Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site

The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.     

Lipid binding to the carotenoid binding site in photosynthetic reaction centers

Lipid binding to the carotenoid binding site near the inactive bacteriochlorophyll monomer was probed in the reaction centers of carotenoid-less mutant, R-26 from Rhodobacter sphaeroides. Recently, a marked light-induced change of the local dielectric constant in the vicinity of the inactive bacteriochlorophyll monomer was reported in wild type that was attributed to structural changes that ultimately lengthened the lifetime of the charge-separated state by 3 orders of magnitude (Deshmukh, S. S.; Williams, J. C.; Allen, J. P.; Kalman, L. Biochemistry 2011, 50, 340). Here in the R-26 reaction centers, the combination of light-induced structural changes and lipid binding resulted in a 5 orders of magnitude increase in the lifetime of the charge-separated state involving the oxidized dimer and the reduced primary quinone in proteoliposomes. Only saturated phospholipids with fatty acid chains of 12 and 14 carbon atoms long were bound successfully at 8 °C by cooling the reaction center protein slowly from room temperature. In addition to reporting a dramatic increase of the lifetime of the charge-separated state at physiologically relevant temperatures, this study reveals a novel lipid binding site in photosynthetic reaction center. These results shed light on a new potential application of the reaction center in energy storage as a light-driven biocapacitor since the charges separated by ～30 ? in a low-dielectric medium can be prevented from recombination for hours.     

Design of novel antibiotics that bind to the ribosomal acyltransfer site

The structure of neamine bound to the A site of the bacterial ribosomal RNA was used in the design of novel aminoglycosides. The design took into account stereo and electronic contributions to interactions between RNA and aminoglycosides, as well as a random search of 273 000 compounds from the Cambridge structural database and the National Cancer Institute 3-D database that would fit in the ribosomal aminoglycoside-binding pocket. A total of seven compounds were designed and subsequently synthesized, with the expectation that they would bind to the A-site RNA. Indeed, all synthetic compounds were found to bind to the target RNA comparably to the parent antibiotic neamine, with dissociation constants in the lower micromolar range. The synthetic compounds were evaluated for antibacterial activity against a set of important pathogenic bacteria. These designer antibiotics showed considerably enhanced antibacterial activities against these pathogens, including organisms that hyperexpressed resistance enzymes to aminoglycosides. Furthermore, analyses of four of the synthetic compounds with two important purified resistance enzymes for aminoglycosides indicated that the compounds were very poor substrates; hence the activity of these synthetic antibiotics does not appear to be compromised by the existing resistance mechanisms, as supported by both in vivo and in vitro experiments. The design principles disclosed herein hold the promise of the generation of a large series of designer antibiotics uncompromised by the existing mechanisms of resistance.     

EPR study of substrate binding to the Mn(II) active site of the bacterial antibiotic resistance enzyme FosA: a better way to examine Mn(II)

FosA is a manganese metalloglutathione transferase that confers resistance to the broad-spectrum antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid. The reaction catalyzed by FosA involves the attack by glutathione on fosfomycin to yield the product 1-(S-glutathionyl)-2-hydroxypropylphosphonic acid. The enzyme is a dimer of 16 kDa subunits, each of which harbors one mononuclear Mn(II) site. The coordination environment of the Mn(II) in the FosA x Mn(2+) complex is composed of a glutamate and two histidine ligands and three water molecules. Here we report EPR spectroscopic studies on FosA, in which EPR spectra were obtained at 35 GHz and 2 K using dispersion-detection rapid-passage techniques. This approach provides an absorption envelope line shape, in contrast to the conventional (slow-passage) derivative line shape, and is a more reliable way to collect spectra from Mn(II) centers with large zero-field splitting. We obtain excellent spectra of FosA bound with substrate, substrate analogue phosphate ion, and product, whereas these states cannot be studied by X-band, slow-passage methods. Simulation of the EPR spectra shows that binding of substrate or analogue causes a profound change in the electronic parameters of the Mn(II) ion. The axial zero-field splitting changes from [D] = 0.06 cm(-1) for substrate-free enzyme to 0.23 cm(-1) for fosfomycin-bound enzyme, 0.28 (1) cm(-1) for FosA with phosphate, and 0.27 (1) cm(-1) with product. Such a large zero-field splitting is uncommon for Mn(II). A simple ligand field analysis of this change indicates that binding of the phosphonate/phosphate group of substrate or analogue changes the electronic energy levels of the Mn(II) 3d orbitals by several thousand cm(-1), indicative of a significant change in the Mn(II) coordination sphere. Comparison with related enzymes (glyoxalase I and MnSOD) suggests that the change in the coordination environment on substrate binding may correspond to loss of the glutamate ligand.     

Investigation on the binding site in heparin by spectrophotometry

Heparin has a variety of biological activities, most of them due to heparin’s high sulfate groups. To gain insight into the mechanism of activation of the spectroscopic probe with sulfate groups of heparin in vitro, we have used a cationic dye by a spectrophotometric method. It is considered that the combination of heparin with methylene blue is due to noncovalent binding forces. Dye binding requires an organic chain structure form with sulfate groups. The solution equilibria of the reaction system are discussed. A new linear regression equation has been proposed, in which the maximum binding number N expresses the binding ability of methylene blue (MB) with sulfate groups of heparin. The linear regression equation can estimate this parameter.     

The auxiliary determination of the binding site of berberine binding to human serum albumin by surface-enhanced Raman scattering

We report on the joint application of fluorescence, ultraviolet-visible (UV-Vis) and Raman spectroscopy to the study of berberine with human serum albumin (HSA). We propose the surface-enhanced Raman scattering (SERS) technique to improve the understanding of the quenching interaction caused by berberine which could be applied in recognition process of fluorescent drugs with large biomolecules. The fluorescence and UV-Vis spectroscopic results show that the fluorescence intensity of HSA is significantly decreased in the presence of berberine, and the quenching mechanism is static. The SERS technique demonstrates clear advantages over direct measurements in physiological conditions. By means of this method, we are able to deduce important information concerning the binding property of berberine when interacting with HSA. We show the nitrogen atom is free but the dioxolane is involved in the spontaneously electrostatic inducement and subsequently hydrophobic binding.     

Elucidating the site of protein-ATP binding by top-down mass spectrometry

A Fourier-transform ion cyclotron resonance (FT-ICR) top-down mass spectrometry strategy for determining the adenosine triphosphate (ATP)-binding site on chicken adenylate kinase is described. Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS), but the ability to detect protein-ligand complexes depends on their stability in the gas phase. Previously, we showed that collisionally activated dissociation (CAD) of protein-nucleotide triphosphate complexes yield products from the dissociation of a covalent phosphate bond of the nucleotide with subsequent release of the nucleotide monophosphate (Yin, S. et al., J. Am. Soc. Mass Spectrom. 2008, 19, 1199–1208). The intrinsic stability of electrostatic interactions in the gas phase allows the diphosphate group to remain noncovalently bound to the protein. This feature is exploited to yield positional information on the site of ATP-binding on adenylate kinase. CAD and electron capture dissociation (ECD) of the adenylate kinase-ATP complex generate product ions bearing monoand diphosphate groups from regions previously suggested as the ATP-binding pocket by NMR and crystallographic techniques. Top-down MS may be a viable tool to determine the ATP-binding sites on protein kinases and identify previously unknown protein kinases in a functional proteomics study.     

Ramoplanin inhibits bacterial transglycosylases by binding as a dimer to lipid II

Ramoplanin is a lipglycodepsipeptide antibiotic that inhibits peptidoglycan biosynthesis. Its mechanism of action has been the subject of debate. It was originally proposed to inhibit the MurG step of peptidoglycan synthesis by binding Lipid I. In this paper, we report that ramoplanin inhibits bacterial transglycosylases by binding to Lipid II, the substrate for these enzymes. The inhibition curves reveal that the inhibitory species has a stoichiometry of 2:1 ramoplanin:Lipid II. A Job titration confirms that ramoplanin binds as a dimer to Lipid II. The apparent dissociation constant is in the nanomolar range, which is unusually low given the nature of the interacting species. We show that Lipid II binding is coupled to the formation of a higher order species, which may explain the tight binding. We also present a testable model for the binding-competent dimeric conformation of ramoplanin.     

Probing the acceptor substrate binding site of Trypanosoma cruzi trans-sialidase with systematically modified substrates and glycoside libraries

Systematically modified octyl galactosides and octyl N-acetyllactosamines were assessed as inhibitors of, and substrates for, T. cruzi trans-sialidase (TcTS) in the context of exploring its acceptor substrate binding site. These studies show that TcTS, which catalyses the α-(2→3)-sialylation of non-reducing terminal β-galactose residues, is largely intolerant of substitution of the galactose 2 and 4 positions whereas substitution of the galactose 6 position is well tolerated. Further studies show that even the addition of a bulky sugar residue (glucose, galactose) does not impact negatively on TcTS binding and turnover, which highlights the potential of 'internal' 6-substituted galactose residues to serve as TcTS acceptor substrates. Results from screening a 93-membered thiogalactoside library highlight a number of structural features (notably imidazoles and indoles) that are worthy of further investigation in the context of TcTS inhibitor development.     

Nature of halide binding to the molybdenum site of sulfite oxidase

Valuable information on the active sites of molybdenum enzymes has been provided from both Mo(V) electron paramagnetic resonance (EPR) spectroscopy and X-ray absorption spectroscopy (XAS). One of three major categories of Mo(V) EPR signals from the molybdenum enzyme sulfite oxidase is the low-pH signal, which forms in the presence of chloride. Two alternative structures for this species have been proposed, one in which the chloride is coordinated directly to Mo and a second in which chloride is held in the arginine-rich basic pocket some 5 ? from Mo. Here we present an independent assessment of the structure of this species by using XAS of the analogous bromide and iodide complexes. We show that there is no evidence of direct Mo-I coordination, and that the data are consistent with a structure in which the halide is bound at ～5 ? from Mo.     

Mapping the binding site of thiopeptide antibiotics by proximity-induced covalent capture

Proximity-induced covalent capture (PICC) has been established for the investigation of ligand binding to composite protein/oligonucleotide target complexes. The RNA-induced attachment of the thiopeptides Thiostrepton and Nosiheptide to engineered Cys mutants of the ribosomal protein L11 was highly position selective and allowed mapping of their binding site at amino acid resolution.     

Determination of binding site concentration and average binding constant by the method of equilibrium sorption: Evidence for lysine as a principal receptor site for collagen-enzyme binding

The contribution of lysyl ϵ-amino groups to the noncovalent binding on enzymes to collagen has been determined by the method of equilibrium sorption. The sorption or binding of enzyme by chemically modified, and by the corresponding unmodified membraneous collagen, was determined as a function of enzyme concentration. Chemical modification of lysyl ϵ-amino groups was accomplished by carbamylation of the collagen membrane with potassium cyanate. The collagen membranes were contacted with a purified β-galactosidase (E. coli K₁₂). The enzyme was purified by affinity chromato- graphy. Analysis of the resultant sorption isotherms allowed determination of the heterogeneity index (a) and the concentration of active binding sites (A_o). Binding constants (K_o) and the free energy of binding (δG) were also computed from the sorption data.The results of these studies have shown that lysyl ϵ-amino groups of collagen are primary receptor sites for enzyme binding (β-galactosidase, E. coli K₁₂) and that carbamylation of the collagen membrane resulted in a decrease in active binding sites with little or no change in the binding constant of the remaining sites.     

Enzyme electrodes with improved mechanical and analytical characteristics obtained by binding enzymes to nylon nets

Enzyme electrodes obtained by binding enzymes on nylon net show improved mechanical and analytical characteristics. The chemical binding process is mild so that the final membrane retains a high enzyme activity. The resulting membrane also has high mechanical strength and can be assembled on the electrode surface several times without damage. Response times without nylon net are excellent. Examples with single and dual enzymes coupled with an oxygen or ammonia electrode are discussed.     

19F NMR in the measurement of binding affinities of chloroeremomycin to model bacterial cell-wall surfaces that mimic VanA and VanB resistance

Background: The emergence of bacteria that are resistant to vancomycin, the drug of choice against methicillin-resistant Staphylococcus aureus, has made the study of the binding characteristics of glycopeptides to biologically relevant depsipeptides important. These depsipeptides, terminating in -d-alanyl-d-lactate, mimic the cell-wall precursors of resistant bacteria.Results: The use of ¹⁹F-labelled ligands in the study of the therapeutically important vancomycin series of antibiotics is demonstrated. The substantial simplification of spectra that occurs when such labelled ligands are employed is used in the measurement of binding affinities of depsipeptides to chloroeremomycin (CE). Large enhancements of binding affinities are found at a model bacterial cell-wall surface (constituted from depsipetides that are anchored into vesicles) relative to those measured in free solution.Conclusions: Surface-enhanced binding, previously shown for strongly dimerising glycopeptide antibiotics to normal -d-alanyl-d-alanine-terminating cell-wall precursors, is now demonstrated for CE to the surface of models of VanA- and VanB-resistant bacteria. The effect of depsipeptide chain length is shown to be critically important in producing and maximising this enhancement.     

Theoretical studies on substrate binding to the active site of carbonic anhydrase

The role of some amino acids and metal ions in the catalytic activity of carbonic anhydrase (carbonate dehydratase EC 4.2.1.1) has been investigated. The additional stabilization of the transition state complex was used as the qualitative measure of the effect of molecular surrounding on CO₂ hydration reaction calculated within the approximate CNDO /2 approach. The effect of the molecular environment has been simulated by inclusion into the SCF LCAO MO Hamiltonian, a term representing the interaction with a set of point charges and atomic dipoles centered on experimentally determined position of Zn²⁺ ion and all atoms of histidine 94, 96, 119 and threonine 199, 200 (or histidine 200 in the case of carbonic anhydrase B). The possible molecular mechanism of CO₂ hydration inside the active site has been also discussed.     

Photo-affinity labeling strategy to study the binding site of G protein-coupled receptors

G protein-coupled receptors (GPCRs) are involved in the control of every aspect of our behavior and physiology. GPCR can be involved in pathological processes as well and are linked to numerous diseases, including cardiovascular and mental disorders, retinal degeneration, cancer, and AIDS. This article reviews the methods of approaching photo-affinity labeling strategy to obtain the possible G protein-coupled receptors’s binding site.