Oligomerizations of deoxyadenosine bis-phosphates and of their 3′-5′, 3′-3′, and 5′-5′ dimers: Effects of a pyrophosphate-linked,poly(t) analog

A pyrophosphate-linked polynucleotide analog based on thymidine 3,5 bis-phosphate (pTp) catalyzes the oligomerization of activated dimers of pdAp in the presence of MgCl₂. Although no catalysis of the oligomerization of the activated monomer (ImpdAplm) was observed in the presence of MgCl₂, there was a significant stimulation of oligomerization by the template in the presence of MnCl₂.     

Characterization of glyoxalase I (E. coli)-inhibitor interactions by electrospray time-of-flight mass spectrometry and enzyme kinetic analysis

Potential inhibitors of the enzyme glyoxalase I from Escherichia coli have been evaluated using a combination of electrospray mass spectrometry and conventional kinetic analysis. An 11-membered library of potential inhibitors included a glutathione analogue resembling the transition-state intermediate in the glyoxalase I catalysis, several alkyl-glutathione, and one flavonoid. The E. coli glyoxalase I quaternary structure was found to be predominantly dimeric, as is the homologous human glyoxalase I. Binding studies by electrospray revealed that inhibitors bind exclusively to the dimeric form of glyoxalase I. Two specific binding sites were observed per dimer. The transition-state analogue was found to have the highest binding affinity, followed by a newly identified inhibitor; S-{2-[3-hexyloxybenzoyl]-vinyl}glutathione. Kinetic analysis confirmed that the order of affinity established by mass spectrometry could be correlated to inhibitory effects on the enzymatic reaction. This study shows that selective inhibitors may exist for the E. coli homologue of the glyoxalase I enzyme.     

Amyloid oligomer formation probed by water proton magnetic resonance spectroscopy

Formation of amyloid oligomers, the most toxic species of amyloids in degenerative diseases, is critically coupled to the interplay with surrounding water. The hydrophobic force driving the oligomerization causes water removal from interfaces, changing the surface-hydration properties. Here, we show that such effects alter the magnetic relaxation response of local water in ways that may enable oligomer detection. By using water proton magnetic resonance spectroscopy, we measured significantly longer transverse magnetic relaxation (T₂) times in mixtures of serum and amyloidogenic Aβ_1-42 peptides versus similar concentration solutions of serum and nonamyloidogenic scrambled Aβ_42-1 peptides. Immunochemistry with oligomer-specific antibodies, electron microscopy and computer simulations demonstrated that the hyperintense magnetic signal correlates with Aβ_1-42 oligomerization. Finding early biophysical markers of the oligomerization process is crucial for guiding the development of new noninvasive imaging techniques, enabling timely diagnosis of amyloid-related diseases and pharmacological intervention.     

Interfacial amino acids support Spa47 oligomerization and shigella type three secretion system activation

Like many Gram-negative pathogens, Shigella rely on a type three secretion system (T3SS) for injection of effector proteins directly into eukaryotic host cells to initiate and sustain infection. Protein secretion through the needle-like type three secretion apparatus (T3SA) requires ATP hydrolysis by the T3SS ATPase Spa47, making it a likely target for in vivo regulation of T3SS activity and an attractive target for small molecule therapeutics against shigellosis. Here, we developed a model of an activated Spa47 homo-hexamer, identifying two distinct regions at each protomer interface that we hypothesized to provide intermolecular interactions supporting Spa47 oligomerization and enzymatic activation. Mutational analysis and a series of high-resolution crystal structures confirm the importance of these residues, as many of the engineered mutants are unable to form oligomers and efficiently hydrolyze ATP in vitro. Furthermore, in vivo evaluation of Shigella virulence phenotype uncovered a strong correlation between T3SS effector protein secretion, host cell membrane disruption, and cellular invasion by the tested mutant strains, suggesting that perturbation of the identified interfacial residues/interactions influences Spa47 activity through preventing oligomer formation, which in turn regulates Shigella virulence. The most impactful mutations are observed within the conserved Site 2 interface where the native residues support oligomerization and likely contribute to a complex hydrogen bonding network that organizes the active site and supports catalysis. The critical reliance on these conserved residues suggests that aspects of T3SS regulation may also be conserved, providing promise for the development of a cross-species therapeutic that broadly targets T3SS ATPase oligomerization and activation.     

Opsin Oligomerization in a Heterologous Cell System

Using bioluminescence resonance energy transfer (BRET) we studied opsin oligomerization in heterologous expression systems and quantitatively assessed its oligomerization state. BRET² saturation and competition experiments were performed with live COS-7 cells expressing Rluc-and GFP²-tagged receptor constructs. BRET² saturation curves obtained were hyperbolic, and the calculated oligomerization state (N = 1 for dimers) suggested that opsin (N = 1.34 ± 0.25) forms higher oligomers. Very high BRET² values obtained for the opsin homo-dimer pair indicated a large energy transfer efficiency (E) and for cases where E ? 0.1 a modified saturation curve was proposed. The existence of homo-dimer complexes was additionally supported by competition assay results and was also observed in HEK-293 cells. Furthermore, evidence was provided for homo-and hetero-dimerization of family A (β₂-adrenergic) and B (gastric inhibitory polypeptide, GIP) receptors. In summary, these experiments demonstrate homo-and hetero-dimerization for opsin, β ₂-adrenergic, and GIP receptors.     

At low water activity α-chymotrypsin is more active in an ionic liquid than in non-ionic organic solvents

The kinetics of the -chymotrypsin catalysed transesterification of N-acetyl-l-phenylalanine ethyl ester with 1-butanol and the competing hydrolysis were evaluated at fixed water activity in two ionic liquids and two non-ionic organic solvents. In most respects the four solvents behaved similarly. However, at a water activity of 0.33, higher catalytic activity was observed in the ionic liquid, 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]amide, than in the other solvents, and at a_w=0.11 catalysis was only observed in this solvent.     

Modifications of amino acids during ferulic acid-mediated,laccase-catalysed cross-linking of peptides

Abstract

Mass spectral analysis demonstrated oligomerization of peptides that had been subjected to oxidation catalysed by Trametes (Coriolus) versicolor laccase. Peptide oligomerization occurred only when cysteines or tyrosines were present in the peptides. MS/MS confirmed the cross-linking in tyrosine-containing peptides to be located between tyrosine residues. Ferulic acid mediated oligomerization of cysteine-containing peptides, but prevented cross-linking of tyrosines when used in the same concentration as the peptides. This suggests an antioxidative effect of ferulic acid in relation to tyrosine oxidation, although incorporation of ferulic acid into peptide oligomers was found in some of the tyrosine-containing peptides. No other modifications to amino acid residues by laccase-catalysed oxidation were observed by mass spectroscopy. Thus, it is suggested that oxidative modifications of other amino acids observed in proteins oxidized by laccase are not major reaction products of laccase-catalysed oxidation.     

Physiological relevance of plant 2‐Cys peroxiredoxin overoxidation level and oligomerization status

Peroxiredoxins are ubiquitous thioredoxin‐dependent peroxidases presumed to display, upon environmental constraints, a chaperone function resulting from a redox‐dependent conformational switch. In this work, using biochemical and genetic approaches, we aimed to unravel the factors regulating the redox status and the conformation of the plastidial 2‐Cys peroxiredoxin (2‐Cys PRX) in plants. In Arabidopsis, we show that in optimal growth conditions, the overoxidation level mainly depends on the availability of thioredoxin‐related electron donors, but not on sulfiredoxin, the enzyme reducing the 2‐Cys PRX overoxidized form. We also observed that upon various physiological temperature, osmotic and light stress conditions, the overoxidation level and oligomerization status of 2‐Cys PRX can moderately vary depending on the constraint type. Further, no major change was noticed regarding protein conformation in water‐stressed Arabidopsis, barley and potato plants, whereas species‐dependent up‐ and down‐variations in overoxidation were observed. In contrast, both 2‐Cys PRX overoxidation and oligomerization were strongly induced during a severe oxidative stress generated by methyl viologen. From these data, revealing that the oligomerization status of plant 2‐Cys PRX does not exhibit important variation and is not tightly linked to the protein redox status upon physiologically relevant environmental constraints, the possible in planta functions of 2‐Cys PRX are discussed.     

Mineral Catalysis of a Potentially Prebiotic Aldol Condensation

Minerals may have played a significant role in chemical evolution. In the course of investigating the chemistry of phosphonoacetaldehyde (PAL), an analogue of glycolaldehyde phosphate, we have observed a striking case of catalysis by the layered hydroxide mineral hydrotalcite ([Mg₂Al(OH)₆][Cl.nH₂O]). In neutral or moderately basic aqueous solutions, PAL is unreactive even at a concentration of 0.1 M. In the presence of a large excess of NaOH (2 M), the compound undergoes aldol condensation to produce a dimer containing a C3–C4 double-bond. In dilute neutral solutions and in the presence of the mineral, however, condensation takes place rapidly, to produce a dimer which is almost exclusively the C2–C3 unsaturated product. Received: 11 February 1998 / Accepted: 12 May 1998     

The Use of Salt Hydrates as Water buffers To Control Enzyme Activity in Organic Solvents

The conversion of o-diphenols to o-quinones was carried out in chloroform using a dry powder prepared from mushrooms as the catalyst. Several salt hydrates proved effective in supplying the small amount of water necessary for catalysis. The efficacy of the hydrates was related to their water activities and their use provided a convenient method for controlling water activity in nearly non-aqueous conditions.     

Synthesis and bioorthogonal coupling chemistry of a novel cyclopentenone-containing unnatural tyrosine analogue

Herein we report the synthesis of a novel amino acid with orthogonal functionality to the natural amino acid side chains. Tyrosine was O-alkylated with a cyclic 5-membered α,β-unsaturated ketone ring (5). We have established that this amino acid analogue can undergo cycloaddition reactions in aqueous media with in situ generated nitrones. Nitrone formation occurred by micellar catalysis can undergo aqueous 1,3-dipolar cycloaddition reactions with the unnatural Tyr. We also performed a linear free energy analysis of the one pot bioconjugation reaction in water using cyclopentenone as a model for the Tyr analogue and seven different aryl nitrones. We found that the Hammett ρ value was −0.94, suggesting that the reaction occurs in a concerted fashion with a slight positive charge buildup in the transition state. The Hammett ρ value also suggests that the bioconjugation reaction is tolerant of different substituents and thus may be useful for introducing novel functionality into peptides and proteins containing the Tyr analogue 5. The aqueous 1,3-dipolar cycloaddition reactions, that use nitrones to trap the O-alkylated Tyr 5, establish a novel strategy for rapid, water compatible bioconjugation reactions.     

Microsecond simulations indicate that ethanol binds between subunits and could stabilize an open-state model of a glycine receptor

Distinct lipid environments, including lipid rafts, are increasingly recognized as a crucial factor affecting membrane protein function in plasma membranes. Unfortunately, an understanding of their role in membrane protein activation and oligomerization has remained elusive due to the challenge of characterizing these often small and transient plasma membrane heterogeneities in live cells. To address this difficulty, we present an experimental model membrane platform based on polymer-supported lipid bilayers containing stable raft-mimicking domains (type I) and homogeneous cholesterol-lipid mixtures (type II) into which transmembrane proteins are incorporated (α_vβ₃ and α₅β₁ integrins). These flexible lipid platforms enable the use of confocal fluorescence spectroscopy, including the photon counting histogram method, in tandem with epifluorescence microscopy to quantitatively probe the effect of the binding of native ligands from the extracellular matrix ligands (vitronectin and fibronectin for α_vβ₃ and α₅β₁, respectively) on domain-specific protein sequestration and on protein oligomerization state. We found that both α_vβ₃ and α₅β₁ sequester preferentially to nonraft domains in the absence of extracellular matrix ligands, but upon ligand addition, α_vβ₃ sequesters strongly into raft-like domains and α₅β₁ loses preference for either raft-like or nonraft-like domains. A corresponding photon counting histogram analysis showed that integrins exist predominantly in a monomeric state. No change was detected in oligomerization state upon ligand binding in either type I or type II bilayers, but a moderate increase in oligomerization state was observed for increasing concentrations of cholesterol. The combined findings suggest a mechanism in which changes in integrin sequestering are caused by ligand-induced changes in integrin conformation and/or dynamics that affect integrin-lipid interactions without altering the integrin oligomerization state.     

Metal-ion-catalyzed hydrolysis of monomethyl and dimethyl esters of 3-(2-imidazoleazo)phthalic acid: Bifunctional catalysis by carboxyl group and the metal ion in the hydrolysis of an alkyl ester

The Cu(II) or Ni(II) ion-catalyzed hydrolysis of methyl 2-carboxy-6-(2-imidazoleazo)benzoate (1) and the corresponding dimethyl ester (2) was studied kinetically at various pH values. For 2, the ester group located at the o position to the azo substiuent was hydrolyzed. From the rate data obtained at various metal concentrations, the values of k_cat and K_f were estimated at each pH value. For the Ni(II)-catalyzed hydrolysis of 1 at pH < 4, k_cat increases as pH is lowered, indicating bifunctional catalysis by the carboxyl group and the metal ion. For most of the reactions investigated under other conditions, the ester hydrolysis was subjected to sole catalysis by the metal ions. Detailed analysis of kinetic data obtained for these reactions indicated that the metal-ion catalysis involves the rate-determining breakdown of the tetrahedral intermediates formed by the addition of a water molecule or hydroxide ion. The bifunctional catalysis by the carboxyl group and Ni(II) ion can be considered as a model for carboxypeptidase A. The kinetic data indicate that the bifunctional catalysis proceeds through the nucleophilic attack of the carboxylate ion at the Ni(II)-coordinated carbonyl group.     

Salvianolic acid B inhibits the amyloid formation of human islet amyloid polypeptideand protects pancreatic beta‐cells against cytotoxicity

The misfolding of human islet amyloid polypeptide (hIAPP) is regarded as one of the causative factors of type 2 diabetes mellitus (T2DM). Salvia miltiorrhiza (Danshen), one of the most commonly used of traditional Chinese medicines, is often used in Compound Recipes for treating diabetes, however with unclear mechanisms. Since salvianolic acid B (SalB) is the most abundant bioactive ingredient of salvia miltiorrhiza water‐extract. In this study, we tested whether SalB has any effect on the amyloidogenicity of hIAPP. Our results clearly suggest that SalB can significantly inhibit the formation of hIAPP amyloid and disaggregate hIAPP fibrils. Furthermore, photo‐crosslinking based oligomerization studies suggest SalB significantly suppresses the toxic oligomerization of hIAPP monomers. Cytotoxicity protection effects on pancreatic INS‐1 cells by SalB were also observed using MTT‐based assays, potentially due to the inhibition on the membrane disruption effects and attenuated mitochondria impairment induced by hIAPP. These results provide evidence that SalB may further be studied on the possible pharmacological treatment for T2DM. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Substrate stabilization and noncompetitive inhibition effects of a water-miscible ionic liquid [BMPy][BF<Subscript>4</Subscript>] in the catalysis of horseradish peroxidase

The inhibition mechanism of a water-miscible ionic liquid, N-butyl-3-methypyridinium tetrafluoroborate ([BMPy][BF₄]), on the catalysis of horseradish peroxidase (HRP) was investigated. The K _m value for the oxidation of guaiacol (2-methoxyphenol) with H₂O₂ catalyzed by HRP increased from 2.8 mM in 100% water to 12.6 mM in 25% (v/v) [BMPy][BF₄]. This increase of K _m by the ionic liquid was elucidated to be caused by the strong stabilization of the ground state of guaiacol by the ionic liquid. On the contrary, the k _cat value for the HRP-catalyzed reaction decreased from 13.8/sec in 100% water to 6.7/sec in 25% (v/v) [BMPy][BF₄]. Such decrease of k _cat value of HRP catalysis by the increasing content of [BMPy][BF₄] was described using the noncompetitive inhibition of the enzyme by the ionic liquid. The value of the inhibition constant of [BMPy][BF₄] was 1.48 M indicating that the ionic liquid exerts a weak noncompetitive inhibition effect on the HRP catalysis.     

1H-nmr studies of the 20-31 fragment of calmodulin and of its cyclic analogue

High-resolution ¹H-nmr spectroscopy at 500 MHz has been used to study the Ca²⁺ binding domain I of bovine brain calmodulin in aqueous solution. All the resonances of the linear dodecapeptide Asp-Lys-Asp-Gly-Asn-Gly-Thr-Ile-Thr-Thr-Lys-Glu and of its cyclic analogue, synthesized by classical solution methods, have been completely assigned using a combination of several one- and two-dimensional nmr experiments, including the zero quantum correlation. Chemical shift values and ³J_CHNH coupling constants indicate that, on the nmr time scale, both peptides are flexible and assume multiple conformations in rapid equilibrium, with no relevant contribution of structured features. Addition of Ca²⁺ causes only minor spectral changes in aqueous solution of both peptides, while larger effects are observed in more hydrophobic mixtures such as water/trifluoroethanol. The linear analogue shows nonspecific interactions, while only Asp³ and Asn⁵ are significantly perturbed in the cyclic peptide. This evidence, together with identical findings in La³⁺ titration studies of the cyclic analogue in pure water, suggest that loop I of calmodulin is endowed with an intrinsic binding ability.     

Role of water in protein folding,oligomerization, amyloidosis and miniprotein

The essential involvement of water in most fundamental extra‐cellular and intracellular processes of proteins is critically reviewed and evaluated in this article. The role of water in protein behavior displays structural ambivalence; it can protect the disordered peptide‐chain by hydration or helps the globular chain‐folding, but promotes also the protein aggregation, as well (see: diseases). A variety of amyloid diseases begins as benign protein monomers but develops then into toxic amyloid aggregates of fibrils. Our incomplete knowledge of this process emphasizes the essential need to reveal the principles of governing this oligomerization. To understand the biophysical basis of the simpler in vitro amyloid formation may help to decipher also the in vivo way. Nevertheless, to ignore the central role of the water's effect among these events means to receive an uncompleted picture of the true phenomenon. Therefore this review represents a stopgap role, because the most published studies—with a few exceptions—have been neglected the crucial importance of water in the protein research. The following questions are discussed from the water's viewpoint: (i) interactions between water and proteins, (ii) protein hydration/dehydration, (iii) folding of proteins and miniproteins, (iv) peptide/protein oligomerization, and (v) amyloidosis. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

DNA and oligosaccharides stimulate oligomerization of human milk lactoferrin

Lactoferrin (LF) is a Fe³⁺-transferring glycoprotein and is contained in human barrier fluids, blood, and milk. LF is an acute phase protein, is involved in nonspecific defense, and displays a unique set of biological functions. Small-angle X-ray scattering and light scattering experiments demonstrated that DNA and oligosaccharides added to LF with various levels of initial oligomerization increased the oligomerization rate. Almost complete dissociation into monomers was observed when 1 M NaCl was added to LF oligomers obtained in the presence of DNA, oligosaccharides, and nucleotides, previously identified as oligomerization effectors. LF complexes obtained with different oligomerization effectors differed in stability. Incubation with 50 mM MgCl₂ completely destructed LF complexes formed in the presence of ATP and oligosaccharides but only partly destructed AMP- and d(pT)₁₀-dependent complexes, which was followed by the formation of new complexes with a higher salt stability. A possible role of oligomerization in various LF functions is discussed.     

Charge modification at conserved positively charged residues of fatty acid binding protein (FABP) from the giant liver fluke Fasciola gigantica: its effect on oligomerization and binding properties

Fatty acid binding proteins (FABPs) are capable of binding hydrophobic ligands with high affinity; thereby facilitating the cellular uptake and intracellular trafficking of fatty acids. In this study, functional characteristics of a cytoplasmic FABP from the giant liver fluke Fasciola gigantica (FgFABP) were determined. Binding of a fluorescent fatty acid analogue 11-[[5-dimethy aminonaphtalene-1-sulphonyl] amino] undecanoic acid (DAUDA) to FgFABP resulted in changes in the emission spectrum. The optimal excitation wavelength and maximum emission of fluorescence for binding activities with DAUDA were 350 nm and 550 nm, respectively. The binding activity for DAUDA was determined from titration experiments and revealed a K_d value of 2.95 ± 0.54 μM. Furthermore, we found that cross-linking profile of FgFABP with dithiobis-(succinimidylpropionate) (DSP) in the presence of DAUDA resulted in increased formation of higher-ordered oligomers compared to that in the absence of DAUDA. We also replaced five highly conserved positively charged residues (K9, K58, K91, R107 and K131) with alanine and studied their oligomerization and binding properties of the modified FgFABPs. The obtained data demonstrate that these residues do not appear to be involved in oligomerization. However, the K58A and R107A substitutions exhibited a reduction in binding affinities. K91A and R107A revealed an increase in maximal specific binding.