Specific H-bonds Research Articles

Conformational alteration in glycan induces phospholipase Cβ1 activation and angiogenesis

BackgroundIn endothelial cells, phospholipase C (PLC) β1-activated Ca2+ is a crucial second messenger for the signaling pathways governing angiogenesis. PLCβ1 is inactivated by complexing with an intracellular protein called translin-associated factor X (TRAX). This study demonstrates specific interactions between Globo H ceramide (GHCer) and TRAX, which highlight a new angiogenic control through PLCβ1 activation.MethodsGlobo-series glycosphingolipids (GSLs), including GHCer and stage-specific embryonic antigen-3 ceramide (SSEA3Cer), were analyzed using enzyme-linked immunosorbent assay (ELISA) and Biacore for their binding with TRAX. Angiogenic activities of GSLs in human umbilical vein endothelial cells (HUVECs) were evaluated. Molecular dynamics (MD) simulation was used to study conformations of GSLs and their molecular interactions with TRAX. Fluorescence resonance energy transfer (FRET) analysis of HUVECs by confocal microscopy was used to validate the release of PLCβ1 from TRAX. Furthermore, the in vivo angiogenic activity of extracellular vesicles (EVs) containing GHCer was confirmed using subcutaneous Matrigel plug assay in mice.ResultsThe results of ELISA and Biacore analysis showed a stable complex between recombinant TRAX and synthetic GHCer with Kd of 40.9 nM. In contrast, SSEA3Cer lacking a fucose residue of GHCer at the terminal showed ~ 1000-fold decrease in the binding affinity. These results were consistent with their angiogenic activities in HUVECs. The MD simulation indicated that TRAX interacted with the glycan moiety of GHCer at amino acid Q223, Q219, L142, S141, and E216. At equilibrium the stable complex maintained 4.6 ± 1.3 H-bonds. TRAX containing double mutations with Q223A and Q219A lost its ability to interact with GHCer in both MD simulation and Biacore assays. Removal of the terminal fucose from GHCer to become SSEA3Cer resulted in decreased H-bonding to 1.2 ± 1.0 by the MD simulation. Such specific H-bonding was due to the conformational alteration in the whole glycan which was affected by the presence or absence of the fucose moiety. In addition, ELISA, Biacore, and in-cell FRET assays confirmed the competition between GHCer and PLCβ1 for binding to TRAX. Furthermore, the Matrigel plug assay showed robust vessel formation in the plug containing tumor-secreted EVs or synthetic GHCer, but not in the plug with SSEA3Cer. The FRET analysis also indicated the disruption of colocalization of TRAX and PLCβ1 in cells by GHCer derived from EVs.ConclusionsOverall, the fucose residue in GHCer dictated the glycan conformation for its complexing with TRAX to release TRAX-sequestered PLCβ1, leading to Ca2+ mobilization in endothelial cells and enhancing angiogenesis in tumor microenvironments.

Synthesis and characterization of a computationally predicted redox and radiation stable deep eutectic solvent

• DFT calculations towards finding suitable HBD and HBA for the formation of redox and radiation stable DES. • Phase diagram to depict the molar ratio of the constituents in the new DES. • Stabilization energy calculation of the predicted new DES. • Experimental synthesis and characterization of the DES predicted from computational calculations. • Radiation stability study and by-product analysis of the as synthesized DES under gamma irradiation. A redox and radiation stable DES has been predicted based on the fundamental electronic properties such as energy gap, ionization potential and electron affinity computed applying suitable density functionals in combination with 6-311++G(d,p) set of atomic basis functions. A selected series of optimized hydrogen bond donors (HBDs) and hydrogen bond acceptors (HBAs) has been screened using density functional theory (DFT). The long range corrected density functionals; ωB97XD and LC-BLYP are found to be cost effective and appropriate towards orbital energy gap calculations of such systems. Choline acetate and malonic acid appeared to be the most appropriate combination among those studied for formation of a chemical and radiation stable DES. Theoretically constructed phase diagram using Gibbs free energy minimization technique is applied to suggest the eutectic point and eutectic composition of the recommended DES. Stabilization energy calculations following electronic structure support the phase diagram data denoting formation of a stable eutectic with 1:2 stoichiometry. Density, viscosity, differential scanning calorimetry (DSC) and Fourier transform infra-red (FTIR) experiments have been carried out with this synthesized DES. Measured glass transition temperature (−75 °C) is observed to be lower than the theoretical eutectic point (−40 °C) indicating strong interspecies interaction within the medium. Experimental FTIR analysis gives an idea of the type and number of H-bonds present within the DES whereas computationally optimized 1:2 geometry identifies the specific H-bonds along with their distances. Irradiation of this new DES has been conducted at a constant dose of 100 kGy to observe the extent of degradation. UV–Vis and FTIR analysis does not denote generation of any new species within the liquid phase upon irradiation, however the yields of the gaseous by-products have been quantified by Gas Chromatography (GC).

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex.

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.

Narcissistic self-sorting of n-acene nano-ribbons yielding energy-transfer and electroluminescence at p-n junctions.

The 2,3-didecyloxy derivative of an n-type anthracene (n-BG) and a p-type tetracene (p-R) have been synthesized and their self-assembly into nano-ribbons studied. Hyperspectral fluorescence imaging revealed their narcissistic self-sorting, leading to separated nanoribbons emitting with very different colors (blue or green for n-BG, depending on the growth solvent, and red for p-R). It is unique that the usual origins of self-sorting, such as specific H-bonding, different growth kinetics, or incompatible steric hindrance can be ruled out. Hence, the narcissistic behaviour is herein proposed to originate from a so-far unconsidered cause: the discrepancy between the quadrupolar character of n-BG and dipolar character of p-R. At the p-n junctions of these nanoribbons, inter-ribbon FRET and electro-luminescence switch-on were observed by fluorescence/luminescence microscopy.

Stable silver nanoparticle doped mesoporous biochar-based nanocomposite for efficient removal of toxic dyes

In this present study, biochar-based silver nanocomposite (Ag-nBC) has been synthesized by combining (i) AgNPs, synthesized biochemically using Shorea robusta leaf extract, and (ii) S. robusta leaf biochar, produced via mild thermal pyrolysis (300 °C) and tested for toxic dye removal efficiency. The Ag-nBC was characterized by FESEM-EDX, BET, XRD, XPS, TGA, and FTIR, found to be irregular, heterogeneous, and mesoporous, containing a significant amount of surface functional groups. The Ag-nBC showed > 90% removal for Congo red (CR) and Rhodamine B (RhB), where the dye removal experiments were found to be spontaneous exothermic, followed Freundlich isotherm and pseudo-second order reaction kinetic model. The adsorption mechanism of CR involved surface complexation through specific electrostatic attraction and H-bonding, while RhB exhibited only surface complexation. Notably, this heterogeneous Ag-nBC system showed excellent stability at wide ranges of pH and promising reusability, suggesting great potential for waste biomass minimization and dye effluent treatment.

Casein-Derived Peptides with Antihypertensive Potential: Production, Identification and Assessment of Complex Formation with Angiotensin I-Converting Enzyme (ACE) through Molecular Docking Studies

Hypertension is nowadays one of the major world concerns in public health. Several food proteins, among which caseins, can be substrates for generating peptides with antihypertensive potential. With the increasingly evolution of computational tools, in silico molecular modeling have gained prominence in studies of protein-ligand complexes in different research fields, such as pharmaceutics and biochemical engineering. However, the application of such methodologies in food-related research can be considered still embryonic. Thus, the central aim of the present work was to apply molecular modelling in order to elucidate the molecular bases of the anti-hypertensive potential of milk caseins-derived peptides. Firstly, hydrolysates obtained from a controlled trypsinolysis of caseins were fractioned according to their molecular weight, by ultrafiltration and RP-HPLC. The obtained fractions were evaluated with regard to their in vitro inhibitory angiotensin-converting enzyme activity (%IACE). Six chromatographic fractions were identified, and three of them displayed high ACE-inhibition (F1: 80.68%; F2: 79.00%; and F4: 62.44%). Finally, intermolecular interactions networks in complexes formed between ACE and the identified peptides were assessed through in silico molecular docking. At the molecular level, a correlation between in vitro and in silico results was found: the peptides FFVAPFPEVFGK (F6), FALPQYLK (F2, F4) and ALNEINQFYQK (F1) presented the lowest biding energies and interacted by specific H-bonds, electrostatic and hydrophobic interactions formed within ACE active site S1 residues (Ala354, Glu384, and Tyr 523) and the Zn2+ coordinated residues (His383, His387, and Glu411). The fraction F3, despite its low total peptide concentration, presented a moderate inhibitory activity for ACE (49.2%), likely due to H-bonds between HQGLPQEVLNENLLR and the active site S1 residues.

Subtle differences in chemical pattern between human toll-like receptor 8 agonists and antagonists: Emerging chemical patterns analysis.

Due to the potencies in the treatments of cancer, infectious diseases, and autoimmune diseases, the developments of human TLR8 (hTLR8) agonists and antagonists have attracted widespread attentions. The hTLR8 agonists and antagonists have similar structures but with completely opposite biological effects. Up to date, the subtle differences in the structures between the hTLR8 agonists and antagonists are still unknown. In this work, emerging chemical pattern (ECP) was successfully used to extract the key chemical patterns of the hTLR8 agonists and antagonists. By using CAEP classifier, an optimal ECP model with only 3 descriptors was established with the overall prediction accuracy larger than 90%. Further hierarchical cluster analysis and molecular docking showed that the H-bond and hydrophobic properties are the key features distinguishing the hTLR8 agonists from antagonists. Comparing with the antagonists, the agonists show stronger specific H-bond properties, while antagonists have stronger non-specific hydrophobic properties. The significant differences in the structural properties may be closely related to the activation/inhibition mechanism of hTLR8.

Structure of an engineered multidrug transporter MdfA reveals the molecular basis for substrate recognition

MdfA is a prototypical H+-coupled multidrug transporter that is characterized by extraordinarily broad substrate specificity. The involvement of specific H-bonds in MdfA-drug interactions and the simplicity of altering the substrate specificity of MdfA contradict the promiscuous nature of multidrug recognition, presenting a baffling conundrum. Here we show the X-ray structures of MdfA variant I239T/G354E in complexes with three electrically different ligands, determined at resolutions up to 2.2 Å. Our structures reveal that I239T/G354E interacts with these compounds differently from MdfA and that I239T/G354E possesses two discrete, non-overlapping substrate-binding sites. Our results shed new light on the molecular design of multidrug-binding and protonation sites and highlight the importance of often-neglected, long-range charge-charge interactions in multidrug recognition. Beyond helping to solve the ostensible conundrum of multidrug recognition, our findings suggest the mechanistic difference between substrate and inhibitor for any H+-dependent multidrug transporter, which may open new vistas on curtailing efflux-mediated multidrug resistance.

Molecular mechanism by which residues at position 481 and 546 of measles virus hemagglutinin protein define CD46 receptor binding using a molecular docking approach

The hemagglutinin (H) protein of measles viruses (MeV) mediates binding to the cellular receptors, CD46,human signaling lymphocyte activation molecule and nectin-4. Vaccine strains primarily contain H-proteins possessing MeV-H: Y481 and can utilize CD46. Reports suggest that a single amino acid change in MeV-H at position 481 in wild type strains renders them inefficient in utilizing CD46. The in-depth molecular mechanism by which substitutions at 481 and another reported critical residue position 546 affects CD46 binding affinity however remains elusive. We used molecular docking studies of CD46 with MeV-H possessing Y481 N/D to understand the in-depth molecular mechanism involved. It was found that loss in either of the hydrogen bond (H-bond) contacts (MeV-H:481–CD46:65, MeV-H:546–CD46:63) in the central contact region prevented efficient CD46 binding. Y481 N could form the specific H-bond, while G546S H-bond could be formed only in conjunction with Y481, revealing the significance of these residues in determining CD46 receptor binding potential. Elucidating the underlying molecular mechanism of receptor usage by the MeV has implications to understanding cellular tropism, viral pathogenesis and therapy.

Impact of Hydrogen Bonding Interactions on Graft–Matrix Wetting and Structure in Polymer Nanocomposites

We present a new coarse-grained (CG) model that captures directional interactions between graft and matrix polymer chains in polymer nanocomposites (PNCs) comprising polymer grafted spherical nanoparticles in a matrix polymer. In this CG model we incorporate acceptor and donor CG beads along with graft and matrix monomer CG beads and optimize the bonded and nonbonded interactions to mimic directional and specific H-bonding between the acceptor and donor sites on graft and matrix chains, respectively. Using this CG model and molecular dynamics simulations we show that H-bonding interactions between graft and matrix polymer chains increase the grafted layer wetting by matrix chains compared to that at the purely entropic limit. One can achieve equivalent grafted layer wetting in PNCs with directional acceptor–donor interactions and PNCs with isotropic graft–matrix interactions, but the directional acceptor–donor interaction strength needs to be much stronger than the isotropic graft–matrix monomer attractio...

Dielectric properties of polyurethane nanocomposites modified by fullerene С60 and nanodiamonds

The paper describes preparation of polyurethane composites infused with nano- and macro-sized carbonaceous fillerswith a different surface nature (with a hydrophobic surface-fullerene C60, fullerene soot, with a hydrophilic surface nano-diamonds, nano-diamond charge), with loading varying from 0.1 to 0.5 wt. % by in situ polymerization. The obtained nano-composites were measured by the method of dielectric spectroscopy to determine the nature of the influence of the surface origin and particle size on the structure and properties of the finished material. It was found that loading of fillers leads to the decrease in the process of α-relaxation activation energycompared to neat polyurethane (PU). It was revealed that the non-specific π-π interaction for nanosized fillers dominates over specific H-bonding, which can be related to the oxygen groups on the shells of nano-diamonds. The dielectric spectroscopy demonstrated that the glass transition temperature values of the nano-composites increase in comparison with neat PU, manifesting the so-called "antiplasticizating phenomenon", while composites with macro-sized filler exhibit a typical plasticizing effect for traditional fillers. The greatest value of the D parameter (fragility) corresponds to a sample with fullerene soot. The coincidence of activation energies of Maxwell-Wagner-Sillars polarization for different fillers means that the dimensions of the hard domains in the polymer have not changed.

Docking and pharmacodynamic studies on hGAT1 inhibition activity in the presence of selected neuronal and astrocytic inhibitors. Part I

Inhibition of 4-aminobutanoic acid (GABA) uptake is a strategy for enhancing GABA transmission. The utility of this approach is demonstrated by the successful development of such agents for the treatment of epilepsy and pain. Existing reports on acute brain slice preparations indicate the intersecting of complementary channels and receptors sets between astrocytes and neurons cells. Thorough analysis of astroglial cells by means of molecular and functional studies demonstrated their active modulatory role in intercellular communication. The chemical interactions between sixteen GABA analogues and isoform of hGAT1 is outlined in the light of molecular docking results. In the in vivo part antinociceptive properties of racemic nipecotic acid, its R and S enantiomers and isonipecotic acid, each administered intraperitoneally at 3 fixed doses (10, 30 and 100 mg/kg), were assessed in a thermally-induced acute pain model i.e. the mouse hot plate test. Docking analyses provided complex binding energies, specific h-bond components, and h-bond properties, such as energies, distances and angles. In vivo tests revealed statistically significant antinociceptive properties of isonipecotic acid (10 and 30 mg/kg), R-nipecotic acid (30 and 100 mg/kg) and S-nipecotic acid (100 mg/kg) in mice. The docking data endorse the hypothesis of correlation between the strength of their chemical interactions with hGAT1 and analgesic action of studied compounds.

The kink-turn in the structural biology of RNA.

The kink-turn (k-turn) is a widespread structural motif found in functional RNA species. It typically comprises a three-nucleotide bulge followed by tandem trans sugar edge-Hoogsteen G:A base pairs. It introduces a sharp kink into the axis of duplex RNA, juxtaposing the minor grooves. Cross-strand H-bonds form at the interface, accepted by the conserved adenine nucleobases of the G:A basepairs. Alternative acceptors for one of these divides the k-turns into two conformational classes N3 and N1. The base pair that follows the G:A pairs (3b:3n) determines which conformation is adopted by a given k-turn. k-turns often mediate tertiary contacts in folded RNA species and frequently bind proteins. Common k-turn binding proteins include members of the L7Ae family, such as the human 15·5k protein. A recognition helix within these proteins binds in the widened major groove on the outside of the k-turn, that makes specific H-bonds with the conserved guanine nucleobases of the G:A pairs. L7Ae binds with extremely high affinity, and single-molecule data are consistent with folding by conformational selection. The standard, simple k-turn can be elaborated in a variety of ways, that include the complex k-turns and the k-junctions. In free solution in the absence of added metal ions or protein k-turns do not adopt the tightly-kinked conformation. They undergo folding by the binding of proteins, by the formation of tertiary contacts, and some (but not all) will fold on the addition of metal ions. Whether or not folding occurs in the presence of metal ions depends on local sequence, including the 3b:3n position, and the -1b:-1n position (5' to the bulge). In most cases -1b:-1n=C:G, so that the 3b:3n position is critical since it determines both folding properties and conformation. In general, the selection of these sequence matches a given k-turn to its biological requirements. The k-turn structure is now very well understood, to the point at which they can be used as a building block for the formation of RNA nano-objects, including triangles and squares.

First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences.

The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition. The molecular features, in this report, explain the mechanism of recognition of both A⋅T and G⋅C bps and are an interesting molecular recognition story. Examination of the experimental structure and the NMR restrained molecular dynamics model suggests that recognition of the G⋅C base pair involves two specific H-bonds. The structure illustrates a wealth of information on different DNA interactions and illustrates an interfacial water molecule that is a key component of the complex.

A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase

Structural comparisons of the cold adapted subtilase VPR and its thermophilic homologue, aqualysin I (AQUI) indicated the presence of additional salt bridges in the latter. Few of those appear to contribute significantly to thermal stability of AQUI. This includes a putative salt bridge between residues Lys142 and Glu172 as its deletion did not have any significant effect on its stability or activity (Jónsdóttir et al. (2014)). Insertion of this putative salt bridge into the structure of VPR, in a double mutant (VPRΔC_Q142K/S172E), however was detrimental to the stability of the enzyme. Incorporation of either the Q142K or S172E mutations into VPR, were found to significantly affect the catalytic properties of the enzyme. The single mutation Q142K was highly effective, as it increased the kcat and kcat/Km more than twofold. When the Q142K mutation was inserted into a thermostabilized, but a low activity mutant of VPR (VPRΔC_N3P/I5P), the activity increased about tenfold in terms of kcat and kcat/Km, while retaining the stability of the mutant. Molecular dynamics simulations of the single mutants were carried out to provide structural rationale for these experimental observations. Based on root mean square fluctuation (RMSF) profiles, the two mutants were more flexible in certain regions of the structure and the Q142K mutant had the highest overall flexibility of the three enzymes. The results suggest that weakening of specific H-bonds resulting from the mutations may be propagated over some distance giving rise to higher flexibility in the active site regions of the enzyme, causing higher catalytic activity in the mutants.

Effect of Stereochemistry on Directed Self-Assembly of Poly(styrene-b-lactide) Films on Chemical Patterns.

We demonstrated here for the first time that the stereochemistry of polylactide (PLA) blocks affected the assembly behaviors of PS-b-PLA on chemical patterns. Two PS-b-PLA block copolymers, where the PLA block is either racemic (PDLLA) or left-handed (PLLA), were synthesized and directed to assemble on chemical patterns with a wide range of Ls/L0. PS-b-PDLLA was stretched up to 70% on chemical patterns, while PS-b-PLLA was only stretched by 20%. The assembly behavior of PS-b-PDLLA was different from AB diblock copolymer, but similar to that of ABA triblock copolymer. The high stretchability might be attributed to the formation of stereocomplexes in PDLLA blocks. Compared to ABA triblock copolymers, stereocomplexed diblock copolymers have much faster assembly kinetics. This observation provides a new concept to achieve large process windows by the introduction of specific interactions, for example, H-bonding, supramolecular interaction, and sterecomplexation, between polymer chains.

Dewetting of S1-Pocket via Water Channel upon Thrombin-Substrate Association Reaction.

Upon protein-substrate association reaction, dewetting of the substrate-binding pocket is one of the rate-limiting processes. However, understanding the microscopic mechanism still remains challenging because of practical limitations of experimental methodologies. We have addressed the problem here by using molecular dynamics (MD) simulation of the thrombin-substrate association reaction. During the MD simulation, ArgP1 in a substrate accessed thrombin's substrate-binding pocket and formed specific hydrogen bonds (H-bonds) with Asp189 in thrombin, while the catalytic serine of thrombin was still away from the substrate's active site. It is assumed that the thrombin-substrate association reaction is regulated by a stepwise mechanism. Furthermore, in the earlier stage of ArgP1 access to the pocket, we observed that ArgP1 was spatially separated from Asp189 by two water molecules in the pocket. These water molecules transferred from the pocket, followed by the specific H-bond formation between thrombin and the substrate. Interestingly, they were not evacuated directly from the pocket to the bulk solvent, but moved to the water channel of thrombin. This observation indicates that the channel plays functional roles in dewetting upon the association reaction.

Structures and dielectric properties of three homonuclear H-bonded 1D chain complexes based on protonated 4,4′-bipyridine-N,N′-dioxide

One-dimensional homonuclear H-bonded complexes of 4,4′-bipyridine-N,N′-dioxide (bp4do) with three kinds of acid [trichloroacetic acid (TCA) 1, hexafluorophosphoric acid 2, perrhenic acid 3] have been synthesized and characterized by single-crystal X-ray diffraction analysis, dielectric measurement, powder X-ray diffraction, IR spectra and UV–Vis spectra. All three complexes form 1D chains of Hbp4do+ cations through the bridge of specific short H-bond with different patterns and further develop into multi-dimensional architecture through π⋯π packing of pyridyl rings. Single crystal X-ray crystallography discloses that 1 shows a parallel ribbon chain structure, 2 exhibits a crossing ribbon chain structure and 3 with a zigzag chain structure. Combined variable temperature structural analysis and dielectric measurements disclose phase transition of 1 and 2 owing to the disorder–order transition of acid anions.

Nitro-Assisted Brønsted Acid Catalysis: Application to a Challenging Catalytic Azidation.

A cocatalytic effect of nitro compounds is described for the B(C6F5)3·H2O catalyzed azidation of tertiary aliphatic alcohols, enabling catalyst turnover for the first time and with a broad range of substrates. Kinetic investigations into this surprising effect reveal that nitro compounds induce a switch from first order concentration dependence in Brønsted acid to second order concentration dependence in Brønsted acid and second order dependence in the nitro compounds. Kinetic, electronic, and spectroscopic evidence suggests that higher order hydrogen-bonded aggregates of nitro compounds and acids are the kinetically competent Brønsted acid catalysts. Specific weak H-bond accepting additives may offer a new general approach to accelerating Brønsted acid catalysis in solution.

Dynamic asymmetry and the role of the conserved active-site thiol in rabbit muscle creatine kinase.

Symmetric and asymmetric crystal structures of the apo and transition state analogue forms, respectively, of the dimeric rabbit muscle creatine kinase have invoked an "induced fit" explanation for asymmetry between the two subunits and their active sites. However, previously reported thiol reactivity studies at the dual active-site cysteine 283 residues suggest a more latent asymmetry between the two subunits. The role of that highly conserved active-site cysteine has also not been clearly determined. In this work, the S-H vibrations of Cys283 were observed in the unmodified MM isoform enzyme via Raman scattering, and then one and both Cys283 residues in the same dimeric enzyme were modified to covalently attach a cyano group that reports on the active-site environment via its infrared CN stretching absorption band while maintaining the catalytic activity of the enzyme. Unmodified and Cys283-modified enzymes were investigated in the apo and transition state analogue forms of the enzyme. The narrow and invariant S-H vibrational bands report a homogeneous environment for the unmodified active-site cysteines, indicating that their thiols are hydrogen bonded to the same H-bond acceptor in the presence and absence of the substrate. The S-H peak persists at all physiologically relevant pH's, indicating that Cys283 is protonated at all pH's relevant to enzymatic activity. Molecular dynamics simulations identify the S-H hydrogen bond acceptor as a single, long-resident water molecule and suggest that the role of the conserved yet catalytically unnecessary thiol may be to dynamically rigidify that part of the active site through specific H-bonding to water. The asymmetric and broad CN stretching bands from the CN-modified Cys283 suggest an asymmetric structure in the apo form of the enzyme in which there is a dynamic exchange between spectral subpopulations associated with water-exposed and water-excluded probe environments. Molecular dynamics simulations indicate a homogeneous orientation of the SCN probe group in the active site and thus rule out a local conformational explanation at the residue level for the multipopulation CN stretching bands. The homogeneous simulated SCN orientation suggests strongly that a more global asymmetry between the two subunits is the cause of the CN probe's broad and asymmetric infrared line shape. Together, these spectral observations localized at the active-site cysteines indicate an intrinsic, dynamic asymmetry between the two subunits that exists already in the apo form of the dimeric creatine kinase enzyme, rather than being induced by the substrate. Biochemical and methodological consequences of these conclusions are considered.