Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics

Minimal Optimized Effective Potentials for Density Functional Theory Studies on Excited-State Proton Dissociation

Recently, a new method [P. Partovi-Azar and D. Sebastiani, J. Chem. Phys. 152, 064101 (2020)] was proposed to increase the efficiency of proton transfer energy calculations in density functional theory by using the T1 state with additional optimized effective potentials instead of calculations at S1. In this work, we focus on proton transfer from six prototypical photoacids to neighboring water molecules and show that the reference proton dissociation curves obtained at S1 states using time-dependent density functional theory can be reproduced with a reasonable accuracy by performing T1 calculations at density functional theory level with only one additional effective potential for the acidic hydrogens. We also find that the extra effective potentials for the acidic hydrogens neither change the nature of the T1 state nor the structural properties of solvent molecules upon transfer from the acids. The presented method is not only beneficial for theoretical studies on excited state proton transfer, but we believe that it would also be useful for studying other excited state photochemical reactions.

Optimized effective potentials to increase the accuracy of approximate proton transfer energy calculations in the excited state

Many fundamental chemical reactions are triggered by electronic excitations. Here, we propose and benchmark a novel approximate first-principles molecular dynamics simulation idea for increasing the computational efficiency of density functional theory-based calculations of the excited states. We focus on obtaining proton transfer energy at the S₁ excited state through actual density functional theory calculations at the T₁ state with additional optimized effective potentials. The potentials are optimized as such to reproduce the excited-state energy surface obtained using time-dependent density functional theory, but can be generalized to other more accurate quantum chemical methods. We believe that the presented method is not only suitable for studies on excited-state proton transfer and ion mobility in general systems but can also be extended to investigate more involved processes, such as photo-induced isomerization.

Influence of local microenvironment on the double hydrogen transfer in porphycene

We performed time-resolved transient absorption and fluorescence anisotropy measurements in order to study tautomerization of porphycene in rigid polymer matrices at cryogenic temperatures. Studies were carried out in poly(methyl methacrylate) (PMMA), poly(vinyl butyral) (PVB), and poly(vinyl alcohol) (PVA). The results prove that in all studied media hydrogen tunnelling plays a significant role in the double hydrogen transfer which becomes very sensitive to properties of the environment below approx. 150 K. We also demonstrate that there exist two populations of porphycene molecules in rigid media: "hydrogen-transferring" molecules, in which tautomerization occurs on time scales below 1 ns and "frozen" molecules in which double hydrogen transfer is too slow to be monitored with nanosecond techniques. The number of "frozen" molecules increases when the sample is cooled. We explain this effect by interactions of guest molecules with a rigid host matrix which disturbs symmetry of porphycene and hinders tunnelling. Temperature dependence of the number of hydrogen-transferring molecules suggests that the factor which restores the symmetry of the double-minimum potential well in porphycene are intermolecular vibrations localized in separated regions of the amorphous polymer.

The role of Brønsted base basicity in estimating carbon acidity at enzyme active sites: a caveat

Many enzymes catalyze the abstraction of a proton from a carbon acid substrate to initiate a variety of reactions; however, the development of a complete quantitative description of enzyme-catalyzed heterolytic cleavage of a C-H bond remains a challenge to enzymologists. To determine the pK value for such substrates bound at the active site, recent studies have estimated the equilibrium for formation of the deprotonated intermediate at the active site, however, accurate knowledge of the pK of the conjugate acid of the Brønsted base catalyst (BH⁺) is also required. Herein, it is shown that using the value of pK of the enzyme-substrate complex can underestimate the value of pK by an amount between zero and pδ, where pδ is the change in basicity of BH⁺ upon going from the enzyme-substrate complex to the enzyme-intermediate complex.

Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants

We propose a simple atomic multipole electrostatic model to rapidly evaluate the effects of mutation on enzyme activity and test its performance on wild-type and mutant ketosteroid isomerase. The predictions of our atomic multipole model are similar to those obtained with symmetry-adapted perturbation theory at a fraction of the computational cost. We further show that this approach is relatively insensitive to the precise amino acid side chain conformation in mutants and may thus be useful in computational enzyme (re)design.

Theoretical study of enzymatically catalyzed tautomerization of carbon acids in aqueous solution: quantum calculations and steered molecular dynamics simulations

The thermodynamics and kinetics of enzymatically assisted reactions of carbon acids were studied theoretically in this work. Quantum electronic (QE) structure calculations and steered molecular dynamics (SMD) simulations were carried out. Three 3-butenal tautomerization reactions that proceed from the β,γ-unsaturated reactant (R) to the α,β-unsaturated carbon acid product (P) and occur in two elementary steps through an intermediate (I) were studied, ignoring or including the surrounding aqueous medium in the calculations. The Gibbs free energies of activation of the R ⇆ I enolization and I ⇆ P ketonization steps were found to decrease considerably when residues simulating enzymes were introduced into these processes. Although the processes became slightly more favorable thermodynamically when the solution was included in the simulations, they became less favorable kinetically. The results from SMD simulations of these reactions were qualitatively consistent with the values we obtained using QE as well as those found by other authors in similar studies. Our simulations also allowed us to perform a detailed study of these reactions in solution.

Prediction of distal residue participation in enzyme catalysis

A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues.

Long-range proton relay shows an inverse linear free energy relationship depending on the pKa of the hydrogen-bonded wire

The long-range proton transfer dependence on the pK_a of hydroxyl molecules in hydrogen (H)-bonded wires was investigated using quantum mechanical calculations.

Challenges in computational studies of enzyme structure, function and dynamics

In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.

Studying allosteric regulation in metal sensor proteins using computational methods

In this chapter, we describe advances made in understanding the mechanism of allosteric regulation of DNA operator binding in the ArsR/SmtB family of metal-sensing proteins using computational methods. The paradigm, zinc-sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Here, we discuss studies that helped to characterize a metal ion-mediated hydrogen-bonding pathway (HBP) that plays a dominant role in the allosteric mechanism of DNA operator binding in these proteins. The chapter discusses computational methods used to provide a molecular basis for the large conformational motions and allosteric coupling free energy (~6kcal/mol) associated with Zn(II) binding in CzrA. We present an accurate and convenient means by which to include metal ions in the nuclear magnetic resonance (NMR) structure determination process using molecular dynamics (MD) constrained by NMR-derived data. The method provides a realistic and physically viable description of the metal-binding site(s) and has potentially broad applicability in the structure determination of metal ion-bound proteins, protein folding, and metal template protein-design studies. Finally, our simulations provide strong support for a proposed HBP that physically connects the metal-binding residue, His97, to the DNA-binding interface through the αR helix that is present only in the Zn(II)-bound state. We find the interprotomer hydrogen bond interaction to be significantly stronger (~8kcal/mol) at functional allosteric metal-binding sites compared to the apo proteins. This interaction works to overcome the considerable disorder at these hydrogen-bonding sites in apo protein and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. This interaction is found to be considerably weaker in nonresponsive metal-binding sites. These findings suggest a conserved functional role of metal-mediated second-shell coordination hydrogen bonds at allosterically responsive sites in zinc-sensing transcription regulators.

Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase

Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and ¹³C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor–acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for significant electrostatic changes in the active site microenvironments due to conformational motion occurring over the catalytic cycle of ecDHFR.

Using unnatural amino acids to probe the energetics of oxyanion hole hydrogen bonds in the ketosteroid isomerase active site

Hydrogen bonds are ubiquitous in enzyme active sites, providing binding interactions and stabilizing charge rearrangements on substrate groups over the course of a reaction. But understanding the origin and magnitude of their catalytic contributions relative to hydrogen bonds made in aqueous solution remains difficult, in part because of complexities encountered in energetic interpretation of traditional site-directed mutagenesis experiments. It has been proposed for ketosteroid isomerase and other enzymes that active site hydrogen bonding groups provide energetic stabilization via "short, strong" or "low-barrier" hydrogen bonds that are formed due to matching of their pKa or proton affinity to that of the transition state. It has also been proposed that the ketosteroid isomerase and other enzyme active sites provide electrostatic environments that result in larger energetic responses (i.e., greater "sensitivity") to ground-state to transition-state charge rearrangement, relative to aqueous solution, thereby providing catalysis relative to the corresponding reaction in water. To test these models, we substituted tyrosine with fluorotyrosines (F-Tyr's) in the ketosteroid isomerase (KSI) oxyanion hole to systematically vary the proton affinity of an active site hydrogen bond donor while minimizing steric or structural effects. We found that a 40-fold increase in intrinsic F-Tyr acidity caused no significant change in activity for reactions with three different substrates. F-Tyr substitution did not change the solvent or primary kinetic isotope effect for proton abstraction, consistent with no change in mechanism arising from these substitutions. The observed shallow dependence of activity on the pKa of the substituted Tyr residues suggests that the KSI oxyanion hole does not provide catalysis by forming an energetically exceptional pKa-matched hydrogen bond. In addition, the shallow dependence provides no indication of an active site electrostatic environment that greatly enhances the energetic response to charge accumulation, consistent with prior experimental results.

Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site

The positioning of catalytic groups within proteins plays an important role in enzyme catalysis, and here we investigate the positioning of the general base in the enzyme ketosteroid isomerase (KSI). The oxygen atoms of Asp38, the general base in KSI, were previously shown to be involved in anion–aromatic interactions with two neighboring Phe residues. Here we ask whether those interactions are sufficient, within the overall protein architecture, to position Asp38 for catalysis or whether the side chains that pack against Asp38 and/or the residues of the structured loop that is capped by Asp38 are necessary to achieve optimal positioning for catalysis. To test positioning, we mutated each of the aforementioned residues, alone and in combinations, in a background with the native Asp general base and in a D38E mutant background, as Glu at position 38 was previously shown to be mispositioned for general base catalysis. These double-mutant cycles reveal positioning effects as large as 10³-fold, indicating that structural features in addition to the overall protein architecture and the Phe residues neighboring the carboxylate oxygen atoms play roles in positioning. X-ray crystallography and molecular dynamics simulations suggest that the functional effects arise from both restricting dynamic fluctuations and disfavoring potential mispositioned states. Whereas it may have been anticipated that multiple interactions would be necessary for optimal general base positioning, the energetic contributions from positioning and the nonadditive nature of these interactions are not revealed by structural inspection and require functional dissection. Recognizing the extent, type, and energetic interconnectivity of interactions that contribute to positioning catalytic groups has implications for enzyme evolution and may help reveal the nature and extent of interactions required to design enzymes that rival those found in biology.

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) simulations constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational sampling in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies.

QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis

Ketosteroid isomerase (Δ⁵-3-keto steroid isomerase or steroid Δ-isomerase) is a highly efficient enzyme at the centre of current debates on enzyme catalysis. We have modelled the reaction mechanism of the isomerization of 3-oxo-Δ⁵-steroids into their Δ⁴-conjugated isomers using high-level combined quantum mechanics/molecular mechanics (QM/MM) methods, and semi-empirical QM/MM molecular dynamics simulations. Energy profiles were obtained at various levels of QM theory (AM1, B3LYP and SCS-MP2). The high-level QM/MM profile is consistent with experimental data. QM/MM dynamics simulations indicate that active site closure and desolvation of the catalytic Asp38 occur before or during formation of dienolate intermediates. These changes have a significant effect on the reaction barrier. A low barrier to reaction is found only when the active site is closed, poising it for catalysis. This conformational change is thus integral to the whole process. The effects on the barrier are apparently largely due to changes in solvation. The combination of high-level QM/MM energy profiles and QM/MM dynamics simulation shows that the reaction involves active site closure, desolvation of the catalytic base, efficient isomerization and re-opening of the active site. These changes highlight the transition between the ligand binding/releasing form and the catalytic form of the enzyme. The results demonstrate that electrostatic interactions (as a consequence of pre-organization of the active site) are crucial for stabilization during the chemical reaction step, but closure of the active site is essential for efficient catalysis to occur.

Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding

The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.

Catalytic efficiency of enzymes: a theoretical analysis

This brief review analyzes the underlying physical principles of enzyme catalysis, with an emphasis on the role of equilibrium enzyme motions and conformational sampling. The concepts are developed in the context of three representative systems, namely, dihydrofolate reductase, ketosteroid isomerase, and soybean lipoxygenase. All of these reactions involve hydrogen transfer, but many of the concepts discussed are more generally applicable. The factors that are analyzed in this review include hydrogen tunneling, proton donor-acceptor motion, hydrogen bonding, pKa shifting, electrostatics, preorganization, reorganization, and conformational motions. The rate constant for the chemical step is determined primarily by the free energy barrier, which is related to the probability of sampling configurations conducive to the chemical reaction. According to this perspective, stochastic thermal motions lead to equilibrium conformational changes in the enzyme and ligands that result in configurations favorable for the breaking and forming of chemical bonds. For proton, hydride, and proton-coupled electron transfer reactions, typically the donor and acceptor become closer to facilitate the transfer. The impact of mutations on the catalytic rate constants can be explained in terms of the factors enumerated above. In particular, distal mutations can alter the conformational motions of the enzyme and therefore the probability of sampling configurations conducive to the chemical reaction. Methods such as vibrational Stark spectroscopy, in which environmentally sensitive probes are introduced site-specifically into the enzyme, provide further insight into these aspects of enzyme catalysis through a combination of experiments and theoretical calculations.

Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF

The periplasmic Cu(+)/Ag(+) chaperone CusF features a novel cation-π interaction between a Cu(+)/Ag(+) ion and Trp44 at the metal binding site. The nature and strength of the Cu(+)/Ag(+)-Trp44 interactions were investigated using computational methodologies. Quantum-mechanical (QM) calculations showed that the Cu(+) and Ag(+) interactions with Trp44 are of similar strength (~14 kcal/mol) and bond order. Quantum-mechanical/molecular-mechanical (QM/MM) calculations showed that Cu(+) binds in a distorted tetrahedral coordination environment in the Trp44Met mutant, which lacks the cation-π interaction. Molecular dynamics (MD) simulations of CusF in the apo and Cu(+)-bound states emphasized the importance of the Cu(+)-Trp44 interaction in protecting Cu(+) from water oxidation. The protein structure does not change over the time scale of hundreds of nanoseconds in the metal-bound state. The metal recognition site exhibits small motions in the apo state but remains largely preorganized toward metal binding. Trp44 remains oriented to form the cation-π interaction in the apo state and faces an energetic penalty to move away from the metal ion. Cu(+) binding quenches the protein's internal motions in regions linked to binding CusB, suggesting that protein motions play an essential role in Cu(+) transfer to CusB.

Water in the active site of ketosteroid isomerase

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two in the Y16S mutant and one in the Y16F and FFF mutants, with intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of (1)H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less probable in WT KSI.

Hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling

Computational studies are performed to analyze the physical properties of hydrogen bonds donated by Tyr16 and Asp103 to a series of substituted phenolate inhibitors bound in the active site of ketosteroid isomerase (KSI). As the solution pK(a) of the phenolate increases, these hydrogen bond distances decrease, the associated nuclear magnetic resonance (NMR) chemical shifts increase, and the fraction of protonated inhibitor increases, in agreement with prior experiments. The quantum mechanical/molecular mechanical calculations provide insight into the electronic inductive effects along the hydrogen bonding network that includes Tyr16, Tyr57, and Tyr32, as well as insight into hydrogen bond coupling in the active site. The calculations predict that the most-downfield NMR chemical shift observed experimentally corresponds to the Tyr16-phenolate hydrogen bond and that Tyr16 is the proton donor when a bound naphtholate inhibitor is observed to be protonated in electronic absorption experiments. According to these calculations, the electronic inductive effects along the hydrogen bonding network of tyrosines cause the Tyr16 hydroxyl to be more acidic than the Asp103 carboxylic acid moiety, which is immersed in a relatively nonpolar environment. When one of the distal tyrosine residues in the network is mutated to phenylalanine, thereby diminishing this inductive effect, the Tyr16-phenolate hydrogen bond becomes longer and the Asp103-phenolate hydrogen bond shorter, as observed in NMR experiments. Furthermore, the calculations suggest that the differences in the experimental NMR data and electronic absorption spectra for pKSI and tKSI, two homologous bacterial forms of the enzyme, are due predominantly to the third tyrosine that is present in the hydrogen bonding network of pKSI but not tKSI. These studies also provide experimentally testable predictions about the impact of mutating the distal tyrosine residues in this hydrogen bonding network on the NMR chemical shifts and electronic absorption spectra.

Transformation of a series of saturated isomeric steroidal diols by Aspergillus tamarii KITA reveals a precise stereochemical requirement for entrance into the lactonization pathway

Four isomers of 5α-androstan-3,17-diol have been transformed by the filamentous fungus Aspergillus tamarii, an organism which has the ability to convert progesterone to testololactone in high yield through an endogenous four step enzymatic pathway. The only diol handled within the lactonization pathway was 5α-androstan-3α,17β-diol which, uniquely underwent oxidation of the 17β-alcohol to the 17-ketone prior to its Baeyer-Villiger oxidation and the subsequent production of 3α-hydroxy-17a-oxa-D-homo-5α-androstan-17-one. This demonstrated highly specific stereochemical requirements of the 17β-hydroxysteroid dehydrogenase for oxidation of this specific steroidal diol to occur. In contrast, the other three diols were transformed within the hydroxylation pathway resulting in functionalization at C-11β. Only 5α-androstan-3β,17α-diol could bind to the hydroxylase in multiple binding modes undergoing monohydroxylation in 6β and 7β positions. Evidence from this study has indicated that hydroxylation of saturated steroidal lactones may occur following binding of ring-D in its open form in which an α-alcohol is generated with close spatial parity to the C-17α hydroxyl position. All metabolites were isolated by column chromatography and were identified by (1)H, (13)C NMR and DEPT analysis and further characterized using infra-red, elemental analysis and accurate mass measurement.

From alcohol dehydrogenase to a "one-way" carbonyl reductase by active-site redesign: a mechanistic study of mannitol 2-dehydrogenase from pseudomonas fluorescens

Directional preference in catalysis is often used to distinguish alcohol dehydrogenases from carbonyl reductases. However, the mechanistic basis underpinning this discrimination is weak. In mannitol 2-dehydrogenase from Pseudomonas fluorescens, stabilization of (partial) negative charge on the substrate oxyanion by the side chains of Asn-191 and Asn-300 is a key feature of catalysis in the direction of alcohol oxidation. We have disrupted this ability through individual and combined substitutions of the two asparagines by aspartic acid. Kinetic data and their thermodynamic analysis show that the internal equilibrium of enzyme-NADH-fructose and enzyme-NAD(+)-mannitol (K(int)) was altered dramatically (10(4)- to 10(5)-fold) from being balanced in the wild-type enzyme (K(int) ≈ 3) to favoring enzyme-NAD(+)-mannitol in the single site mutants, N191D and N300D. The change in K(int) reflects a selective slowing down of the mannitol oxidation rate, resulting because Asn --> Asp replacement (i) disfavors partial abstraction of alcohol proton by Lys-295 in a step preceding catalytic hydride transfer, and (ii) causes stabilization of a nonproductive enzyme-NAD(+)-mannitol complex. N191D and N300D appear to lose fructose binding affinity due to deprotonation of the respective Asp above apparent pK values of 5.3 ± 0.1 and 6.3 ± 0.2, respectively. The mutant incorporating both Asn-->Asp substitutions behaved as a slow "fructose reductase" at pH 5.2, lacking measurable activity for mannitol oxidation in the pH range 6.8-10. A mechanism is suggested in which polarization of the substrate carbonyl by a doubly protonated diad of Asp and Lys-295 facilitates NADH-dependent reduction of fructose by N191D and N300D under optimum pH conditions. Creation of an effectively "one-way" reductase by active-site redesign of a parent dehydrogenase has not been previously reported and holds promise in the development of carbonyl reductases for application in organic synthesis.

Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations

The two proton transfer reactions catalyzed by ketosteroid isomerase (KSI) involve a dienolate intermediate stabilized by hydrogen bonds with Tyr14 and Asp99. Molecular dynamics simulations based on an empirical valence bond model are used to examine the impact of mutating these residues on the hydrogen-bonding patterns, conformational changes, and van der Waals and electrostatic interactions during the proton transfer reactions. While the rate constants for the two proton transfer steps are similar for wild-type (WT) KSI, the simulations suggest that the rate constant for the first proton transfer step is smaller in the mutants due to the significantly higher free energy of the dienolate intermediate relative to the reactant. The calculated rate constants for the mutants D99L, Y14F, and Y14F/D99L relative to WT KSI are qualitatively consistent with the kinetic experiments indicating a significant reduction in the catalytic rates along the series of mutants. In the simulations, WT KSI retained two hydrogen-bonding interactions between the substrate and the active site, while the mutants typically retained only one hydrogen-bonding interaction. A new hydrogen-bonding interaction between the substrate and Tyr55 was observed in the double mutant, leading to the prediction that mutation of Tyr55 will have a greater impact on the proton transfer rate constants for the double mutant than for WT KSI. The electrostatic stabilization of the dienolate intermediate relative to the reactant was greater for WT KSI than for the mutants, providing a qualitative explanation for the significantly reduced rates of the mutants. The active site exhibited restricted motion during the proton transfer reactions, but small conformational changes occurred to facilitate the proton transfer reactions by strengthening the hydrogen-bonding interactions and by bringing the proton donor and acceptor closer to each other with the proper orientation for proton transfer. Thus, these calculations suggest that KSI forms a preorganized active site but that the structure of this preorganized active site is altered upon mutation. Moreover, small conformational changes due to stochastic thermal motions are required within this preorganized active site to facilitate the proton transfer reactions.

Solvation response along the reaction coordinate in the active site of ketosteroid isomerase

A light-activated reaction analog has been developed to mimic the catalytic reaction cycle of Delta(5)-3-ketosteroid isomerase to probe the functionally relevant protein solvation response to the catalytic charge transfer. Delta(5)-3-ketosteroid isomerase from Pseudomonas putida catalyzes a C-H bond cleavage and formation through an enolate intermediate. Conversion of the ketone substrate to the enolate intermediate is simulated by a photoacid bound to the active site oxyanion hole. In the ground state, the photoacid electrostatically resembles the enolate intermediate while the low pK(a) excited state resembles the ketone starting material. Time-resolved fluorescence experiments with photoacids coumarin 183 and equilenin show the active site of Delta(5)-3-ketosteroid isomerase to be largely unperturbed by the light-activated reaction. The small solvation response for the photoacid at the active site as compared with a simple solvent suggests the active site does not significantly change its electrostatic environment during the catalytic cycle. Instead, the reaction takes place in an electrostatically preorganized environment.