low-barrier hydrogen bonds (LBHBs). This reversible protonation of the phosphate group, which changes both the electrostatic properties of the phosphate group and the strength of the hydrogen bond, provides a possible mechanism in regulating protein function.

Altered specificity in DNA binding by the lac repressor: a mutant lac headpiece that mimics the gal repressor

Recognition of the lac operator by the lac repressor involves specific interactions between residues in the repressor's recognition helix and bases in the DNA major groove. Tyr17 and Gln18, at positions 1 and 2 in the lac repressor recognition helix, can be exchanged for other amino acids to generate mutant repressors that display altered specificity. We have solved the solution structure of a protein-DNA complex of an altered-specificity mutant lac headpiece in which Tyr17 and Gln18 were exchanged for valine and alanine, respectively, as found in the recognition helix of the gal repressor. As previously described by Lehming et al. (EMBO J. 1987, 6, 3145-3153), this altered-specificity mutant of the lac repressor recognizes a variant lac operator that is similar to the gal operator Oe. The mutant lac headpiece showed the predicted specificity and is also able to mimic the gal repressor by recognizing and bending the natural gal operator Oe. These structural data show that, while most of the anchoring points that help the lac headpiece to assemble on the lac operator were preserved, a different network of protein-DNA interactions connecting Ala17 and Val18 to bases in the DNA major groove drives the specificity towards the altered operator.

Characterization of the Cation and Temperature Dependence of DNA Quadruplex Hydrogen Bond Properties Using High-Resolution NMR

Variations in the hydrogen bond network of the Oxy-1.5 DNA guanine quadruplex have been monitored by trans-H-bond scalar couplings, (h2)J(N2N7), for Na(+)-, K(+)-, and NH(4)(+)-bound forms over a temperature range from 5 to 55 degrees C. The variations in (h2)J(N2N7) couplings exhibit an overall trend of Na(+) > K(+) > NH(4)(+) and correlate with the different cation positions and N2-H2...N7 H-bond lengths in the respective structures. A global weakening of the (h2)J(N2N7) couplings with increasing temperature for the three DNA quadruplex species is accompanied by a global increase of the acceptor (15)N7 chemical shifts. Above 35 degrees C, spectral heterogeneity indicates thermal denaturation for the Na(+)-bound form, whereas spectral homogeneity persists up to 55 degrees C for the K(+)- and NH(4)(+)-coordinated forms. The average relative change of the (h2)J(N2N7) couplings amounts to approximately 0.8 x 10(-3)/K and is thus considerably smaller than respective values reported for nucleic acid duplexes. The significantly higher thermal stability of H-bond geometries in the DNA quadruplexes can be rationalized by their cation coordination of the G-quartets and the extensive H-bond network between the four strands. A detailed analysis of individual (h2)J(N2N7) couplings reveals that the 5' strand end, comprising base pairs G1-G9* and G4*-G1, is the most thermolabile region of the DNA quadruplex in all three cation-bound forms.

Visualization of the phosphorylated active site loop of the cytoplasmic B domain of the mannitol transporter II(Mannitol) of the Escherichia coli phosphotransferase system by NMR spectroscopy and residual dipolar couplings

The solution structure of a stably phosphorylated form of the cytoplasmic B domain of the mannitol-specific transporter (IIB(Mtl)) of the Escherichia coli phosphotransferase system, containing a mutation of the active site Cys384 to Ser, has been solved by NMR. The strategy employed relies principally on backbone residual dipolar couplings recorded in three different alignment media, supplemented by nuclear Overhauser enhancement data and torsion angle restraints related specifically to the active site loop (residues 383-393). As judged from the dipolar coupling data, the remainder of the structure is unchanged upon phosphorylation within the errors of the coordinates of the previously determined solution structure of unphosphorylated wild-type IIB(Mtl). Thus, only the active site loop was refined. Phosphorylation results in a backbone atomic rms shift of approximately 0.7 angstroms in the active site loop. The resulting conformation is less than 0.5 angstroms away from the equivalent P-loop in both the low and high molecular mass eukaryotic tyrosine phosphatases. 3J(NP) coupling constant measurements using quantitative J-correlation spectroscopy provide a direct demonstration of a hydrogen bond between the phosphoryl group and the backbone amide of Ser391 at position i + 7 from phospho-Ser384, with an approximately linear P-O-H(N) bond angle. The structure also reveals additional hydrogen bonding interactions involving the backbone amides of residues at positions i + 4 and i + 5, and the hydroxyl groups of two serine residues at positions i + 6 and i + 7 that stabilize the phosphoryl group.

Cofactor-Apoprotein Hydrogen Bonding in Oxidized and Fully Reduced Flavodoxin Monitored by Trans-Hydrogen-Bond Scalar Couplings

Hydrogen bonding plays a key role in the tight binding of the FMN cofactor and the regulation of its redox properties in flavodoxins. Hydrogen bonding interactions can be directly observed in solution by multidimensional heteronuclear NMR spectroscopy through the scalar couplings between donor and acceptor nuclei. Here we report on the detection of intermolecular trans-hydrogen-bond couplings ((h)J) between the flavin ring system and the backbone of Desulfovibrio vulgaris flavodoxin in the oxidized and the two-electron reduced states. For this purpose, experiments are adapted from pulse sequences previously applied to determining (h)J coupling constants in nucleic acid-base pairs and proteins. The resulting (h2)J(N,N), (h4)J(N,N), (h3)J(C,N), and (h1)J(H,N) couplings involve the (15)N(1), (13)C(2), and (15)N(3) nuclei of the pyrimidine moiety of FMN, whereas no such interactions are detectable for (13)C(4) and (15)N(5). Several long-range (15)N-(15)N, (13)C-(15)N, and (1)H-(15)N J-coupling constants within the flavin are obtained as "by-products". The magnitudes of both (h)J and regular J couplings are found to be dependent on the redox state. In general, good correlations between (h)J coupling constants and donor-group (1)H chemical shifts and also crystallographic donor-acceptor distances are observed.

The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics

The emerging antibiotics-resistance problem has underlined the urgent need for novel antimicrobial agents. Lantibiotics (lanthionine-containing antibiotics) are promising candidates to alleviate this problem. Nisin, a member of this family, has a unique pore-forming activity against bacteria. It binds to lipid II, the essential precursor of cell wall synthesis. As a result, the membrane permeabilization activity of nisin is increased by three orders of magnitude. Here we report the solution structure of the complex of nisin and lipid II. The structure shows a novel lipid II-binding motif in which the pyrophosphate moiety of lipid II is primarily coordinated by the N-terminal backbone amides of nisin via intermolecular hydrogen bonds. This cage structure provides a rationale for the conservation of the lanthionine rings among several lipid II-binding lantibiotics. The structure of the pyrophosphate cage offers a template for structure-based design of novel antibiotics.

NMR Detection of Intermolecular NH···OP Hydrogen Bonds between Guanidinium Protons and Bisposphonate Moieties in an Artificial Arginine Receptor

Hydrogen bonding plays a major role in the selective recognition of guanidinium groups by receptor molecules. The present NMR investigation provides direct experimental evidence of hydrogen bonds in an artificial arginine receptor complex consisting of alpha-N-benzoylarginine ethyl ester and a bisphosphonate tweezers molecule. trans-Hydrogen bond 2hJHP couplings between the phosphonate moieties and individual guanidinium protons as well as the amide proton have been detected by [1H,31P]-HMBC and [31P,1H]-INEPT experiments. The detected hydrogen bonding network in the investigated artificial arginine receptor shows a symmetrical end-on interaction of the guanidinium moiety, which enables concerted rotations and deviates from the structure proposed for the biological arginine fork.

(3h)J((15)N-(31)P) spin-spin coupling constants across N[bond]H....O[bond]P hydrogen bonds

Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) calculations have been performed to evaluate three-bond (15)N-(31)P coupling constants ((3h)J(N[bond]P)) across N[bond]H....O[bond]P hydrogen bonds in model cationic and anionic complexes including NH(4)(+):OPH, NH(4)(+):OPH(3), NH(3):(-)O(2)PH(2), NFH(2):(-)O(2)PH(2), and NF(2)H:(-)O(2)PH(2). Three-bond coupling constants can be appreciable when the phosphorus is P(V), but are negligible with P(III). (3h)J(N[bond]P) values in complexes with cyclic or open structures are less than 1 Hz, a consequence of the nonlinear arrangement of N, H, O, and P atoms. For complexes with these structures, (3h)J(N[bond]P) may not be experimentally measurable. In contrast, complexes in which the N, H, O, and P atoms are collinear or nearly collinear have larger values of (3h)J(N[bond]P), even though the N[bond]P distances are longer than N[bond]P distances in cyclic and open structures. In linear complexes, (3h)J(N[bond]P) is dominated by the Fermi-contact term, which is distance dependent. Therefore, N[bond]P (and hydrogen-bonding N[bond]O) distances in these complexes can be determined from experimentally measured (15)N-(31)P coupling constants.

Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR

The temperature-dependence of a large number of NMR parameters describing hydrogen bond properties in the protein ubiquitin was followed over a range from 5 to 65 degrees C. The parameters comprise hydrogen bond (H-bond) scalar couplings, h3JNC', chemical shifts, amide proton exchange rates, 15N relaxation parameters as well as covalent 1JNC' and 1JNH couplings. A global weakening of the h3JNC' coupling with increasing temperature is accompanied by a global upfield shift of the amide protons and a decrease of the sequential 1JNC' couplings. If interpreted as a linear increase of the N...O distance, the change in h3JNC' corresponds to an average linear thermal expansion coefficient for the NH-->O hydrogen bonds of 1.7 x 10(-4)/K, which is in good agreement with overall volume expansion coefficients observed for proteins. A residue-specific analysis reveals that not all hydrogen bonds are affected to the same extent by the thermal expansion. The end of beta-sheet beta1/beta5 at hydrogen bond E64-->Q2 appears as the most thermolabile, whereas the adjacent hydrogen bond I3-->L15 connecting beta-strands beta1 and beta2 is even stabilized slightly at higher temperatures. Additional evidence for the stabilization of the beta1/beta2 beta-hairpin at higher temperatures is found in reduced hydrogen exchange rates for strand end residue V17. This reduction corresponds to a stabilizing change in free energy of 9.7 kJ/mol for the beta1/beta2 hairpin. The result can be linked to the finding that the beta1/beta2 hairpin behaves as an autonomously folding unit in the A-state of ubiquitin under changed solvent conditions. For several amide groups the temperature-dependencies of the amide exchange rates and H-bond scalar couplings are uncorrelated. Therefore, amide exchange rates are not a sole function of the hydrogen bond "strength" as given by the electronic overlap of donors and acceptors, but are clearly dependent on other blocking mechanisms.

Identifying hydrogen bond alignments in multistranded DNA architectures by NMR

NMR studies of nucleic acids have benefited tremendously from the discovery of trans-hydrogen-bond scalar coupling constants, which have enabled direct determination of N-H...N and N-H...O=C hydrogen bonds using a combination of (2h)J(NN)-, (4h)J(NN)-, and (3h)J(NC)-based spectroscopy. This is especially true of multistranded DNA architectures containing intricate hydrogen-bonded networks mediated primarily through mismatched base pairing, which often resist identification by posing serious technical, spectroscopic, and physicochemical challenges. In this Account, we present a suite of NMR pulse sequences that have been developed in our laboratory to address these issues. We demonstrate the utility of these methods for identifying hydrogen bonds in two quadruplex DNA structures, containing triad, tetrad, and hexad motifs involving Watson-Crick, G.G and sheared G.A mismatch base pairing.

NMR methodology for the study of nucleic acids

During the past few years, NMR methodology for the study of nucleic acids has benefited from new developments that greatly improved state-of-the-art technology for the precise determination of three-dimensional structures. Substantial progress has been made in designing experimental protocols for the measurement of residual dipolar couplings, in sensitivity optimization of triple-resonance experiments and in detection of hydrogen bonds and in developing computational methods for structure refinement using NMR restraints.