Enzymes are extremely efficient catalysts. Here, part of the mechanisms proposed to explain this catalytic power will be compared to quantitative experimental results and computer simulations. Influence of the enzymatic environment over species along the reaction coordinate will be analysed. Concepts of transition state stabilisation and reactant destabilisation will be confronted. Divided site model and near-attack conformation hypotheses will also be discussed. Molecular interactions such as covalent catalysis, general acid-base catalysis, electrostatics, entropic effects, steric hindrance, quantum and dynamical effects will also be analysed as sources of catalysis. Reaction mechanisms, in particular that catalysed by protein tyrosine phosphatases, illustrate the concepts.
The preparation of enantiomerically pure or enriched substances is of fundamental importance to pharmaceutical, food, agrochemical, and cosmetics industries and involves a growing market of hundreds of billions of dollars. However, most chemical processes used for their production are not environmentally friendly because in most cases, stoichiometric amounts of chiral inductors are used and substantial waste is produced. In this context, asymmetric catalysis has emerged as an efficient tool for the synthesis of enantiomerically enriched compounds using chiral catalysts. More specifically, considering the current scenario in the Brazilian chemical industry, especially that of pharmaceuticals, the immediate prospect for the use of synthetic routes developed in Brazil in an enantioselective fashion or even the discovery of new drugs is practically null. Currently, the industrial production of drugs in Brazil is primarily focused on the production of generic drugs and is basically supported by imports of intermediates from China and India. In order to change this panorama and move forward toward the gradual incorporation of genuinely Brazilian synthetic routes, strong incentive policies, especially those related to continuous funding, will be needed. These incentives could be a breakthrough once we establish several research groups working in the area of organic synthesis and on the development and application of chiral organocatalysts and ligands in asymmetric catalysis...
Arginine kinase belongs to the family of enzymes, including creatine kinase, that catalyze the buffering of ATP in cells with fluctuating energy requirements and that has been a paradigm for classical enzymological studies. The 1.86-Å resolution structure of its transition-state analog complex, reported here, reveals its active site and offers direct evidence for the importance of precise substrate alignment in the catalysis of bimolecular reactions, in contrast to the unimolecular reactions studied previously. In the transition-state analog complex studied here, a nitrate mimics the planar γ-phosphoryl during associative in-line transfer between ATP and arginine. The active site is unperturbed, and the reactants are not constrained covalently as in a bisubstrate complex, so it is possible to measure how precisely they are pre-aligned by the enzyme. Alignment is exquisite. Entropic effects may contribute to catalysis, but the lone-pair orbitals are also aligned close enough to their optimal trajectories for orbital steering to be a factor during nucleophilic attack. The structure suggests that polarization, strain toward the transition state, and acid-base catalysis also contribute, but, in contrast to unimolecular enzyme reactions...
Gromova, I I; Kjeldsen, E; Svejstrup, J Q; Alsner, J; Christiansen, K; Westergaard, O
Fonte: PubMedPublicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 11/02/1993Português
Relevância na Pesquisa
We investigated topoisomerase I activity at a specific camptothecin-enhanced cleavage site by use of a partly double-stranded DNA substrate. The cleavage site belongs to a group of DNA topoisomerase I sites which is only efficiently cleaved by wild-type topoisomerase I (topo I-wt) in the presence of camptothecin. With a mutated camptothecin-resistant form of topoisomerase I (topo I-K5) previous attempts to reveal cleavage activity at this site have failed. On this basis it was questioned whether the mutant enzyme has an altered DNA sequence recognition or a changed rate of catalysis at the site. Utilizing a newly developed assay system we demonstrate that topo I-K5 not only recognizes and binds to the strongly camptothecin-enhanced cleavage site but also has considerable cleavage/religation activity at this particular DNA site. Thus, topo I-K5 has a 10-fold higher rate of catalysis and a 10-fold higher affinity for DNA relative to topo I-wt. Our data indicate that the higher cleavage/religation activity of topo I-K5 is a result of improved DNA binding and a concomitant shift in the equilibrium between cleavage and religation towards the religation step. Thus, a recently identified point mutation which characterizes the camptothecin-resistant topo I-K5 has altered the enzymatic catalysis without disturbing the DNA sequence specificity of the enzyme.
Unfolded RNase A is known to contain an equilibrium mixture of two forms, a slow-folding form (U1) and a fast-folding form (U2). If U1 is produced after unfolding by the slow cis-trans isomerization of proline residues about X-Pro imide bonds, then the formation of U1 should be catalyzed by strong acids. Therefore, the rate of formation of U1 has been measured at different HClO4 concentrations. After rapid unfolding of the native protein in concentrated HClO4 at 0°, the slow formation of U1 was measured by use of refolding assays. Catalysis of its formation was found at HClO4 concentrations above 5 M. The uncatalyzed reaction follows apparent first-order kinetics but, in the acid-catalyzed range, two reactions are found. The faster reaction produces two-thirds of the slow-folding species and shows acid catalysis above 5 M HClO4. Catalysis of the slower reaction begins at 8 M HClO4. The faster reaction shows a 100-fold increase in rate at 10.6 M HClO4 over the rate of the uncatalyzed reaction of 5 M. The activation enthalpy of the uncatalyzed reaction has been measured in two sets of unfolding conditions: ΔH‡ is 21.5 kcal/mol (1 kcal = 4.2 × 103 J) in 3.3 M HClO4 and 21.0 kcal/mol in 5 M guanidine HCl, pH 2.5.
The Fischer indole synthesis is perhaps the most powerful method for indole preparation, but it often suffers from low regioselectivities with unsymmetric aliphatic ketone substrates and strong acidic conditions and is not suitable for α,β-unsaturated ketones. In this article, we disclose an efficient synthesis of N-protected indoles from N-arylhydroxamic acids/N-aryl-N-hydroxycarbamates and a variety of alkynes via a cooperative gold and zinc catalysis. The zinc catalysis is similar to the related zinc ion catalysis in metalloenzymes such as human carbonic anhydrase II and substantially enhances the O-nucleophilicity of N-acylated hydroxamines by forming the corresponding Zn chelates. The Zn chelates can attack gold-activated alkynes to form O-alkenyl-N-arylhydroxamates, which can undergo facile 3,3-sigmatropic rearrangements and subsequent cyclodehydrations to yield N-protected indole products. This new chemistry offers several important improvements over the Fischer indole synthesis: a) the reaction conditions are mildly acidic and can tolerate sensitive groups such as Boc; b) broader substrate scopes including substrates with pendant carbonyl groups (reactive in the Fischer chemistry) and alkyl chlorides (e.g., 3f); c) better regioselectivities for the formation of 2-substituted indoles under much milder conditions; d) 2-alkenylindoles can be prepared readily in good to excellent yields...
The trigger loop (TL) in the RNA polymerase (RNAP) active center plays key roles in the reactions of nucleotide addition and RNA cleavage catalyzed by RNAP. The adjacent F loop (FL) was proposed to contribute to RNAP catalysis by modulating structural changes in the TL. Here, we investigate the interplay between these two elements during transcription by bacterial RNAP. Thermodynamic analysis of catalysis by RNAP variants with mutations in the TL and FL suggests that the TL is the key element required for temperature activation in RNAP catalysis, and that the FL promotes TL transitions during nucleotide addition. We reveal characteristic differences in the catalytic parameters between thermophilic Thermus aquaticus and mesophilic Deinococcus radiodurans RNAPs and identify the FL as an adaptable element responsible for the observed differеnces. Mutations in the FL also significantly affect the rate of intrinsic RNA cleavage in a TL-dependent manner. In contrast, much weaker effects of the FL and TL mutations on GreA-assisted RNA cleavage suggest that the FL-dependent TL transitions are not required for this reaction. Thus, functional interplay between the FL and TL is essential for various catalytic activities of RNAP and plays an adaptive role in catalysis by thermophilic and mesophilic enzymes.
Progressing green chemical technologies is significant to the sustainable development of chemical industry in China, as the energy and environment problems increasingly became great challenges to the whole society. The scientific connotation of sustainable energy chemical engineering can be generalized as green carbon/hydrogen science which means optimization of carbon/hydrogen atom economics based on high efficient catalysis and low-carbon emission. This review illustrated recent advances in developing sustainable technologies for applied catalysis in chemical industry of China, including the fields of high efficient conversion of heavy oil, green petrochemical catalytic technologies, clean utilization of coal and natural gas, promoting sustainable resources and clean energy, etc. Moreover, from the view of industrial point, some important common scientific problems were discussed and summarized, such as the relation between molecular diffusion and catalyzing efficiency, homogeneous catalysis in heterogeneous catalysts, in situ or operando characterization of industrial catalysis, etc., aiming to supplying a forward roadmap to academia and/or industry.
Most of the chemical reactions used to produce the molecules and materials that our societies need—for example, in the petrochemical and pharmaceutical industries, the synthesis of plastics and other materials, and the production of foods and drinks—make use of catalysts. These speed up the rate at which atoms and molecules rearrange themselves into new forms, and provide a degree of control over the shape and form of those rearrangements. Catalysts let us drive a chemical reaction in a selected direction, in preference to others that could occur. In this way they turn chemistry from crude cookery into a rational and precise form of molecular engineering. And always we can draw inspiration, and sometimes borrow tricks, from the delicate and precise catalytic processes that occur in nature, where enzymes carry out processes in aqueous solution and at mild temperatures and pressures that often we struggle to achieve with far more extreme conditions—such as the fixation of atmospheric nitrogen into useful forms. It is often claimed that this particular catalytic process—the Haber–Bosch process for converting nitrogen into ammonia, discovered just over a century ago—has, by making possible the synthesis of artificial fertilizers...
I report on two class III ACs of Mycobacterium tuberculosis which possess very different structural as well as catalytic characteristics: the mammalian-like membrane-anchored Rv1625c and the transcription-factor-attached Rv0386. As a complementary study to published data (Guo et al., 2001), additional point mutations were made which demonstrated the essential role of the six canonical amino acids for catalysis in Rv1625c. The cytosolic mutants of Rv1625c N372A, N372T and D300S were used to investigate dimerization with mammalian AC catalytic units. Rv1625c engineered to contain forskolin binding amino acids cannot be stimulated by the diterpene. The similarities in conformation and mechanisms of catalysis between ACs and GCs was confirmed through the formation of functional chimeras between Mycobacterium Rv1625c and a guanylyl cyclase of Paramecium. The versatility of the class III cyclase homology domains concerning their modular architectures and mechanisms of catalysis was demonstrated with the biochemical characterization of Rv0386. This enzyme has a substrate-defining mechanism distinctly different of that of mammalian ACs. In addition by using ATP as well as GTP as a substrate it is a unique AC isoform unknown so far. Mutational studies of the Rv0386 AC domain proved the essential role that is played by a glutamine and an asparagine instead of the canonical lysine and aspartate for recognition of ATP and GTP as substrates. Diffraction-quality crystals of this AC domain were obtained as a first step to decipher the molecular and structural particularities of its catalytic function. Sequence comparisons identified an ATPase...
Understanding enzymatic reactions has many invaluable implications that could lead to useful pharmaceutical and commercial applications. Phosphoryl transfer reactions are perhaps the most prevalent chemical transformations in Nature. Phosphate esters are highly resistant to hydrolytic and nucleophilic degradation in the absence of catalysts, and enzymes that faciliate phosphoryl transfer reactions are among the most catalytically efficient enzymes in Nature.
A common strategy for understanding enzyme catalysis involves designing small molecule enzyme mimics. Our approach is to focus on the reaction medium inside the enzyme active sites, which is generally accepted to be non-aqueous and have an effective dielectric constant like organic solvents. We find that by switching from water to light alcohols (methanol and ethanol), a dinuclear Zn(II) complex can accelerate the solvolytic cleavages of simple phosphate diesters (both DNA and RNA models) by 12 orders of magnitude relative to the background reactions. A series of detailed mechanistic investigations revealed that the catalyzed cleavage of phosphate diesters proceeds via a multi-step process. Furthermore, comparison between the catalysis observed in methanol and ethanol is provided. In addition...
The hairpin ribozyme catalyzes RNA cleavage in partially hydrated RNA films in the absence of added divalent cations. This reaction exhibits the characteristics associated with the RNA cleavage reaction observed under standard conditions in solution. Catalysis is a site-specific intramolecular transesterification reaction, requires the 2'-hydroxyl group of substrate nucleotide A(-1), and generates 2',3'-cyclic phosphate and 5'-hydroxyl termini. Mutations in both ribozyme and substrate abolish catalysis in hydrated films. The reaction is accelerated by cations that may enhance binding, conformational stability, and catalytic activity, and is inhibited by Tb3+. The reaction has an apparent temperature optimum of 4 degrees C. At this temperature, cleavage is slow (k(obs): 2 d(-1)) and progressive, with accumulation of cleavage products to an extent of 40%. The use of synthetic RNAs, chelators, and analysis of all reaction components by inductively coupled plasma-optical spectrophotometry (ICPOES) effectively rules out the possibility of contaminating divalent metals in the reactions. Catalysis is minimal under conditions of extreme dehydration, indicating that the reaction requires hydration of RNA by atmospheric water. Our results provide a further caution for those studying the biochemical activity of ribozymes in vitro and in cells...
Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether...
There exists a linear correlation between the effect of a salt on the rate of an enzymic reaction and its effect on the activation volume (delta V++) of the reaction. Salts that increase delta V++ invariably decrease the rate of the reaction, and vice versa. The salt effects on reaction rate are, however, much larger than would be predicted solely on the basis of pressure-volume work changes deriving from the observed alterations in delta V++. Different inorganic salts affect reaction rates and activation volumes in a manner that reflects the salts' positions in the Hofmeister series. These observations, taken in conjunction with data on the effects of salts on protein functional group (aminoacid side-chains and peptide linkages) hydration, lead us to propose the following hypothesis to account for salt activation and inhibition of catalysis. Aminoacid side-chains and peptide linkages located on or near the protein surface change their exposure to water during conformational events in catalysis. These protein group transfers are accompanied by large volume and energy changes that are due largely to changes in the organization of water around these groups. When these transfer processes occur during the rate-limiting step in catalysis...
1. Oxaloacetate synthesis catalysed by pyruvate carboxylase from a thermophilic Bacillus in the absence of acetyl-CoA required addition of high concentrations of pyruvate, MgATP2− and HCO3−, and at 45°C occurred at a maximum rate approx. 20% of that in the presence of a saturating concentration of acetyl-CoA. The apparent Km for HCO3− at pH7.8 was 400mm without acetyl-CoA, and 16mm with a saturating activator concentration. The relationship between reciprocal initial rate and reciprocal MgATP2− concentration was non-linear (convex-down) in the absence of acetyl-CoA, but the extent of deviation decreased as the activator concentration was increased. The relationship between reciprocal initial rate and reciprocal pyruvate concentration was non-linear (convex-down) in the presence or absence of acetyl-CoA. 2. The optimum pH for catalysis of oxaloacetate synthesis was similar in the presence or absence of acetyl-CoA. The variation with pH of apparent Km for HCO3− implicated residue(s) with pKa 8.6 in catalysis of the activator-independent oxaloacetate synthesis. 3. Linear Arrhenius and van't Hoff plots were observed for the temperature-dependence of oxaloacetate synthesis in the absence of acetyl-CoA over the range 25–55°C. Ea (activation energy) was 56.3kJ/mol and ΔH‡ (HCO3−) (enthalpy of activation) was −38.6kJ/mol. In the presence of acetyl-CoA...
For the novel interpretation of Raman spectrum from molecule at metal surface, the plasmon driven surface catalysis (PDSC) reactions have become an interesting topic in the research field of surface enhanced Raman scattering (SERS). In this work, the selective PDSC reactions of p,p’-dimercaptoazobenzene (DMAB) produced from para-aminothiophenol (PATP) or 4-nitrobenzenethiol (4NBT) were demonstrated in the Ag nanowires dimer-Au film systems. The different SERS spectra collected at individual part and adjacent part of the same nanowire-film system pointed out the importance of the electromagnetic field redistribution induced by image charge on film in this selective surface catalysis, which was confirmed by the simulated electromagnetic simulated electro- magnetic field distributions. Our result indicated this electromagnetic field redistribution induced selective surface catalysis was largely affected by the polarization and wavelength of incident light but slightly by the difference in diameters between two nanowires. Our work provides a further understanding of PDSC reaction in metal nanostructure and could be a deep support for the researches on surface catalysis and surface analysis.
The possibility of accelerating molecular reactions by lasers has attracted
considerable theoretical and experimental interest. A particular example of
laser-modified reaction dynamics is laser catalysis, a process in which the
tunneling through a potential barrier is enhanced by transient excitation to a
bound electronic state. We have performed detailed calculations of pulsed laser
catalysis on one- and two-dimensional potentials, as a function of the
reactants' collision energy and the laser's central frequency. In agreement
with previous CW results, the reactive lineshapes are Fano-type curves,
resulting from interference between nonradiative tunneling and the optically
assisted pathway. In contrast to the CW process, the power requirements of
pulsed laser catalysis are well within the reach of commonly used pulsed laser
sources, making an experimental realization possible. The laser catalysis
scenario is shown to be equivalent in the ``dressed'' state picture, to
resonant tunneling through a double-barrier potential, admitting perfect
transmission when the incident energy matches a quasibound state of the well
within the barriers. Possible applications for atom optics, solid-state
devices, and scanning tunneling microscopy, are discussed.; Comment: 13 pages...
Catalyzed symmetry breaking arises from a parametric enhancement of critical
fluctuations independently of the coupling strength. Symmetry-breaking
fermionic long-range fluctuations exhibit such an enhancement on negatively
curved spaces, as is known from mean-field studies. We study gravitational
catalysis from the viewpoint of the functional renormalization group using the
3d Gross-Neveu model as a specific example. We observe gravitational catalysis
towards a phase of broken discrete chiral symmetry both on a maximally
symmetric (AdS) and on a purely spatially curved manifold for constant negative
curvature (Lobachevsky plane). The resulting picture for gravitational
catalysis obtained from the renormalization flow is closely related to that of
magnetic catalysis. As an application, we estimate the curvature required for
subcritical systems of finite length to acquire a gravitionally catalyzed gap.; Comment: 13 pages, 3 figures
The key aspect of the remarkable organic catalysis that is observed to occur at the organic/water phase boundary, the so-called 'on-water' catalysis (Narayan et al 2005 Angew. Chem. 44 3275), was recently proposed to be the protruding OH groups of water molecules at the interface that interact with the transition state (TS) via hydrogen bonding and lower activation barriers (Jung and Marcus 2007 J. Am. Chem. Soc. 129 5492). In particular, the cycloaddition reaction of quadricyclane (Q) with dimethyl azodicarboxylate (DMAD) on-water was calculated to be more than 100 000 times more efficient in terms of rate constant than the neat reaction. In this paper, we review and consider a related reaction of Q with dimethyl acetylenedicarboxylate, where nitrogen, a good H-bond acceptor, in DMAD is replaced by carbon, a poor H-bond acceptor. A very low rate acceleration of acetylenedicarboxylate on-water relative to the neat reaction is obtained theoretically, as compared to DMAD on-water, due to the relatively low H-bonding ability of acetylenedicarboxylate with water at the TS relative to the reactants. We suggest that there may also be an 'intrinsic steric effect' or orientational advantage in the on-water catalysis in general, and both electronic and steric effects may be in operation for the smaller on-water catalysis for the cycloaddition reaction of quadricyclane and acetylenedicarboxylate. A preliminary quantum mechanical/molecular mechanical (QM/MM) simulation including 1264 water molecules for the on-water reaction of DMAD + Q also suggests that there are indeed approximately two–four more H-bonds between the TS and the dangling OH groups than between the reactants and the surface.
The present review surveys current chemical understanding of catalysis by addition and removal of an electron. As an overarching theme of this type of catalysis, we introduce the role of redox scales in oxidation and reduction reactions as a direct analogue of pK_a scales in acid/base catalysis. Each scale is helpful in determining the type of reactivity to be expected. In addition, we describe several means of generating electrons and holes via chemical reactions, plasmonic resonance, radiolytic, photochemical and electrochemical methods. We specifically draw parallels between the now well-established fields of photoredox catalysis and chemical opportunities made available by electrochemical methods. We highlight accessible potential ranges for a series of electrochemical solvents and provide a discussion on experimental design, pitfalls and some remaining challenges in preparative organic electrochemistry.