Potential Of Mean Force Profiles Research Articles

A quantum mechanical/molecular mechanical study of the aspartic protease plasmepsin IV complexed with allophenylnorstatine-based inhibitor

Plasmepsin IV (PM IV) is a potential target for developing drugs against malaria. This Letter presents results of QM/MM dynamic simulations applied to the study of the protonation state of two aspartates (Asp34 and Asp214) catalytic residues of PM IV in complex with KNI-764 inhibitor. The potential of mean force profile was used to assign the protonation state of the two catalytic aspartates in PM IV–KNI-764 complex. The results indicate that protonation of the 214 residue is more favorable. In addition, energy terms decomposition was used to explore key interactions between the main residues and KNI-764 inhibitor.

Brownian Dynamics Simulations of Ion Transport through the VDAC

It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions.

Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD–PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

Potential of mean force for separation of the repeating units in cellulose and hemicellulose

As a first step toward understanding the energetics of removal of cello-oligomers from the cellulose surface, we have performed umbrella sampling calculations to determine the free energy required for separation of repeating units of cellulose and hemicellulose from each other. Molecular dynamics (MD) simulations were performed for both the stacked and non-stacked arrangements of the cellobiose pair system and the xylobiose pair system. These stacked and non-stacked arrangements were taken as representative systems for the crystalline and amorphous domains in cellulose and hemicellulose. In addition, similar calculations were also carried out to determine the energetics involved in the separation of the cellobiose–xylobiose molecule pair in the non-stacked arrangement. The potential of mean force profiles exhibit a single minimum in all cases and are qualitatively similar. Our results show that the location of the minimum as well as the depth of the well can be correlated with the size of the disaccharide molecules.

Understanding the nitrate coordination to Eu3+ ions in solution by potential of mean force calculations

Coordination of nitrate anions with lanthanoid cations (Ln(3+)) in water, methanol and octanol-1 has been studied by means of molecular dynamics simulations with explicit polarization. Potential of mean force (PMF) profiles have been calculated for a mono-complex of lanthanoid nitrate (Ln(NO(3))(2+)) in these solvents using umbrella-sampling molecular dynamics. In pure water, no difference in the nitrato coordination to lanthanoids (Nd(3+), Eu(3+) and Dy(3+)) is observed, i.e. the nitrate anion prefers the monodentate coordination, which promotes the salt dissociation. Then, the influence of the nature of the solvating molecules on the nitrato coordination to Eu(3+) has been investigated. PMF profiles point out that both monodenate and bidentate coordinations are stable in neat methanol, while in neat octanol, only the bidentate one is. MD simulations of Eu(NO(3))(3) in water-octanol mixtures with different concentrations of water have been then performed and confirm the importance of the water molecules' presence on the nitrate ion's coordination mode.

Active Participation of the Mg2+ Ion in the Reaction Coordinate of RNA Self-Cleavage Catalyzed by the Hammerhead Ribozyme

We report results from combined quantum mechanical/molecular mechanical (QM/MM) free energy simulations to explore metal-assisted phosphoryl transfer and general acid catalysis in the extended hammerhead ribozyme. The mechanisms considered here assume that the 2′OH group of C17 has already been activated (i.e., is deprotonated) and acts as a nucleophile to go on an in-line attack to the adjacent scissile phosphate, passing through a pentavalent phosphorane intermediate/transition state, followed by acid-catalyzed departure of the O5′ leaving group of C1.1. A series of six two-dimensional potential of mean force profiles are reported in this study, requiring an aggregate of over 100 ns of QM/MM simulation. The simulations employ the AM1/d-PhoT semiempirical quantum model and linear-scaling QM/MM-Ewald method and explore mechanistic pathways for the self-cleavage. Results support the plausibility of a cleavage mechanism where phosphoryl transfer and general acid catalysis are stepwise, and where the catalytic divalent metal ion plays an active role in the chemical steps of catalysis.

Role of the Bile Salt Surfactant Sodium Cholate in Enhancing the Aqueous Dispersion Stability of Single-Walled Carbon Nanotubes: A Molecular Dynamics Simulation Study

Very recently, bile salt biosurfactants have been utilized extensively to disperse individual single-walled carbon nanotubes (SWNTs) in aqueous solution with high weight fractions, as well as to sort SWNTs according to their electronic properties with the aid of ultracentrifugation. To help elucidate the role of bile salts in the SWNT dispersion process, we report the first detailed large-scale all-atomistic molecular dynamics (MD) simulation study of the adsorption and surface self-assembly of a common bile salt surfactant, sodium cholate (SC), on a SWNT in aqueous solution. We find that the cholate ions wrap around the SWNT like a ring and have a small tendency to orient perpendicular to the cylindrical axis of the SWNT, a unique feature that has not been observed for conventional linear surfactants such as sodium dodecyl sulfate (SDS). In addition, we carry out a series of simulations to compute the potential of mean force (PMF) between two parallel SC-covered SWNTs as a function of the intertube separation. By comparing our simulated PMF profile of SC with the PMF profile of SDS reported in the literature, we found that, at the saturated surface coverages, SC is a better stabilizer than SDS, a finding that is consistent with the widespread use of SC to disperse SWNTs in aqueous media. Indeed, the superior dispersion-induced stability of SC over SDS results from a higher repulsive energy barrier and a shallower attractive energy well induced by SC in the PMF profile. In particular, we found that the shallower attractive energy well induced by SC is due to the rigid, bean-like structure of SC which allows this bile salt surfactant to more effectively accommodate the intertube gap.

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel.

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.

Barnase–Barstar: From first encounter to final complex

Formation of transient protein complexes is an important process in cells. Details of the association process as well as the energy landscapes of association are not well understood. In particular, the nature, height and position of the energy barriers during complexation are debated. Computational studies are well suited for atomistically investigating protein association processes. The Barnase-Barstar complex constitutes a well-studied target for computational studies as a small system with fast association rates. Here, we performed constraint biased Molecular Dynamics simulations along the reaction coordinate reaching from the diffusion regime to the bound complex. We simulated the wild-type and different mutants at different salt concentrations. A structural analysis of our simulation trajectories revealed not a single, but two distinct association patterns dominated by an interplay between two charged contact points near the binding site. Electrostatics and/or mutations influence the relative population of these patterns. Further, we computed the energy landscape of association as PMF (Potential of Mean Force) profiles within a reasonable agreement to experiment. We find a single energy barrier at a distance of ~0.3 nm, which corresponds to the final desolvation transition. Electrostatics has a profound influence on the height of this energy barrier, but not on its position.

Membrane/Toxin Interaction Energetics via Serial Multiscale Molecular Dynamics Simulations.

Computing free energies of complex biomolecular systems via atomistic (AT) molecular dynamics (MD) simulations remains a challenge due to the need for adequate sampling and convergence. Recent coarse-grained (CG) methodology allows simulations of significantly larger systems (∼10(6) to 10(8) atoms) over longer (μs/ms) time scales. Such CG models appear to be capable of making semiquantitative predictions. However, their ability to reproduce accurate thermodynamic quantities remains uncertain. We have recently used CG MD simulations to compute the potential of mean force (PMF) or free energy profile of a small peptide toxin interacting with a lipid bilayer along a 1D reaction coordinate. The toxin studied was VSTx1 (Voltage Sensor Toxin 1) from spider venom which inhibits the archeabacterial voltage-gated potassium (Kv) channel KvAP by binding to the voltage-sensor (VS) domains. Here, we re-estimate this PMF profile using (i) AT MD simulations with explicit membrane and solvent and (ii) an implicit membrane and solvent (generalized Born; GBIM) model where only the peptide was explicit. We used the CG MD free energy simulations to guide the setup of the corresponding AT MD simulations. The aim was to avoid local minima in the AT simulations which would be difficult over shorter AT time scales. A cross-comparison of the PMF profiles revealed a conserved topology, although there were differences in the magnitude of the free energies. The CG and AT simulations predicted a membrane/water interface free energy well of -27 and -23 kcal/mol, respectively (with respect to water). The GBIM model, however, gave a reduced interfacial free energy well (-12 kcal/mol). In addition, the CG and GBIM models predicted a free energy barrier of +61 and +96 kcal/mol, respectively, for positioning the toxin at the center of the bilayer, which was considerably smaller in the AT simulations (+26 kcal/mol). Thus, we present a framework for serially combining CG and AT simulations to estimate the free energy of peptide/membrane interactions. Such approaches for combining simulations at different levels of granularity will become increasingly important in future studies of complex membrane/protein systems.

Molecular Dynamics Investigation of Anesthetic Halothane Interactions with the Proton-Gated Ion Channel GLIC

Experimental studies found that general anesthetics inhibited the function of GLIC. To investigate the underlying inhibition mechanism, we studied the interaction of halothane with GLIC and determined the potential of mean force (PMF) for transporting a sodium ion across the GLIC channel in the presence and absence of halothane. Multiple halothane binding sites were identified through docking and multi-nanosecond molecular dynamics (MD) simulations; three important ones are: A) inter-subunit site near TM2-3 loop; B) inter-subunit site near D86; and C) intra-subunit site near W160. MD simulations demonstrated that halothane altered GLIC dynamics and electrostatic interactions between critical residues. Halothane near W160 reduced the stability of salt-bridges between D32 and R192, whose homologous electrostatic interaction was suggested to be important for channel gating in the ligand-gated ion channels. To assess potential impact of halothane binding to channel conductance, we calculated PMF using adaptive biased force method. Protonation state of E222 is a determinant for the PMF. PMF profile with five deprotonated E222 residues in the pentamer showed a significantly deeper energy well than that with three deprotonated E222, suggesting that five deprotonated E222 may trap an ion and that partial protonation of E222 is necessary for ion leaving the trap. While halothane near sites A and B introduced comparatively small effects on PMF, a profound PMF change near E222 was observed in the presence of halothane at W160. This change may likely affect the single channel conductance. Taken together, halothane may modulate GLIC function through altering salt bridges crucial for gating, coupled with a breaking of the fivefold symmetry of the pore-lining helices, leading to a change in the energy profile for ion passage through the channel. Supported by NIH (R01GM66358 and R01GM56257) and NCSA through PSC.

Quantitative analysis of Poisson–Boltzmann implicit solvent in molecular dynamics

A critical issue in the development of implicit solvent models is their quality in realistic simulations of non-trivial systems. In a previous study, we quantitatively compared the reaction field energies of static structures calculated with the Poisson-Boltzmann implicit solvent and the TIP3P explicit solvent and found an overall agreement, though a discrepancy was also observed in the electrostatic potentials of mean force for salt-bridging and hydrogen-bonding dimers (see J. Phys. Chem. B, 2006, 110, 18680). In this study, we are interested in how the implicit solvent performs in molecular dynamics simulations. To guarantee sampling convergence in simulated observables in the explicit solvent, we explored to use a high-temperature constant-volume simulation setting at 450 K but with the water density at 300 K. The relevance of the artificial simulation setting to room-temperature simulations of biomolecules was first investigated by systematic comparisons of the polar and nonpolar solvation free energies of 23 amino acid analogues at 300 K and 450 K, respectively. Assisted by the artificial simulation setting, we found the simulated secondary structure populations agree very well between the implicit and explicit solvents for tested dipeptides and peptides. In addition, the agreement in the populations of hydrophobic contacts is reasonable. However, our analysis also shows that the populations of the salt bridges are too low in the implicit solvent. The low salt-bridge population perhaps results from a combination of the atomic-centered modified van der Waals surface and the small solvent probe radius optimized to best reproduce the polar potential of mean force profiles. In addition, the lower accuracy of the electrostatic forces and the lack of water-bridged minima in the implicit solvents may also contribute to the instability of the salt bridge populations.

Potential of Mean Force Between Ionizable Amino Acid Side Chains in Lipid Bilayer

Potentials of mean force (PMF) between ionizable amino acid side chains (Arg, Lys, His, Glu/Asp) in different protonation states in palmitoyl oleoyl phosphatidylcholine lipid bilayer were obtained from all-atom explicit solvent molecular dynamics simulations and the adaptive biasing force approach available with NAMD.1,2 Side chains (SC) were constrained in different orientations: collinear, stacked and T-shaped and placed into the bilayer interface. The most structured PMFs were observed for unlike-charged ions or pairs with neutral SCs in collinear orientation. Contact pairs (CP) occurred at a distance of 2.6-3.1 A with the strongest interaction of −9.6 kcal/mol between Arg+ and Glu- ions. Like-charged SCs in this orientation displayed less stable contact minima at greater distances or solvent separated minima. All pairs in stacking approach showed similar, well-structured PMF profiles with CPs at ∼3.8 A. The strongest interaction between like-charged pairs was observed for stacked arginines. Like-charged pairs constrained in T-shaped geometry mostly displayed slightly stable solvent separated minima. A relationship between water and phosphate coordination numbers, contact pair minima and free energy barriers was found. There is also dependence of PMF shapes on H-bonding between amino acids. Generally, interactions between ionizable SCs are more attractive and the PMFs are more structured in a lipid bilayer than in water.31 Darve, E.; Pohorille, A. J. Chem. Phys. 2001, 115, 9169.2 Darve, E.; Wilson, M.; Pohorille, A. Mol. Simul.2002, 28, 113.3 Masunov, A.; Lazaridis, T.J. Am. Chem. Soc.2003125, 1722.

Ion Selectivity of α-Hemolysin with a β-Cyclodextrin Adapter. I. Single Ion Potential of Mean Force and Diffusion Coefficient

The alpha-hemolysin (alphaHL) is a self-assembling exotoxin that binds to the membrane of a susceptible host cell and causes its death. Experimental studies show that electrically neutral beta-cyclodextrin (betaCD) can insert into the alphaHL channel and significantly increase its anion selectivity. To understand how betaCD can affect ion selectivity, molecular dynamics simulations and potential of mean force (PMF) calculations are carried out for different alphaHL channels with and without the betaCD adapter. A multiscale approach based on the generalized solvent boundary potential is used to reduce the size of the simulated system. The PMF profiles reveal that betaCD has no anion selectivity by itself but can increase the Cl(-) selectivity of the alphaHL channel when lodged into the pore lumen. Analysis shows that betaCD causes a partial desolvation of ions and affects the orientation of nearby charged residues. The ion selectivity appears to result from increased electrostatic interaction between the ion and the channel due to a reduction in dielectric shielding by the solvent. These observations suggest a reasonable explanation of the ion selectivity and provide important information for further ion channel modification.

An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies.

Base flipping is a common strategy utilized by many enzymes to gain access to the functional groups of nucleic acid bases in duplex DNA which are otherwise protected by the DNA backbone and hydrogen bonding with their partner bases. Several X-ray crystallography studies have revealed flipped conformations of nucleotides bound to enzymes. However, little is known about the base-flipping process itself, even less about the role of the enzymes. Computational studies have used umbrella sampling to elicit the free energy profile of the base-flipping process using a pseudodihedral angle to represent the reaction coordinate. In this study, we have used an unrestrained trajectory in which a flipped base spontaneously reinserted into the helix in order to evaluate and improve the previously defined pseudodihedral angle. Our modified pseudodihedral angles use a new atom selection to improve the numerical stability of the restraints and also provide better correlation to the extent of flipping observed in simulations. Furthermore, on the basis of the comparison of potential of mean force (PMF) generated using different reaction coordinates, we observed that the shape of a flipping PMF profile is strongly dependent on the definition of the reaction coordinate, even for the same data set.

On the Mechanism of Surfactant Adsorption on Solid Surfaces: Free-Energy Investigations

The adsorption free-energy of surfactant on solid surfaces has been calculated by molecular dynamics (MD) simulation for a model surfactant/solvent system. The umbrella-sampling with the weight histogram analysis method (WHAM) was applied. The entropic and enthalpic contributions to the full potential of mean force (PMF) were obtained to evaluate the detailed thermodynamics of surfactant adsorption in solid/liquid interfaces. Although we observed that this surfactant adsorption process is driven mainly by a favorable enthalpy change, a highly unfavorable entropic contribution still existed. By decomposing the free energy (including its entropic and enthalpic components) into the solvent-induced contribution and the surfactant-wall term, the effect of surface and solvent on the adsorption free-energy has been distinguished. The contribution to the PMF from the surface effect is thermodynamically favorable, whereas the solvent term displays an obviously unfavorable component with a monotonic increase as the surfactant approaches to the surface. The impact of various interactions from the surfaces (both solvent-philic and solvent-phobic) and the solvent on the adsorption PMF of surfactant has been compared and discussed. Compared to the solvent-philic surface, the solvent-phobic surface generates more stable site for the surfactant adsorption. However, the full PMF profile for the solvent-phobic system shows a clear positive maximum value at the bulk-interface transition region, which leads to a considerable long-range free-energy barrier to the surfactant adsorption. These results have been analyzed in terms of the local interfacial structures. In summary, this comprehensive study is expected to reveal the microscopic interaction mechanisms determining the surfactant adsorption on solid surfaces.

Calculation of the absolute thermodynamic properties of association of host-guest systems from the intermolecular potential of mean force

The authors report calculations of the intermolecular potential of mean force (PMF) in the case of the host-guest interaction. The host-guest system is defined by a water soluble calixarene and a cation. With an organic cation such as the tetramethylammonium cation, the calixarene forms an insertion complex, whereas with the Lanthane cation, the supramolecular assembly is an outer-sphere complex. The authors apply a modified free energy perturbation method and the force constraint technique to establish the PMF profiles as a function of the separation distance between the host and guest. They use the PMF profile for the calculation of the absolute thermodynamic properties of association that they compare to the experimental values previously determined. They finish by giving some structural features of the insertion and outer-sphere complexes at the Gibbs free energy minimum.

Steered Molecular Dynamics Studies of the Potential of Mean Force of a Na+ or K+ Ion in a Cyclic Peptide Nanotube

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport.

Adaptive Brownian Dynamics Simulation for Estimating Potential Mean Force in Ion Channel Permeation

Ion channels are biological nanotubes formed by large protein molecules in the cell membrane. This paper presents a novel multiparticle simulation methodology, which we call adaptive controlled Brownian dynamics, for estimating the force experienced by a permeating ion at each discrete position along the ion-conducting pathway. The profile of this force, commonly known as the potential of mean force, results from the electrostatic interactions between the ions in the conduit and all the charges carried by atoms forming the channel the protein, as well as the induced charges on the protein wall. The current across the channel is solely determined by the potential of mean force encountered by the permeant ions. The simulation algorithm yields consistent estimates of this profile. The algorithm operates on an angstrom unit spatial scale and femtosecond time scale. Numerical simulations on the gramicidin ion channel show that the algorithm yields the potential of mean force profile that accurately reproduces experimental observations.

On the Nature of the Transition State in Catechol O-Methyltransferase. A Complementary Study Based on Molecular Dynamics and Potential Energy Surface Explorations

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.