Ground State and Transition State Contributions to the Rates of Intramolecular and Enzymatic Reactions

Bruice, Thomas C.; Lightstone, Felice C.

doi:10.1021/ar960131y

Cited by 280 publications

(230 citation statements)

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“…One such reference state is the is the 'near-attack conformer' (NAC). [46,47] The NAC can be viewed as a point, or an area, on the potential energy surface, located between the bound enzyme-substrate complex and the TS, where the geometry of the system is preorganized for forming the TS and the atoms of the bonds that are formed in the TS are within van der Waals distance. Since the geometry of the NAC is similar to the TS, the interactions between the active site and the substrate(s) are similar in the NAC and the TS, except for those that directly influence the bond breaking/forming.…”

Section: Kinetics and Binding Dynamicsmentioning

confidence: 99%

“…If the diene binds tightly to the active site and in a geometry that is close to the NAC geometry, ∆G NAC will be low; typically for a natural enzyme binding a natural substrate, ∆G NAC is in the order of 0.5-2 kcal·mol −1 . [46,47] However, if the substrate binds loosely to the active site and retains substantial freedom of moment, ∆G NAC will be higher. Even higher values of ∆G NAC are expected if the substrate binds tightly but in a nonproductive fashion, i.e.…”

Section: Kinetics and Binding Dynamicsmentioning

confidence: 99%

“…We have used a slightly less rigorous definition that the original one stated by Bruice and colleagues, [46,47] as this allows us to reduce the sampling of data. Most important for our model to be valid is that the NAC definition is identical in both the MD and QC regime (see section 2.1).…”

Section: Simulations Of Substratesmentioning

confidence: 99%

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Computational design of a lipase for catalysis of the Diels-Alder reaction

et al. 2010

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Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the Diels-Alder reaction by a modified lipase. Six variants of the versatile enzyme {\em Candida Antarctica} lipase B (CALB) have been rationally engineered {\em in silico} based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity shape and size, and can be controlled by a few rational mutations. The well-documented S105A mutation is essential to enable sufficient space in the vicinity of the oxyanion hole. Moreover, bulky residues on the edge of the active site hinders the formation of a sandwich-like near-attack conformer (NAC), and the I189A mutation is needed to obtain enough space above the face of the $\alpha$,$\beta$-double bond on the dienophile. The double mutant S105A/I189A performs quite well for two of three dienophiles. Based on binding constants and NAC energies obtained from MD simulations combined with activation energies from DFT computations, relative catalytic rates ($v_{cat}/v_{uncat}$) of up to $10^3$ are predicted.Response to Reviewers: We are happy with the favorable comments by the reviewers. We have have corrected the manuscript as suggested by reviewer 1 1. A sentence explaining catalytic promiscuity has been added. 2. A paragraph discussing the relationship between the NAC concept and the Reaction Force has been added.We have shortened the manuscript as suggested by reviewer 2. In particular, we have moved information regarding the structural relaxation of protein structure in MD simulations to the supplementary material. Abstract Combined molecular docking, molecular dynamics (MD) and density functional theory (DFT) studies have been employed to study catalysis of the DielsAlder reaction by a modified lipase. Six variants of the versatile enzyme Candida Antarctica lipase B (CALB) have been rationally engineered in silico based on the specific characteristics of the pericyclic addition. A kinetic analysis reveals that hydrogen bond stabilization of the transition state and substrate binding are key components of the catalytic process. In the case of substrate binding, which has the greater potential for optimization, both binding strength and positioning of the substrates are important for catalytic efficiency. The binding strength is determined by hydrophobic interactions and can be tuned by careful selection of solvent and substrates. The MD simulations show that substrate positioning is sensitive to cavity s...

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Section: Kinetics and Binding Dynamicsmentioning

confidence: 99%

Section: Kinetics and Binding Dynamicsmentioning

confidence: 99%

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Computational design of a lipase for catalysis of the Diels-Alder reaction

et al. 2010

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“…A related issue addressed here is the question of whether certain thermal Brownian motions of an enzymesubstrate complex (E⅐S) participate in lowering the energy barrier of activation (6) by creating the most reactive groundstate conformations [near-attack conformers (NACs) (7)]. One such possibility is that ground-state conformations, which lead directly to the lowest energy-transition state (NACs), are formed with assistance of anticorrelated motions of residues proximal to the active site.…”

mentioning

confidence: 99%

Anticorrelated motions as a driving force in enzyme catalysis: The dehydrogenase reaction

Luo

Bruice

2004

Proc. Natl. Acad. Sci. U.S.A.

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A present issue concerns the occurrence of rate-promoting vibrations, which assist in lowering barrier height in enzyme catalysis (1-5). A related issue addressed here is the question of whether certain thermal Brownian motions of an enzymesubstrate complex (E⅐S) participate in lowering the energy barrier of activation (6) by creating the most reactive groundstate conformations [near-attack conformers (NACs) (7)]. One such possibility is that ground-state conformations, which lead directly to the lowest energy-transition state (NACs), are formed with assistance of anticorrelated motions of residues proximal to the active site.From Eq. 1, the free energy of activation is equal to the sum of the standard free energies for formation of reactive E⅐NAC conformers (⌬GЊ NAC ) plus the activation energy (⌬G TS ‡ ) for conversion of E⅐NAC to E⅐TS as shown in Eq. 2.We report here the findings of a study of correlated and anticorrelated motions of an E⅐S complex, the role of certain anticorrelated motions in the formation of E⅐NAC, as well as the demonstration that reactions that pass through E⅐NAC follow a kinetically favored trajectory. The reaction of interest is the oxidation of a primary alcohol by horse liver alcohol dehydrogenase (HLADH⅐NAD ϩ ). The computational tools used have been molecular dynamics (MD) simulations, crosscorrelation analysis, and quantum mechanics (QM)͞molecular mechanics (MM).HLADH (EC 1.1.1.1) (8) consists of two subunits of identical composition in which a 12-stranded ␤-sheet makes up the central core (9). Each subunit binds a molecule of NAD ϩ and a Zn 2ϩ at the active site and an additional Zn 2ϩ , which is structural. Alcohol oxidation by NAD ϩ involves first the proton dissociation of RCH 2 OH followed by transfer of a hydride equivalent from RCH 2 O Ϫ to NAD ϩ (Eq. 3).In an earlier study we carried out MD simulations (10) for 1-2 ns the structures of HLADH⅐NAD ϩ ⅐PhCH 2 OH, HLADH⅐NAD ϩ ⅐PhCH 2 O Ϫ , and HLADH⅐NADH⅐PhCHO using one subunit covered by a 32-Å-radius pool of transferable intermolecular potential three-point water molecules. By doing so we were able to derive an ensemble of dynamic conformations for the reactive HLADH⅐NAD ϩ ⅐PhCH 2 O Ϫ species, define the paths of H ϩ transfer to water, and established the presence of a water channel, which facilitates proton shuttling (10). We reported that the Michaels complex assumed the conformation of a reactive conformer [NAC (7)] 60% of the time. We defined the NAC as a conformer in which the distances between the transferring of an H Ϫ equivalent from C7 of PhCH 2 O Ϫ and acceptor C4 of NAD ϩ are Յ3.0 Å (3.9 Å for the heavy atoms C7 and C4) and the angles of C7-H-NC4 range from 132°to 180°. Concurrently, an investigation from Karplus and coworkers (11) appeared in which the kinetic features, the adiabatic potential barrier heights, the rate constants (including quantum mechanical effects such as tunneling), and potential of mean force of the HLADH⅐NAD ϩ ⅐PhCH 2 O Ϫ species were described by use of self-consistent charge density functio...

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“…Bruice 29 introduziu o conceito de conformação próxima ao ataque (NAC), definido como a configuração estrutural que os reagentes precisam assumir para chegar ao TS. A análise conformacional de uma série de reações intramoleculares de ciclização de ácidos dicarboxílicos indicou que a fração molar dos reagentes em NACs (definidas de acordo com critérios geométricos como distância e ângulo da ligação em formação) era diretamente proporcional à velocidade da ciclização intramolecular e formação de anidrido (Figura 4) 29 .…”

Section: Conformação Próxima Ao Ataqueunclassified

Uma perspectiva computacional sobre catálise enzimática

Arantes¹

2008

Quím. Nova

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Recebido em 24/11/06; aceito em 18/5/07; publicado na web em 19/12/07 A COMPUTATIONAL PERSPECTIVE ON ENZYMATIC CATALYSIS. 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.Keywords: enzymatic catalysis; computer simulation; reaction mechanism. INTRODUÇÃOEnzimas são catalisadores de extraordinária eficiência. Os aumentos de velocidade de reações alcançados por enzimas podem chegar a vinte ordens de magnitude 1 ! Por outro lado, enzimas possuem uma grande especificidade pelos substratos, sua atividade é controlável e totalmente seletiva.Sob uma perspectiva teórica, a sugestão de Fischer 2 , conhecida como a hipótese da "chave e fechadura", foi a primeira proposta para explicar o poder catalítico das enzimas. Com o advento da teoria do estado de transição 3 nos anos 1930, Pauling 4 propôs que esta espécie seria preferencialmente ligada pelo sítio ativo enzimático. Já em 1969, Jencks 5 escreveu que "o estudo dos mecanismos moleculares de catálise enzimática é necessariamente empírico e qualitativo". No entanto, nos últimos 30 anos, simulações computacionais que permitem determinações quantitativas de propriedades termodinâmicas têm alterado este panorama, apontando e quantificando os mecanismos catalíticos empregados por enzimas.Cabem aqui duas definições. O termo "mecanismo catalítico" é usado para descrever as forças ou interações microscópicas utilizadas pelas enzimas para amplificar a velocidade de reações. Já "mecanismo de reação" é a seqüência de transformações (quebra e formação de ligações químicas) e mudanças de estrutura do complexo enzimático observadas ao longo do progresso da reação.Diversos mecanismos catalíticos já foram propostos para explicar as acelerações enzimáticas em nível microscópico. Por exemplo, Menger contabilizou 21 teorias sobre catálise enzimática 6 . Este número é elevado em conseqüência de diferentes interpretações semânticas e imprecisas definições de quantidades termodinâmicas nas teorias propostas, e também porque a maior parte destas teorias não foi (ou não pode ser) testada quantitativamente. Portanto, há muita controvérsia sobre a importância de cada um dos diferentes mecanismos e teorias propostos para explicar o poder catalítico das enzimas 7-9 . Sem dúvida, cada enzima possui sua própria "receita" 6 para catálise, em que uma combinação das interações prop...

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Ground State and Transition State Contributions to the Rates of Intramolecular and Enzymatic Reactions

Cited by 280 publications

References 40 publications

Computational design of a lipase for catalysis of the Diels-Alder reaction

Computational design of a lipase for catalysis of the Diels-Alder reaction

Anticorrelated motions as a driving force in enzyme catalysis: The dehydrogenase reaction

Uma perspectiva computacional sobre catálise enzimática

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