The Effect of a Covalent and a Noncovalent Small-Molecule Inhibitor on the Structure of Abg β-Glucosidase in the Gas-Phase

The effects of binding two small-molecule inhibitors to Agrobacterium sp. strain ATCC 21400 (Abg) β-glucosidase on the conformations and stability of gas-phase ions of Abg have been investigated. Biotin-iminosugar conjugate (BIC) binds noncovalently to Abg while 2,4-dinitro-2-deoxy-2-fluoro-β-d-glucopyranoside (2FG-DNP) binds covalently with loss of DNP. In solution, Abg is a dimer. Mass spectra show predominantly dimer ions, provided care is taken to avoid dissociation of dimers in solution and dimer ions in the ion sampling interface. When excess inhibitor, either covalent or noncovalent, is added to solutions of Abg, mass spectra show peaks almost entirely from 2:2 inhibitor-enzyme dimer complexes. Tandem mass spectrometry experiments show similar dissociation channels for the apo-enzyme and 2FG-enzyme dimers. The +21 dimer produces +10 and +11 monomers. The internal energy required to dissociate the +21 2FG-enzyme to its monomers (767?±?30 eV) is about 36 eV higher than that for the apo-enzyme dimer (731?±?6 eV), reflecting the stabilization of the free enzyme dimer by the 2FG inhibitor. The primary dissociation channels for the noncovalent BIC-enzyme dimer are loss of neutral and charged BIC. The internal energy required to induce loss of BIC is 482?±?8 eV, considerably less than that required to dissociate the dimers. For a given charge state, ions of the covalent and noncovalent complexes have about 15 % and 25 % lower cross sections, respectively, compared with the apo-enzyme. Thus, binding the inhibitors causes the gas-phase protein to adopt more compact conformations. Noncovalent binding surprisingly produces the greatest change in protein ion conformation, despite the weaker inhibitor binding.

Mechanism of immunoglobulin G4 Fab-arm exchange

Immunoglobulin G (IgG) antibodies are symmetrical molecules that may be regarded as covalent dimers of 2 half-molecules, each consisting of a light chain and a heavy chain. Human IgG4 is an unusually dynamic antibody, with half-molecule exchange ("Fab-arm exchange") resulting in asymmetrical, bispecific antibodies with two different antigen binding sites, which contributes to its anti-inflammatory activity. The mechanism of this process is unknown. To elucidate the elementary steps of this intermolecular antibody rearrangement, we developed a quantitative real-time FRET assay to monitor the kinetics of this process. We found that an intrinsic barrier is the relatively slow dissociation of the CH3 domains that noncovalently connect the heavy chains, which becomes rate determining in case disulfide bonds between the heavy chains are reduced or absent. Under redox conditions that mimic the previously estimated in vivo reaction rate, i.e., 1 mM of reduced glutathione, the overall rate is ca. 20 times lower because only a fraction of noncovalent isomers is present (with intra- rather than interheavy chain disulfide bonds), formed in a relatively fast pre-equilibrium from covalent isomers. Interestingly, Fab arms stabilize the covalent isomer: the amount of noncovalent isomers is ca. 3 times higher for Fc fragments of IgG4 (lacking Fab domains) compared to intact IgG4, and the observed rate of exchange is 3 times higher accordingly. Thus, kinetic data obtained from a sensitive and quantitative real-time FRET assay as described here yield accurate data about interdomain interactions such as those between Fab and/or Fc domains. The results imply that in vivo, the reaction is under control of local redox conditions.     

双卟啉化合物的构象平衡及π-π作用研究

制备并表征了一系列以柔韧烷氧化相连的自由双卟啉及其锌配合物,以＾１Ｈ－ＮＭＲ考察了烷氧链长度及锌离子对双卟啉构象平衡的影响。结果表明,双卟啉存在开放式及闭合式构象平衡,随烷氧链的增长,构象平衡由开放式向闭合式移动,当链上碳原子数为４时最有利于双卟啉形成闭合式构象。     

Synthesis of defined ubiquitin dimers

Many proteins are post-translationally modified by the attachment of poly-ubiquitin (Ub) chains. Notably, the biological function of the attached Ub chain depends on the specific lysine residue used for conjugate formation. Here, we report an easy and efficient method to synthesize site-specifically linked Ub dimers by click reaction between two artificial amino acids. In fact, we were able to synthesize all seven naturally occurring Ub connectivities, providing the first example of a method that gives access to all Ub dimers. Furthermore, these synthetic Ub dimers are recognized by the natural ubiquitination machinery and are proteolytically stable, making them optimal candidates to further investigate the function of differently linked Ub chains.     

Electron hopping in pi-stacked covalent and self-assembled perylene diimides observed by ENDOR spectroscopy

We have carried out room-temperature, solution-phase electron paramagnetic resonance and electron-nuclear double resonance studies on a series of radical anions based upon perylene-3,4:9,10-bis(dicarboximide) (PDI). The following systems were studied: two PDI monomers, a covalent, cofacial dimer, and two covalent trefoil-PDI3 molecules, one of which self-assembles into pi-stacked dimers. Full sharing of the unpaired electron in the covalent and self-assembled dimers is revealed by a halving of the hyperfine coupling constants in these species, relative to those of the monomers. These results and the electronic absorption spectra show that electron hopping on a >107 Hz time scale occurs between a reduced and neutral chromophoric pair.     

A Study of peptide-peptide interaction by matrix-assisted laser desorption/ionization

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to study peptide-peptide interaction. The interaction was seen when 6-aza-2-thiothymine was used as a matrix (pH 5.4), but was disrupted with a more acidic matrix, alpha-cyano-4-hydroxycinnamic acid (pH 2.0). In the present study, we show that dynorphin, an opioid peptide, and five of its fragments that contain two adjacent basic residues (Arg6-Arg7), all interact noncovalently with peptides that contain two to five adjacent acidic residues (Asp or Glu). Two other nonrelated peptides containing two (Arg6-Arg7) or three (Arg1-Lys2-Arg3) adjacent basic amino acid residues were studied and exhibited the same behavior. However, peptides containing adjacent Lys or His did not form noncovalent complexes with acidic peptides. The noncovalent bonding was sufficiently stable that digestion with trypsin only cleaved Arg and Lys residues that were not involved in hydrogen bonding with the acidic residues. In an equimolar mixture of dynorphin, dynorphin fragments (containing the motif RR), and an acidic peptide (minigastrin), the acidic peptide preferentially complexed with dynorphin. If the concentration of minigastrin was increased 10 fold, noncovalent interaction was seen with dynorphin and all its fragments containing the motif RR. In the absence of dynorphin, minigastrin formed noncovalent complexes with all dynorphin fragments. These findings suggest that conformation, equilibrium, and concentration do play a role in the occurrence of peptide-peptide interaction. Observations from this study include: (1) ionic bonds were not disrupted by enzymatic digests, (2) conformation and concentration influenced complex formation, and (3) the complex did not form with fragments of dynorphin or unrelated peptides that did not contain the motifs RR or RKR, nor with a fragment of dynorphin where Arg7 was mutated to a phenylalanine residue. These findings strongly suggest that peptide-peptide interaction does occur, and can be studied by MALDI if near physiologic pH is maintained.     

Effects of noncovalently functionalized multiwalled carbon nanotube with hyperbranched polyesters on mechanical properties of epoxy composites

In order to improve the dispersibility and interface properties of multi-walled carbon nanotubes (MWCNTs) in epoxy resin (EP), aromatic hyperbranched polyesters with terminal carboxyl (HBP) and aromatic hyperbranched polyesters with terminal amino groups (HBPN) were used for noncovalent functionalization of MWCNTs. Epoxy composites reinforced by different types of MWCNT were prepared. The effects of noncovalent functionalization of MWCNTs on the dispersibility, wettability, interface properties and mechanical properties of epoxy composites were investigated. The results show that the dispersibility and wettability of MWCNTs are significantly improved after noncovalent functionalization. A large number of terminal primary amines (NH₂) on noncovalently functionalized MWCNT with HBPN (HBPN-MWCNT) form covalent bonds with EP matrix, and thus the interfacial adhesion is enhanced significantly, resulting in high load transfer efficiency and substantial increase in mechanical properties. The interface with covalent bonding formed between the flexible hyperbranched polyester layer on the surface of HBPN-MWCNT and the EP matrix promotes plastic deformation of the surrounding EP matrix. The toughening mechanisms of HBPN-MWCNT are MWCNT pull-out and a large amount of plastic deformation of the surrounding EP matrix.     

Dimerization of the keto tautomer of acetohydroxamic acid-infrared matrix isolation and theoretical study

Dimerization of the keto tautomer of acetohydroxamic acid has been studied using FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-31+G(d,p) calculations. Analysis of CH3CONHOH/Ar matrix spectra indicates formation of two dimers in which two intramolecular CO...HON bonds within two interacting acetohydroxamic acid molecules are retained. A chain dimer I is stabilized by the intermolecular CO...HN hydrogen bond, whereas the cyclic dimer II is stabilized by two intermolecular NH...O(H)N bonds. Twelve vibrations were identified for dimer I and six vibrations for dimer II; the observed frequency shifts show a good agreement with the calculated ones for the structures I and II. Both dimers have comparable binding energies (DeltaE(ZPE)(CP)I, II=-7.02, -6.34 kcal mol-1) being less stable than calculated structures III and IV (DeltaE(ZPE)(CP)III, IV=-9.50, -8.87 kcal mol-1) in which one or two intramolecular hydrogen bonds are disrupted. In the most stable 10-membered cyclic dimer III, two intermolecular CO...HON hydrogen bonds are formed at expense of intramolecular hydrogen bonds of the same type. The formation of the less stable (AHA)2 dimers in the studied matrixes indicates that the formation of (AHA)2 is kinetically and not thermodynamically controlled.     

Noncovalent associations of glutathione S-transferase and ligands: A study using electrospray quadrupole/time-of-flight mass spectrometry

Human glutathione S-transferase A1-1 was observed predominantly as dimeric ions (51 kDa) during electrospray mass spectrometric analysis from aqueous solution at pH 7.4, in keeping with the known dimeric structure in solution. When analyses were performed on solutions of the enzyme containing glutathione (GSH), noncovalent adducts of protein dimer and one or two ligand molecules were observed; each mass increment, which exceeded the mass of GSH alone, was provisionally interpreted to indicate concomitant association of two water molecules per bound GSH. Noncovalent adducts of ligand and protein dimer were similarly observed for oxidized glutathione and for two glutathione inhibitors, both incorporating substituted thiol structures. In these instances, the mass increments exactly matched the ligand masses, suggesting that the apparent concomitant binding of water was associated with the presence in the ligand of a free thiol group. Collisionally activated decomposition during tandem mass spectrometry analyses of noncovalent adducts incorporating protein dimer and ligands yielded initially the denuded dimer; at higher collision energies the monomer and a protein fragment were formed.     

Amphotericin B covalent dimers forming sterol-dependent ion-permeable membrane channels

Polyenemacrolides such as amphotericin B (AmB) were thought to assemble together and form an ion channel across plasma membranes. Their antimicrobial activity has been accounted for by this assemblage, whose stability and activity are dependent on sterol constituents of lipid bilayer membranes. The structure of this channel-like assemblage formed in biomembranes has been a target of extensive investigations for a long time. For the first step to this goal, we prepared several AmB dimers with various linkers and tested for their channel-forming activity. Among these, AmB dimers that bore an aminoalkyl-dicarboxylate tether covalently linked between amino groups of AmB showed potent hemolytic activity. Furthermore, K+ influx actions monitored by measuring the pH of the liposome lumen by 31P NMR revealed that the dimers formed the molecular assemblage similar to that of AmB in phospholipid membrane. Judging from changes in 31P NMR spectra, the dimers appeared to induce "all-or-none"-type ion flux across the liposome membrane in the presence of ergosterol, which suggested that the ion channel formed by ergosterol/dimer is similar to that of AmB. With these data in hand, we are now trying to elucidate the structure of the ion-channel complex by making the labeled conjugates of AmB for NMR measurements.     

Semi-synthesis of disulfide-linked branched tri-ubiquitin mimics

Ubiquitin (Ub) chain isopeptide bond mimics are useful molecules for biochemical and biophysical studies. Herein, we report the semi-synthesis of the disulfide-linked K11/K48-branched tri-Ub (Ub₃^11/48(S–S)), the first example of an isopeptide mimic for the branched Ub chains, which have recently emerged as an interesting category of Ub modifications. Our strategy comprised the E1-dependent synthesis of the Ub conjugate of aminoethanethiol, followed by disulfide formation with Ub(K11C, K48C). The structure of the synthetic isopeptide bond mimics was verified by the crystal structure of Ub₃^11/48(S–S). Deubiquitination and pulldown assays indicated that the synthetic Ub₃^11/48(S–S) could be hydrolyzed by linkage-specific deubiquitinases (K11-specific Cezanne and K48-specific OTUB1), and recognized by proteasomal ubiquitin receptor S5a.     

In-silico exploration of noble gas dimer enforced by noncovalent interaction

Density functional calculations have been carried out to investigate the possibility of trapping of noble gas dimers by cyclo[18]carbon dimer. Parallel-displaced conformation of the cyclo[18]carbon dimer is found to be the minimum energy structure. Noncovalent interaction is found to hold the noble gas dimers. The lighter noble gases (He, Ne) posses weaker attractive interactions while the heavier one (Ar, Kr) are held by stronger attractive interactions forming genuine bonds. Each of the noble gas atoms in turn forms noncovalent interaction with the cyclo[18]carbon monomers. The bond dissociation energy of the noble gas dimers dramatically increases inside the cyclo[18]carbon dimer. Energy decomposition analysis reveals that dispersion plays the major role toward the stabilization energy.     

Fluoride-mediated capture of a noncovalent bound state of a reversible covalent enzyme inhibitor: X-ray crystallographic analysis of an exceptionally potent α-ketoheterocycle inhibitor of fatty acid amide hydrolase

Two cocrystal X-ray structures of the exceptionally potent α-ketoheterocycle inhibitor 1 (K(i) = 290 pM) bound to a humanized variant of rat fatty acid amide hydrolase (FAAH) are disclosed, representing noncovalently and covalently bound states of the same inhibitor with the enzyme. Key to securing the structure of the noncovalently bound state of the inhibitor was the inclusion of fluoride ion in the crystallization conditions that is proposed to bind the oxyanion hole precluding inhibitor covalent adduct formation with stabilization of the tetrahedral hemiketal. This permitted the opportunity to detect important noncovalent interactions stabilizing the binding of the inhibitor within the FAAH active site independent of the covalent reaction. Remarkably, noncovalently bound 1 in the presence of fluoride appears to capture the active site in the same "in action" state with the three catalytic residues Ser241-Ser217-Lys142 occupying essentially identical positions observed in the covalently bound structure of 1, suggesting that this technique of introducing fluoride may have important applications in structural studies beyond inhibiting substrate or inhibitor oxyanion hole binding. Key insights to emerge from the studies include the observations that noncovalently bound 1 binds in its ketone (not gem diol) form, that the terminal phenyl group in the acyl side chain of the inhibitor serves as the key anchoring interaction overriding the intricate polar interactions in the cytosolic port, and that the role of the central activating heterocycle is dominated by its intrinsic electron-withdrawing properties. These two structures are also briefly compared with five X-ray structures of α-ketoheterocycle-based inhibitors bound to FAAH recently disclosed.     

Unexpected stable dimerisation of an anionic imidopyrrolecarboxylate in polar solution

The imidopyrrolecarboxylate 3(-) unexpectedly forms stable dimers (K(ass) = 130 M(-1) in CHCl(3)/DMSO, 1?:?1, v/v) despite the fact that two anions have to interact. The dimer is more stable than an analogous neutral amidopyrrolecarboxylic acid dimer (K(ass) < 10 M(-1)) underlining the importance of charged H-bonds compared to neutral ones.     

Forging isopeptide bonds using thiol-ene chemistry: site-specific coupling of ubiquitin molecules for studying the activity of isopeptidases

Chemical methods for modifying proteins can enable studies aimed at uncovering biochemical function. Herein, we describe the use of thiol-ene coupling (TEC) chemistry to report on the function of branched (also referred to as forked) ubiquitin trimers. We show how site-specific isopeptide (Nε-Gly-L-homothiaLys) bonds are forged between two molecules of Ub, demonstrating the power of TEC in protein conjugation. Moreover, we demonstrate that the Nε-Gly-L-homothiaLys isopeptide bond is processed to a similar extent by deubiquitinases (DUBs) as that of a native Nε-Gly-L-Lys isopeptide bond, thereby establishing the utility of TEC in the generation of Ub-Ub linkages. TEC is then applied to the synthesis of branched Ub trimers. Interrogation of these branched derivatives with DUBs reveals that the relative orientation of the two Ub units has a dramatic impact on how they are hydrolyzed. In particular, cleavage of K48C-linkages is suppressed when the central Ub unit is also conjugated through K6C, whereas cleavage proceeds normally when the central unit is conjugated through either K11C or K63C. The results of this work presage a role for branched polymeric Ub chains in regulating linkage-selective interactions.     

Computational study of the release of H2 from ammonia borane dimer (BH3NH3)2 and its ion pair isomers

High-level electronic structure calculations have been used to map out the relevant portions of the potential energy surfaces for the release of H2 from dimers of ammonia borane, BH3NH3 (AB). Using the correlation-consistent aug-cc-pVTZ basis set at the second-order perturbation MP2 level, geometries of stationary points were optimized. Relative energies were computed at these points using coupled-cluster CCSD(T) theory with the correlation-consistent basis sets at least up to the aug-cc-pVTZ level and in some cases extrapolated to the complete basis set limit. The results show that there are a number of possible dimers involving different types of hydrogen-bonded interactions. The most stable gaseous phase (AB)2 dimer results from a head-to-tail cyclic conformation and is stabilized by 14.0 kcal/mol with respect to two AB monomers. (AB)2 can generate one or two H2 molecules via several direct pathways with energy barriers ranging from 44 to 50 kcal/mol. The diammoniate of diborane ion pair isomer, [BH4-][NH3BH2NH3+] (DADB), is 10.6 kcal/mol less stable than (AB)2 and can be formed from two AB monomers by overcoming an energy barrier of approximately 26 kcal/mol. DADB can also be generated from successive additions of two NH3 molecules to B2H6 and from condensation of AB with separated BH3 and NH3 molecules. The pathway for H2 elimination from DADB is characterized by a smaller energy barrier of 20.1 kcal/mol. The alternative ion pair [NH4+][BH3NH2BH3-] is calculated to be 16.4 kcal/mol above (AB)2 and undergoes H2 release with an energy barrier of 17.7 kcal/mol. H2 elimination from both ion pair isomers yields the chain BH3NH2BH2NH3 as product. Our results suggest that the neutral dimer will play a minor role in the release of H2 from ammonia borane, with a dominant role from the ion pairs as observed experimentally in ionic liquids and the solid state.     

Radical para-benzoic acid derivatives: transmission of ferromagnetic interactions through hydrogen bonds at long distances

Investigation of the transmission of magnetic interactions through hydrogen bonds has been carried out for two different benzoic acid derivatives which bear either a tert-butyl nitroxide (NOA) or a poly(chloro)triphenylmethyl (PTMA) radical moiety. In the solid state, both radical acids formed dimer aggregates by the complementary association of two carboxylic groups though hydrogen bonding. This association ensured that atoms with most spin density are separated from one another by more than 15 A. Thus, no competing through-space magnetic exchange interactions are expected in these dimers and, hence, they provide good models to investigate whether noncovalent hydrogen bonds play a role in the long-range transmission of magnetic interactions. The nature of the magnetic exchange interaction and their strengths within similar dimer aggregates in solution was assessed by electron spin resonance (ESR) spectroscopy. In the case of radical NOA, low-temperature ESR experiments showed a weak ferromagnetic interaction between the two radicals in the dimer aggregates (which have the same geometry as in the solid state). In contrast, the corresponding solution ESR study performed with radical PTMA did not lead to any conclusive results, as aggregates were formed by noncovalent interactions other than hydrogen bonds. However, the bulkiness of the poly(chloro)triphenylmethyl radical prevented interdimer contacts in the solid state between regions of high spin density. Hence, solid-state measurements of the alpha phase of PTMA radical provided evidence of the intradimer interaction to confirm the transmission of a weak ferromagnetic interaction through the carboxylic acid bridges, as found for the NOA radical. Moreover, crystallization of the PTMA radical in presence of ethanol to form the beta phase of PTMA radical prevented the dimer formation; this resulted in the suppression of this interaction and provides further evidence of the magnetic exchange mechanism through noncovalent hydrogen bonds at long distances.     

Bis(phenylthienyl)ethene-tethered beta-cyclodextrin dimers as photoswitchable hosts

Two beta-cyclodextrin dimers tethered by photoswitchable bis(phenylthienyl)ethene moieties were synthesized as potentially tunable receptor molecules. The cyclodextrin cavities of these dimers were linked via their secondary sides, with the photochromic bis(phenylthienyl)ethene unit either directly connected to the secondary rim (7) or via propyl spacers (10). By irradiation with light the dimers were reversibly switched between a relatively flexible (open) form and a rigid (closed) form. The photostationary states for both dimers consisted of 92% of the open and 8% of the closed form, enabling the nearly complete conversion between the two forms. The binding properties of the open and closed forms of dimers 7 and 10 were assessed by complexation studies with meso-tetrakis(4-sulfonatophenyl)porphyrin (TSPP) using isothermal titration calorimetry. For the rigidly tethered dimer 7, a factor 8 difference in binding affinity between the open and closed form of the dimer was found. This difference in binding affinity reflects the difference in enthalpy of binding for the two dimers, indicating that the beta-cyclodextrin cavities of the closed dimer 7b are spaced too far apart from each other by the rigid closed bis(phenylthienyl)ethene tether to cooperatively bind TSPP. The difference in binding affinity was sufficient to enable the phototriggered release of TSPP from dimer. The thermodynamic parameters obtained for dimer 10 suggested that the closed tether substantially contributes to the binding of TSPP. The open and closed form of dimer 10 bound TSPP with similar association constants, although the enthalpy of binding for the complexation of TSPP by the closed form of dimer 10 was more favorable than that found for the open form of the dimer.     

Interaction of thiamine with anions in the triclinic form of thiamine iodide: 3‐[(4‐amino‐2‐methylpyrimidin‐5‐yl)methyl]‐5‐(2‐hydroxyethyl)‐4‐methyl‐1,3‐thiazol‐3‐ium iodide 1.25‐hydrate

The asymmetric unit of the title compound, C₁₂H₁₇N₄OS⁺·I⁻·1.25H₂O, contains two crystallographically independent molecules. Both formula units assume the usual F conformation and have the hydroxyethyl group disordered over two sites, each with half occupation. Two thiamine cations are linked by hydrogen bonds into a cyclic dimer. These dimers are further connected by base‐pairing hydrogen bonds into a chain along [010]. The stacked dimers form channels, which are occupied by iodide anions. The cations and anions are associated by N—H...I hydrogen bonds, C—H...I interactions and I...thiazolium ring close contacts. The interactions between thiamine and the iodide anions are similar to those observed in monoclinic thiamine iodide 1.5‐hydrate [Hu & Zhang (1993). J. Inclusion Phenom. Mol. Recognit. Chem. 16 , 273–281].     

Cyclophane‐Type Chlorin Dimers from Dynamic Covalent Chemistry of 2,18‐Porphyrinyl Dicyanomethyl Diradicals

2,18‐Bis(dicyanomethyl)‐substituted Ni^II porphyrin 8 and Zn^II porphyrin 11 were prepared and subjected to oxidation with PbO₂ in CH₂Cl₂ at 298 K to give cyclophane‐type chlorin dimers ( 9 )₂ and ( 12 )₂ as a consequence of double recombination of biradicals 9 and 12 , respectively. Dimer ( 9 )₂ takes a syn‐conformation of two distorted Ni^II chlorins but ( 12 )₂ takes an anti‐conformation of relatively planar Zn^II chlorins. At 298 K, dimer ( 9 )₂ is stable and its ¹H NMR spectrum is sharp but becomes broad at high temperature, while the ¹H NMR spectrum of ( 12 )₂ is considerably broad even at 298 K but becomes sharper at low temperature. These results indicate that the chlorin dimers dissociate to radical species, but the activation barrier of the dissociation of ( 12 )₂ is much less than that of ( 9 )₂. The involvement of diradicals in dynamic covalent chemistry has been suggested by thermal scrambling of hetero dimer ( 16 )₂ to give homo dimers ( 9 )₂ and ( 15 )₂.