We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp(128)beta in a reaction dominated by tunneling over approximately 0.6 angstroms. The role of long-range coupled motions in promoting tunneling is controversial. We show that, in this enzyme system, tunneling is promoted by a short-range motion modulating proton-acceptor distance and no long-range coupled motion is required.

The accurate prediction of enzyme kinetics from first principles is one of the central goals of theoretical biochemistry. Currently there is considerable debate [1][2][3] about the applicability of transition state theory (TST) to compute rate constants of enzyme-catalyzed reactions. Classical TST is known to be insufficient in some cases, but corrections for dynamical recrossing and quantum mechanical tunneling can be included. [1,2,4] Many effects that go beyond the framework of TST have been proposed, particularly focusing on the possible role of protein dynamics and conformational effects on the enzyme activity. Unfortunately, the overall importance of these effects for the effective reaction rate is difficult (if not impossible) to determine experimentally. However, if one could compute the quasi-thermodynamical free energy of activation with chemical accuracy (i.e. 1 kcal mol À1 ), comparison with the effective measured free energy of activation would directly show the importance of other effects.Combined quantum mechanical/molecular mechanical (QM/MM) methods have become an important tool for computational modeling of enzyme-catalyzed reactions. Only the substrate(s) and relevant residues in the active site are treated quantum mechanically, the rest of the protein is described at the empirical MM level. This lowers the computational expense, making it possible to treat large enzyme systems and the surrounding solvent, and to sample phase space. Nevertheless, the number of QM atoms is still relatively large, and until now only low levels of QM theory, such as semiempirical methods or density functional theory (DFT), have been feasible. Semiempirical methods, though applicable to large systems, are generally not accurate enough because computed free energies of activation may have an error of ten or more kcal mol À1 . DFT (especially with the B3LYP functional [5] ) offers improved accuracy but still lacks key physical interactions (e.g., dispersion). Often, DFT underestimates barrier heights by several kcal mol À1 , which cannot be systematically improved. Thus, when theoretical barriers do not agree with those from experiment, it is not clear whether the discrepancy arises from deficiencies in the electronic structure theory and the sampling, in the experimental observations, or in the underlying theoretical framework of QM/MM and TST.Consequently, there is a need for high-level electronic structure calculations for reliable predictions of enzyme reactivity. The ab initio electron correlation methods MP2 (Møller-Plesset second-order perturbation theory), CCSD (coupled-cluster theory with single and double excitations), and CCSD(T) (CCSD with a perturbative treatment of triple excitations) provide a well-established hierarchy that converge reliably to give high accuracy, and rate constants of gasphase reactions involving only a few atoms can be predicted with error bars comparable to those found experimentally. [6,7] However, the computational expense of these methods increases very rapidly with the number o...

Chorismate mutase is a key model system in the development of theories of enzyme catalysis. To analyze the physical nature of catalytic interactions within the enzyme active site and to estimate the stabilization of the transition state (TS) relative to the substrate (differential transition state stabilization, DTSS), we have carried out nonempirical variation-perturbation analysis of the electrostatic, exchange, delocalization, and correlation interactions of the enzyme-bound substrate and transition-state structures derived from ab initio QM/MM modeling of Bacillus subtilis chorismate mutase. Significant TS stabilization by approximately -23 kcal/mol [MP2/6-31G(d)] relative to the bound substrate is in agreement with that of previous QM/MM modeling and contrasts with suggestions that catalysis by this enzyme arises purely from conformational selection effects. The most important contributions to DTSS come from the residues, Arg90, Arg7, Glu78, a crystallographic water molecule, Arg116, and Arg63, and are dominated by electrostatic effects. Analysis of the differential electrostatic potential of the TS and substrate allows calculation of the catalytic field, predicting the optimal location of charged groups to achieve maximal DTSS. Comparison with the active site of the enzyme from those of several species shows that the positions of charged active site residues correspond closely to the optimal catalytic field, showing that the enzyme has evolved specifically to stabilize the TS relative to the substrate.

To investigate fundamental features of enzyme catalysis, there is a need for high-level calculations capable of modelling crucial, unstable species such as transition states as they are formed within enzymes. We have modelled an important model enzyme reaction, the Claisen rearrangement of chorismate to prephenate in chorismate mutase, by combined ab initio quantum mechanics/molecular mechanics (QM/MM) methods. The best estimates of the potential energy barrier in the enzyme are 7.4-11.0 kcal mol(-1)(MP2/6-31+G(d)//6-31G(d)/CHARMM22) and 12.7-16.1 kcal mol(-1)(B3LYP/6-311+G(2d,p)//6-31G(d)/CHARMM22), comparable to the experimental estimate of Delta H(++)= 12.7 +/- 0.4 kcal mol(-1). The results provide unequivocal evidence of transition state (TS) stabilization by the enzyme, with contributions from residues Arg90, Arg7, and Arg63. Glu78 stabilizes the prephenate product (relative to substrate), and can also stabilize the TS. Examination of the same pathway in solution (with a variety of continuum models), at the same ab initio levels, allows comparison of the catalyzed and uncatalyzed reactions. Calculated barriers in solution are 28.0 kcal mol(-1)(MP2/6-31+G(d)/PCM) and 24.6 kcal mol(-1)(B3LYP/6-311+G(2d,p)/PCM), comparable to the experimental finding of Delta G(++)= 25.4 kcal mol(-1) and consistent with the experimentally-deduced 10(6)-fold rate acceleration by the enzyme. The substrate is found to be significantly distorted in the enzyme, adopting a structure closer to the transition state, although the degree of compression is less than predicted by lower-level calculations. This apparent substrate strain, or compression, is potentially also catalytically relevant. Solution calculations, however, suggest that the catalytic contribution of this compression may be relatively small. Consideration of the same reaction pathway in solution and in the enzyme, involving reaction from a 'near-attack conformer' of the substrate, indicates that adoption of this conformation is not in itself a major contribution to catalysis. Transition state stabilization (by electrostatic interactions, including hydrogen bonds) is found to be central to catalysis by the enzyme. Several hydrogen bonds are observed to shorten at the TS. The active site is clearly complementary to the transition state for the reaction, stabilizing it more than the substrate, so reducing the barrier to reaction.

No abstract

Terpenoids form the largest and stereochemically most diverse class of natural products, and there is considerable interest in producing these by biocatalysis with whole cells or purified enzymes, and by metabolic engineering. The monoterpenes are an important class of terpenes and are industrially important as flavors and fragrances. We report here structures for the recently discovered Streptomyces clavuligerus monoterpene synthases linalool synthase (bLinS) and 1,8-cineole synthase (bCinS), and we show that these are active biocatalysts for monoterpene production using biocatalysis and metabolic engineering platforms. In metabolically engineered monoterpene-producing E. coli strains, use of bLinS leads to 300-fold higher linalool production compared with the corresponding plant monoterpene synthase. With bCinS, 1,8-cineole is produced with 96% purity compared to 67% from plant species. Structures of bLinS and bCinS, and their complexes with fluorinated substrate analogues, show that these bacterial monoterpene synthases are similar to previously characterized sesquiterpene synthases. Molecular dynamics simulations suggest that these monoterpene synthases do not undergo large-scale conformational changes during the reaction cycle, making them attractive targets for structured-based protein engineering to expand the catalytic scope of these enzymes toward alternative monoterpene scaffolds. Comparison of the bLinS and bCinS structures indicates how their active sites steer reactive carbocation intermediates to the desired acyclic linalool (bLinS) or bicyclic 1,8-cineole (bCinS) products. The work reported here provides the analysis of structures for this important class of monoterpene synthase. This should now guide exploitation of the bacterial enzymes as gateway biocatalysts for the production of other monoterpenes and monoterpenoids.

Proton tunneling dominates the oxidative deamination of tryptamine catalyzed by the enzyme aromatic amine dehydrogenase. For reaction with the fast substrate tryptamine, a H/D kinetic isotope effect (KIE) of 55 +/- 6 has been reported-one of the largest observed in an enzyme reaction. We present here a computational analysis of this proton-transfer reaction, applying combined quantum mechanics/molecular mechanics (QM/MM) methods (PM3-SRP//PM3/CHARMM22). In particular, we extend our previous computational study (Masgrau et al. Science 2006, 312, 237) by using improved energy corrections, high-level QM/MM methods, and an ensemble of paths to estimate the tunneling contributions. We have carried out QM/MM molecular dynamics simulations and variational transition state theory calculations with small-curvature tunneling corrections. The results provide detailed insight into the processes involved in the reaction. Transfer to the O2 oxygen of the catalytic base, Asp128beta, is found to be the favored reaction both thermodynamically and kinetically, even though O1 is closer in the reactant complex. Comparison of quantum and classical models of proton transfer allows estimation of the contribution of hydrogen tunneling in lowering the barrier to reaction in the enzyme. A reduction of the activation free energy due to tunneling of 3.1 kcal mol-1 is found, which represents a rate enhancement due to tunneling by 2 orders of magnitude. The calculated KIE of 30 is significantly elevated over the semiclassical limit, in agreement with the experimental observations; a semiclassical value of 6 is obtained when tunneling is omitted. A polarization of the C-H bond to be broken is observed due to the close proximity of the catalytic aspartate and the (formally) positively charged imine nitrogen. A comparison is also made with the related quinoprotein methylamine dehydrogenase (MADH)-the much lower KIE of 11 that we obtain for the MADH/methylamine system is found to arise from a more endothermic potential energy surface for the MADH reaction.

The accurate prediction of enzyme kinetics from first principles is one of the central goals of theoretical biochemistry. Currently there is considerable debate [1][2][3] about the applicability of transition state theory (TST) to compute rate constants of enzyme-catalyzed reactions. Classical TST is known to be insufficient in some cases, but corrections for dynamical recrossing and quantum mechanical tunneling can be included. [1,2,4] Many effects that go beyond the framework of TST have been proposed, particularly focusing on the possible role of protein dynamics and conformational effects on the enzyme activity. Unfortunately, the overall importance of these effects for the effective reaction rate is difficult (if not impossible) to determine experimentally. However, if one could compute the quasi-thermodynamical free energy of activation with chemical accuracy (i.e. 1 kcal mol À1 ), comparison with the effective measured free energy of activation would directly show the importance of other effects.Combined quantum mechanical/molecular mechanical (QM/MM) methods have become an important tool for computational modeling of enzyme-catalyzed reactions. Only the substrate(s) and relevant residues in the active site are treated quantum mechanically, the rest of the protein is described at the empirical MM level. This lowers the computational expense, making it possible to treat large enzyme systems and the surrounding solvent, and to sample phase space. Nevertheless, the number of QM atoms is still relatively large, and until now only low levels of QM theory, such as semiempirical methods or density functional theory (DFT), have been feasible. Semiempirical methods, though applicable to large systems, are generally not accurate enough because computed free energies of activation may have an error of ten or more kcal mol À1 . DFT (especially with the B3LYP functional [5] ) offers improved accuracy but still lacks key physical interactions (e.g., dispersion). Often, DFT underestimates barrier heights by several kcal mol À1 , which cannot be systematically improved. Thus, when theoretical barriers do not agree with those from experiment, it is not clear whether the discrepancy arises from deficiencies in the electronic structure theory and the sampling, in the experimental observations, or in the underlying theoretical framework of QM/MM and TST.Consequently, there is a need for high-level electronic structure calculations for reliable predictions of enzyme reactivity. The ab initio electron correlation methods MP2 (Møller-Plesset second-order perturbation theory), CCSD (coupled-cluster theory with single and double excitations), and CCSD(T) (CCSD with a perturbative treatment of triple excitations) provide a well-established hierarchy that converge reliably to give high accuracy, and rate constants of gasphase reactions involving only a few atoms can be predicted with error bars comparable to those found experimentally. [6,7] However, the computational expense of these methods increases very rapidly with the number o...