Heteroassociation of antibiotic norfloxacin with aromatic vitamins in aqueous solution

Heteroassociation of antibacterial antibiotic norfloxacin with aromatic vitamins nicotinamide and flavin mononucleotide in aqueous solution was studied by ¹H NMR spectroscopy (500 MHz). Equilibrium constants, induced proton chemical shifts, and thermodynamic parameters (ΔH, ΔS) for the reactions of heteroassociation of the molecules were determined on the basis of the concentration and temperature dependences of proton chemical shifts for interacting aromatic molecules. The analysis of the results obtained indicates the formation of heterocomplexes between vitamin molecules and norfloxacin owing to stacking interactions between aromatic chromophores and additional intermolecular hydrogen bonding in norfloxacin-nicotinamide. The most probable spatial structures of 1:1 norfloxacin-flavin mononucleotide and norfloxacin-nicotinamide heterocomplexes were determined by molecular modeling methods using X-PLOR software on the basis of analysis of induced proton chemical shifts.     

Calcium-Lipid Interactions Observed with Isotope-Edited Infrared Spectroscopy

Calcium ions bind to lipid membranes containing anionic lipids; however, characterizing the specific ion-lipid interactions in multicomponent membranes has remained challenging because it requires nonperturbative lipid-specific probes. Here, using a combination of isotope-edited infrared spectroscopy and molecular dynamics simulations, we characterize the effects of a physiologically relevant (2 mM) Ca²⁺ concentration on zwitterionic phosphatidylcholine and anionic phosphatidylserine lipids in mixed lipid membranes. We show that Ca²⁺ alters hydrogen bonding between water and lipid headgroups by forming a coordination complex involving the lipid headgroups and water. These interactions distort interfacial water orientations and prevent hydrogen bonding with lipid ester carbonyls. We demonstrate, experimentally, that these effects are more pronounced for the anionic phosphatidylserine lipids than for zwitterionic phosphatidylcholine lipids in the same membrane.     

Studies in a model system on the effect of hydrogen bonding at hetero atoms of oxidized flavin on its electron acceptability

The effect of hydrogen bonding at hetero atoms of oxidized flavin on its electron acceptability was studied by the ab initio molecular orbital method. The calculations were carried out for all possible lumiflavin-H2O complexes and for some lumiflavin-formamide complexes. Calculated data showed that the magnitudes of hydrogen bonding energy at the hetero atoms are in the order of N(3)H greater than N(5) greater than O(12) greater than N(1) greater than O(14). It was found that the atomic orbital coefficient of the lowest unoccupied molecular orbital is the largest at N(5) and that hydrogen bonding at N(1), N(5), O(12), and O(14) increases the electron acceptability of the oxidized flavin at N(5), while hydrogen bonding at N(3)H decreases it.     

Thioamide, urea and thiourea bridged rhenium(I) complexes as luminescent anion receptors

Thioamides, urea and thiourea derivatives of 2,6-pyridinedicarbonyl dichloride, isophthaloyl dichloride and terephthaloyl dichloride have been synthesized. These ligands have been incorporated in dinuclear rhenium(I) diimine tricarbonyl complexes and the anion recognition properties of these complexes have been studied by luminescence, UV-Vis and ¹H NMR spectroscopic methods. The complexes act as receptors for anions via hydrogen bonding and electrostatic interactions. The anion sensing properties of the complexes are compared to earlier amide-based dinuclear rhenium(I) tricarbonyl complexes.     

Conformation dependence of the CαDα stretch mode in peptides. II. Explicitly hydrated alanine peptide structures

Our previous studies of the potential utility of the C^αD^α stretch frequency, ν(CD), as a tool for determining conformation in peptide systems (Mirkin and Krimm, J Phys Chem A 2004, 108, 10923–10924; 2007, 111, 5300–5303) dealt with the spectroscopic characteristics of isolated alanine peptides with α_R, β, and polyproline II structures. We have now extended these ab initio calculations to include various explicit‐water environments interacting with such conformers. We find that the structure‐discriminating feature of this technique is in fact enhanced as a result of the conformation‐specific interactions of the bonding waters, in part due to our finding (Mirkin and Krimm, J Phys Chem B 2008, 112, 15268) that C^α? D^α…O(water) hydrogen bonds can be present in addition to those expected between water and the CO and NH of the peptide groups. In fact, ν(CD) is hardly affected by the latter bonding but can be shifted by up to 70 cm^?1 by the former hydrogen bonds. We also discuss the factors that will have to be considered in developing the molecular dynamics (MD) treatment needed to satisfactorily take account of the influence of outer water layers on the structure of the first‐layer water molecules that hydrogen bond to the peptide backbone. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 791–800, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

<Superscript>1</Superscript>H, <Superscript>13</Superscript>C and <Superscript>15</Superscript>N resonance assignments for a chemokine receptor-binding domain of FROUNT,a cytoplasmic regulator of chemotaxis

FROUNT is a cytoplasmic protein that interacts with the membrane-proximal C-terminal regions (Pro-Cs) of the CCR2 and CCR5 chemokine receptors. The interactions between FROUNT and the chemokine receptors play an important role in the migration of inflammatory immune cells. Therefore, FROUNT is a potential drug target for inflammatory diseases. However, the structural basis of the interactions between FROUNT and the chemokine receptors remains to be elucidated. We previously identified the C-terminal region (residues 532–656) of FROUNT as the structural domain responsible for the Pro-C binding, referred to as the chemokine receptor-binding domain (CRBD), and then constructed its mutant, bearing L538E/P612S mutations, with improved NMR spectral quality, referred to as CRBD_LEPS. We now report the main-chain and side-chain ¹H, ¹³C, and ¹⁵N resonance assignments of CRBD_LEPS. The NMR signals of CRBD_LEPS were well dispersed and their intensities were uniform on the ¹H–¹⁵N HSQC spectrum, and thus almost all of the main-chain and side-chain resonances were assigned. This assignment information provides the foundation for NMR studies of the three-dimensional structure of CRBD_LEPS in solution and its interactions with chemokine receptors.     

Deuterium isotope effects on <Superscript>15</Superscript>N backbone chemical shifts in proteins

Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the ¹⁵N chemical shift of backbone amides of proteins, ¹Δ¹⁵N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for ¹Δ¹⁵N(D) including the backbone dihedral angles, Φ and Ψ, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N–H bond length. Another contributing factor is the effect of increased anharmonicity of the N–H stretching vibrational state upon hydrogen bonding, which results in an altered N–H/N–D equilibrium bond length ratio. The N–H stretching anharmonicity contribution falls off with the cosine of the N–H···O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, ¹Δ¹⁵N(D) can provide insights into hydrogen bonding geometries. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Transient hydrogen bonding in uniformly ¹³C,¹⁵N-labeled carbohydrates in water

We report NMR studies of transient hydrogen bonding in a polysaccharide (PS) dissolved in water without cosolvent at ambient temperature. The PS portion of the Escherichia coli O142 lipopolysaccharide is comprised of repeating pentasaccharide units of GalNAc (N-acetyl galactosamine), GlcNAc (N-acetyl glucosamine), and rhamnose in a 3:1:1 ratio, respectively. A 105-ns molecular dynamics (MD) simulation on one pentasaccharide repeat unit predicts transient inter-residue hydrogen bonds from the GalNAc NH groups in the PS. To investigate these predictions experimentally, the PS was uniformly ¹³C,¹⁵N enriched and the NH, carbonyl, C2, C4, and methyl resonances of the GalNAc and GlcNAc residues assigned using through-bond triple-resonance NMR experiments. Temperature dependence of amide NH chemical shifts and one-bond NH J couplings support that NH groups on two of the GalNAc residues are donors in transient hydrogen bonds. The remaining GalNAc and GlcNAc NHs do not appear to be donors from either temperature-dependent chemical shifts or one-bond NH J couplings. These results substantiate the presence of weak or partial hydrogen bonds in carbohydrates, and that MD simulations of repeating units in PSs provide insight into overall PS structure and dynamics. Published 2011 Wiley Periodicals, Inc. Biopolymers 97: 145–154, 2012.     

Joint Functions of Protein Residues and NADP(H) in Oxygen Activation by Flavin-containing Monooxygenase

The reactivity of flavoenzymes with dioxygen is at the heart of a number of biochemical reactions with far reaching implications for cell physiology and pathology. Flavin-containing monooxygenases are an attractive model system to study flavin-mediated oxygenation. In these enzymes, the NADP(H) cofactor is essential for stabilizing the flavin intermediate, which activates dioxygen and makes it ready to react with the substrate undergoing oxygenation. Our studies combine site-directed mutagenesis with the usage of NADP⁺ analogues to dissect the specific roles of the cofactors and surrounding protein matrix. The highlight of this “double-engineering” approach is that subtle alterations in the hydrogen bonding and stereochemical environment can drastically alter the efficiency and outcome of the reaction with oxygen. This is illustrated by the seemingly marginal replacement of an Asn to Ser in the oxygen-reacting site, which inactivates the enzyme by effectively converting it into an oxidase. These data rationalize the effect of mutations that cause enzyme deficiency in patients affected by the fish odor syndrome. A crucial role of NADP⁺ in the oxygenation reaction is to shield the reacting flavin N5 atom by H-bond interactions. A Tyr residue functions as backdoor that stabilizes this crucial binding conformation of the nicotinamide cofactor. A general concept emerging from this analysis is that the two alternative pathways of flavoprotein-oxygen reactivity (oxidation versus monooxygenation) are predicted to have very similar activation barriers. The necessity of fine tuning the hydrogen-bonding, electrostatics, and accessibility of the flavin will represent a challenge for the design and development of oxidases and monoxygenases for biotechnological applications.     

Mechanism of metal-promoted catalysis of nucleic acid hydrolysis by Escherichia coli ribonuclease H

 Catalytic activation of Escherichia coli ribonuclease H by a series of inert chromium complexes [Cr(NH₃)_6-x(H₂O)_x]³⁺ (x = 0–6) that bear water and ammine ligands in well-defined geometries in the inner coordination shell has been examined. Such complexes are observed to function by transition state stabilization. The importance of hydrogen bonding and electrostatics to catalytic activation of this reaction were quantitatively evaluated. The availability of [Cr(NH₃)_6-x(H₂O)_x]³⁺ complexes of varying coordination geometry also affords a probe of the preferred structural arrangement for hydrogen-bonding interactions. Under the solution conditions employed, a facial array of bound water molecules is required to promote catalysis, as expected from comparison with the ligation of the enzyme-bound Mg²⁺–cofactor. These results exclude a structural role for the essential metal cofactor. Hydrogen bonding appears to be the dominant stabilizing interaction. In the absence of bound water ligands (for example, in the specific cases of Cr(NH₃)₆ ³⁺ and Co(NH₃)₆ ³⁺), hydrogen bond stabilization is precluded: however, catalysis is observed as a result of the increased positive charge on the complex. Apparently the trivalent charge offsets the poorer hydrogen bonding abilities of the ammine ligands. Received: 11 June 1996 / Accepted: 31 July 1996     

Structural Evidence for Inter-Residue Hydrogen Bonding Observed for Cellobiose in Aqueous Solution

The structure of the disaccharide cellulose subunit cellobiose (4-O-β-D-glucopyranosyl-D-glucose) in solution has been determined via neutron diffraction with isotopic substitution (NDIS), computer modeling and nuclear magnetic resonance (NMR) spectroscopic studies. This study shows direct evidence for an intramolecular hydrogen bond between the reducing ring HO3 hydroxyl group and the non-reducing ring oxygen (O5′) that has been previously predicted by computation and NMR analysis. Moreover, this work shows that hydrogen bonding to the non-reducing ring O5′ oxygen is shared between water and the HO3 hydroxyl group with an average of 50% occupancy by each hydrogen-bond donor. The glycosidic torsion angles φ_H and ψ_H from the neutron diffraction-based model show a fairly tight distribution of angles around approximately 22^° and −40^°, respectively, in solution, consistent with the NMR measurements. Similarly, the hydroxymethyl torsional angles for both reducing and non-reducing rings are broadly consistent with the NMR measurements in this study, as well as with those from previous measurements for cellobiose in solution.     

Studies on the synthesis of ether-, substituted alkyl-, or aryl-linked C-disaccharide derivatives

A series of ether-, substituted alkyl-, or aryl-linked disaccharide derivatives have been synthesized in relatively good yield and characterized using different spectral techniques including single-crystal X-ray diffraction (XRD). β-Anomeric forms of sugar moiety in these derivatives were identified from ¹H NMR studies. The existence of inter- and intramolecular hydrogen bonding interactions were identified from single-crystal XRD studies.     

Syntheses and characterizations of four mixed-ligand hydrogen bonding supramolecular architectures with different structural motifs

The reactions of 4-aminobenzoic acid (4-abaH), 4,4′-bipyridine (4,4′-bipy) and transitional metal ions (Zn^II, Mn^II and Cu^II) gave rise to four supramolecular architectures, namely, [(4-abaH)₂(4,4′-bipy)] (1), {[Zn₂(4,4′-bipy)₂(4-aba)₄] (H₂O)₅}_n (2), {[Mn(4,4′-bipy)₂(H₂O)₄] (4-aba)Br(H₂O)₃} (3) and {[Cu₂(4,4′-bipy)₃(H₂O)₂(4-aba)₂](NO₃)₂(H₂O)₄}_n (4). Their crystal structures were determined by X-ray diffraction and show different structural motifs. 1 is a one-dimensional hydrogen bonding ladder constructed by 4-abaH and 4,4′-bipy. In 2, 4,4′-bipy bridges Zn(4-aba)₂ units forming a one-dimensional zigzag chain, which is extended into a three-dimensional framework by crystalline water molecules through hydrogen bonding interactions. Three-dimensional network of 3 is constructed by mononuclear [Mn(4,4′-bipy)₂(H₂O)₄]²⁺ cations, neutral crystalline water molecules, and 4-aba and Br⁻ anions through extensive hydrogen bonding and π-π interactions. However, one-dimensional ladder formed by 4,4′-bipy and Cu(4-aba) units in 4 is extended into a three-dimensional architecture through interpenetration of the lateral 4-aba arms into squares of the adjacent Cu-(4,4′-bipy) ladders and extensive hydrogen bonding interactions.     

π-Facial hydrogen bonding in the chiral resolving agent 2,2,2-trifluoro-1-(9-anthryl)-ethanol and its racemic modification

2,2,2-Trifluoro-(9-anthryl)-ethanol (TFAE) has been extensively used, in its pure enantiomeric forms, as a chiral solvating agent in nuclear magnetic resonance spectroscopy (NMR). It has also played an important role in the development of chiral stationary phases in liquid chromatography (LC). X-ray crystallography of the enantiomeric and racemic crystals shows, in both cases, the formation of an intermolecular hydrogen bond between the O? H and the π-face of one of the rings of the anthracene aromatic system.¹ Few examples of such hydrogen bonding have been published previously, and those that have are not as clear cut as in this case. An explanation for the hydrogen bonding is sought using molecular modelling via the PM3 analytically derived molecular electrostatic potentials. Using NMR and dynamic lineshape analysis, the barrier to rotation about the aryl-carbon bond is estimated, indicating the C? CF₃ bond to be perpendicular to the anthracene axis in nonpolar solution. This conformation is identical to the conformation in the crystal. Evidence is also presented to support the formation of intermolecular π-facial hydrogen bonding in TFAE solutions. It is thought that such hydrogen bonding may be implicated in chiral recognition using this compound. © 1994 Wiley-Liss, Inc.     

The effects of reversible freezing inactivation and inhibitor binding on redox properties of l-amino-acid oxidase

We measured the redox potentials of frozen inactivated l-amino-acid oxidase (l-amino-acid:oxygen oxidoreductase (deaminating), EC 1.4.3.2) and inhibitor-bound (anthranilic acid) enzyme, and compared these redox properties to those of active l-amino-acid oxidase and benzoate-bound d-amino-acid oxidase (EC 1.4.3.3), respectively. The redox properties of the inactive enzyme are similar to the properties of free flavin; the potential is within 0.015 V of free flavin and no radical stabilization is seen. This corresponds to the loss of most interactions between apoprotein and flavin. In contrast, the anthranilic acid lowers the amount of radical stabilized from 85% to 35%. The potentials are still 0.150 V positive of free flavin, indicating that in the presence of inhibitor, many flavin-protein interactions remain intact. The difference between this behavior and that of d-amino-acid oxidase bound to benzoate, where the amount of radical declined from 95% to 5%, is explained on the basis of the relative tightness of binding of apoprotein to FAD. d-Amino-acid oxidase apoprotein has a relatively low K_a (10⁶) for FAD, and benzoate has a relatively high K_a (10⁵) for the enzyme. Therefore, the binding of benzoate increases the tightness of FAD binding to apo-d-amino-acid oxidase (10¹¹), indicating significant changes in flavin-protein interactions. In contrast, apo-l-amino-acid oxidase binds flavin tightly (the K_a is greater than 10⁷) and the enzyme binds to anthranilate much less tightly, with a K_a of 10³. The l-amino-acid oxidase apoprotein binding to FAD is tight initially, and the binding of anthranilate changes it only slightly. Therefore, redox studies indicate that the ability of a flavoprotein to be regulated may be influenced by the strength of the interaction of flavin with the apoprotein, as well as the strength of interaction of the substrate or activator.     

77Se Enrichment of Proteins Expands the Biological NMR Toolbox

Sulfur, a key contributor to biological reactivity, is not amendable to investigations by biological NMR spectroscopy. To utilize selenium as a surrogate, we have developed a generally applicable ⁷⁷Se isotopic enrichment method for heterologous proteins expressed in Escherichia coli. We demonstrate ⁷⁷Se NMR spectroscopy of multiple selenocysteine and selenomethionine residues in the sulfhydryl oxidase augmenter of liver regeneration (ALR). The resonances of the active-site residues were assigned by comparing the NMR spectra of ALR bound to oxidized and reduced flavin adenine dinucleotide. An additional resonance appears only in the presence of the reducing agent and disappears readily upon exposure to air and subsequent reoxidation of the flavin. Hence, ⁷⁷Se NMR spectroscopy can be used to report the local electronic environment of reactive and structural sulfur sites, as well as changes taking place in those locations during catalysis.     

Use of amide 1H-nmr titration shifts for studies of polypeptide conformation

This paper shows that backbone amide proton titration shifts in polypeptide chains are a very sensitive manifestation of intramolecular hydrogen bonding between carboxylate groups and backbone amide protons. The population of specific hydrogen-bonded structures in the ensemble of species that constitutes the conformation of a flexible nonglobular linear peptide can be determined from the extent of the titration shifts. As an illustration, an investigation of the molecular conformation of the linear peptide H-Gly-Gly-L -Glu-L -Ala-OH is described. The proposed use of amide proton titration shifts for investigating polypeptide conformation is based on 360-MHz ¹H-nmr studies of selected linear oligopeptides in H₂O solutions. It was found that only a very limited number of amide protons in a polypeptide chain show sizable intrinsic intration shifts arising from through-bond interactions with ionizable groups. These are the amide proton of the C-terminal amino acid residue, the amide protons of Asp and the residues following Asp, and possibly the amide proton of the residue next to the N-terminus. Since the intrinsic titration shifts are upfield, the downfield titration shifts arising from conformation-dependent through-space interactions, in particular hydrogen bonding between the amide protons and carboxylate groups, can readily be identified.     

The competition of C-X⋯O=P halogen bond and π-hole⋯O=P bond between halopentafluorobenzenes C6F5X (X=F, Cl, Br, I) and triethylphosphine oxide

Calculation predicted the interacting forms of halopentafluorobenzene C₆F₅X (X=F, Cl, Br, I) with triethylphosphine oxide which is biologically interested and easily detected by ³¹P NMR. The interaction energy and geometric parameters of resultant halogen or π-hole bonding complexes were estimated and compared. Moreover, the bonding constants were determined by ³¹P NMR. Both theory and experiments indicated the C₆F₆ and C₆F₅Cl interact with triethylphosphine oxide by π-hole bonding pattern, while C₆F₅I by halogen/σ-hole bonding form. For C₆F₅Br, two interactions are comparative and should coexist competitively. The calculated interaction energies of σ-hole bonding complexes, ?5.07 kcal mol^?1 for C₆F₅Br?O=P and ?8.25 kcal mol^?1 for C₆F₅I?O=P, and π-hole bonding complexes, ?7.29 kcal mol^?1 for C₆F₆?O=P and ?7.24 kcal mol^?1 for C₆F₅Cl?O=P, are consistent with the changing tendency of bonding constants measured by ³¹P NMR, 4.37, 19.7, 2.42 and 2.23 M^?1, respectively.