Chemical Basis for Enzyme Catalysis

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In aqueous solution, Medicago savita chalcone isomerase (CHI) enhances the reaction rate for the unimolecular rearrangement of chalcone (CHN) into flavanone by seven orders of magnitude. Conformations of CHN and their relative free energies in water and CHI were investigated by the thermodynamic perturbation method. In water, CHN adopts two conformations (I and II) with conformation I being higher in energy than conformation II by 3 kcal͞mol. Only I can give rise to a near attack conformer (NAC) where the nucleophile O2 and the electrophile C9 are placed in proximity. In CHI, I binds less tightly than II by Ϸ2 kcal͞mol, resulting in the free energy for NAC formation being Ϸ2 kcal͞mol higher in the enzyme than in water. This unfavorable feature in the ground state of the CHI reaction requires the predominant catalytic advantage to be taken in the step of NAC 3 transition state (TS). From the molecular dynamics simulations of apo-CHI, CHI complexed with CHN (CHI⅐CHN) and CHI⅐TS, we found: (i) Lys-97-general-acid catalysis of the O2 ؊ nucleophilic addition; (ii) expulsion of three water molecules in the process of TS formation; (iii) release of enzyme structural distortion on TS formation. In the conclusion, CHI's remarkable efficiency of stabilizing the TS and its relatively poor ability in organizing the ground state is compared with chorismate mutase whose catalytic prowess, when compared with water, originates predominantly from the enhanced NAC population at the active site.T he intramolecular ring-closure reaction of chalcone 3 flavanone (see Scheme 1) has been studied extensively structurally and mechanistically (1-3). The rate constant k cat is 38 s Ϫ1 for the enzymatic reaction, and k non is 10 Ϫ6 s Ϫ1 for the water reaction (1). The pH dependences of the noncatalyzed and catalyzed reactions are much the same, suggesting that ionization of the substrate phenolic O2Ј occurs in water for both enzymatic and nonenzymatic reactions (1). The crystal structures of chalcone isomerase (CHI) complexed with flavanones reveal an absence of an enzyme-based nucleophilic species near the substrate, showing that CHI is not directly involved in the enzymatic reaction through covalent interaction (3). Drawing on all experimental data, Noel and colleagues (2, 3) explain the catalytic mechanism of CHI as a combination of two effects. One is active site molding of the substrate into the reactive conformation and the other is stabilization of the enolate-like transition state (TS) by forming a hydrogen-bonding network with Thr-48 and Tyr-106 at the ketone O7. However, quantitative comparison of these two contributions has not been reached because of the experimental difficulty of perturbing each component selectively. Here we report our computational studies to assess the relative importance of ground state and TS effects in the CHI catalysis.We have used two methods to achieve this goal. First, we measure the free energies (⌬G N°v alues) for forming reactive ground-state conformers [near attack conformers (NACs), ref. 4] in ...

Section: Resultsmentioning

confidence: 99%

“…First, we measure the free energies (⌬G N°v alues) for forming reactive ground-state conformers [near attack conformers (NACs), ref. 4] in water and at the enzyme active site. Formation of NAC is a prerequisite for reactants to enter the reaction regardless of the environment.…”

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confidence: 99%

Transition state stabilization by general acid catalysis, water expulsion, and enzyme reorganization in Medicago savita chalcone isomerase

Hur

Newby²,

Bruice³

2004

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“…Sterically constraining chorismate in a "near attack conformation" (NAC) (15)(16)(17)21), in which the reacting centers are confined to contact distances, would be expected to increase the probability of reaction. Ground state destabilization through conformational compression has been shown to afford large rate accelerations for Claisen rearrangements in synthetic model systems (22).…”

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confidence: 99%

Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis

Burschowsky

Eerde

Ökvist

et al. 2014

For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrates, thereby lowering the activation energy compared with that of the corresponding uncatalyzed process. This paradigm has been challenged for chorismate mutase (CM), a well-characterized metabolic enzyme that catalyzes the rearrangement of chorismate to prephenate. Calculations have predicted the decisive factor in CM catalysis to be ground state destabilization rather than transition state stabilization. Using X-ray crystallography, we show, in contrast, that a sluggish variant of Bacillus subtilis CM, in which a cationic active-site arginine was replaced by a neutral citrulline, is a poor catalyst even though it effectively preorganizes chorismate for the reaction. A series of high-resolution molecular snapshots of the reaction coordinate, including the apo enzyme, and complexes with substrate, transition state analog and product, demonstrate that an active site, which is only complementary in shape to a reactive substrate conformer, is insufficient for effective catalysis. Instead, as with other enzymes, electrostatic stabilization of the CM transition state appears to be crucial for achieving high reaction rates.pericyclic reaction | catalysis | enzyme mechanism | near attack conformation | X-ray crystal structures

“…catalysis ͉ polymer ͉ polyolefin E nzymes achieve superior reactivity and selectivity, in part, by their efficacy in creating high local reagent concentrations and special, conformationally advantageous active site-substrate proximities and interactions (1)(2)(3)(4). In this regard, the possibility of unique and more efficient abiotic catalytic transformations based on cooperative effects between adjacent active centers in multinuclear transition metal complexes is currently of great interest.…”

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confidence: 99%

Nuclearity and cooperativity effects in binuclear catalysts and cocatalysts for olefin polymerization

Marks

2006

225

109

A series of bimetallic organo-group 4 ''constrained geometry'' catalysts and binuclear bisborane and bisborate cocatalysts have been synthesized to probe catalyst center-catalyst center cooperativity effects on olefin enchainment in homogenous olefin polymerization and copolymerization processes. Significant nuclearity effects are found versus mononuclear controls, and the effect can be correlated with metal-metal approach distances and ion pairing effects. Novel polymer structures can be obtained by using such binuclear catalyst͞cocatalyst systems.catalysis ͉ polymer ͉ polyolefin E nzymes achieve superior reactivity and selectivity, in part, by their efficacy in creating high local reagent concentrations and special, conformationally advantageous active site-substrate proximities and interactions (1-4). In this regard, the possibility of unique and more efficient abiotic catalytic transformations based on cooperative effects between adjacent active centers in multinuclear transition metal complexes is currently of great interest. Within the context of the rapidly advancing and technologically significant field of homogeneous single-site olefin polymerization catalysis (5-10), the conjecture that cooperative effects involving two or more metal centers in close proximity might achieve more efficient chain propagation and͞or novel polymer architectures motivated the research that is the subject of this contribution. Single-Site Olefin Polymerization ProcessesOne of the most exciting developments in the areas of catalysis, organometallic chemistry, and polymer science in recent years has been the intense development of new polymerization technologies based on well defined single-site metallocene and coordination complex olefin polymerization catalysts (5-10). The active catalytic species is typically generated by combining a transition-metal organometallic precursor with an activator or cocatalyst. The resulting electrophilic͞coordinatively unsaturated, strongly ionpaired species then undergoes rapid olefin enchainment. In optimum cases (e.g., group 4 metal and cyclopentadienyl-type ligand), catalysts with truly exceptional productivities and selectivities for high-molecular-weight polyolefins are produced. Constrained Geometry Catalysts: Testbeds for Multinuclear Cooperativity EffectsGroup 4 ''constrained geometry'' catalysts (CGCs) (A; Fig. 1) are well known single-site polymerization agents (16, 17) that produce unusual branched, hence far more processable, polyethylenes with high productivity and selectivity. One of the key features of these catalysts is the coordinatively open nature of the active site, which allows rapid enchainment of sterically encumbered olefin comonomers into the polyethylene backbone. Under certain conditions, these catalysts yield vinyl-terminated, chain-transferred macromonomers (a macromolecule that acts as a monomer) that diffuse away and then undergo competitive reinsertion into a growing polymer chain to produce macromolecules with long chain branching (Fig. 19, which is published ...