The free energy–reaction coordinate profile for α-chymotryptic hydrolysis of a series of N-acetyl-α-L-amino acid methyl esters

The effect of added nucleophiles (methanol and 1,4-butanediol) on the steady-state kinetics of α-chymotryptic hydrolysis of a series of N-acetyl-L-amino acid methyl esters, R-CH(NHCOCH₃)C(O)OCH₃, has been studied. As a result, the rate and equilibrium constants of the ‘elementary’ steps of the enzyme process have been determined. It has also been demonstrated how the free energy–reaction coordinate profile changes if the structure (the size of the hydrocarbon chain) of the ‘chemically inert’ substrate fragment R is varied. The effects observed can be described by the following equation: where ΔG_s and ΔG_a are the free energies of formation of metastable intermediates, i.e., the enzyme–substrate complex and the acylenzyme, respectively, ΔG₂≠ and ΔG₃≠ are the free energies of activation for the chemical steps, i.e., enzyme acylation and acylenzyme hydrolysis, respectively; and ΔG_trans^(R) is the free energy of transfer of substrate group R from water into a nonaqueous solvent. To explain the results obtained, a mechanism for enzyme–substrate interaction is suggested according to which the potential free energy of sorption of substrate group R on the enzyme is 2 ΔG_trans^(R). Such a high gain in the free energy of hydrophobic interaction may only be realized if (a) in the free enzyme the sorption region has a thermodynamically unfavorable contact with the aqueous medium, and (b) water is forced out of the active center as a result of the hydrophobic interaction of substrate group R with the enzyme. Such a model is in agreement with the published x-ray data on the structure of the crystalline enzyme. The kinetic experiment has proved that not all the potential free energy of sorption is realized as binding force. Thus the true free energy of the binding of substrate group R with the protein does not exceed half the maximum value, both in the enzyme–substrate complex and acylenzyme.     

Entropy,Binding Energy,and Enzymic Catalysis

Why are enzyme-catalyzed reactions so much faster than uncatalyzed reactions, and why are enzymes so specific? What is the effect of mere approximation of enzyme and substrate, and what is the influence of the strain energy? Attempts to answer these questions have led to comparisons between entropy changes in intermolecular and intramolecular reactions, and to determinations of the intrinsic energy of the bond arising by non-covalent interaction between enzyme and substrate.     

Solvent effects on glycine II. Water-assisted tautomerization

The water-assisted tautomerization of glycine has been investigated at the B3LYP/6-31+G** level using supermolecules containing up to six water molecules as well as considering a 1:1 glycine-water complex embedded in a continuum. The conformations of the tautomers in this mechanism do not display an intramolecular H bond, instead the functional groups are bridged by a water molecule. The replacement of the intramolecular H bond by the bridging water reduces the polarity of the N-H bond in the zwitterion and increases that of the O-H bond in the neutral, stabilizing the zwitterion. Both the charge transfer effects and electrostatic interactions stabilize the nonintramolecularly H-bonded zwitterion conformer over the intramolecularly hydrogen bonded one. The nonintramolecularly H-bonded neutral is favored only by charge transfer effects. Although there is no strong evidence whether the intramolecularly hydrogen bonded or non hydrogen bonded structures are favored in the bulk solution represented as a dielectric continuum, it is likely that the latter species are more stable. The free energy of activation of the water-assisted mechanism is higher than the intramolecular proton transfer channel. However, when the presumably higher conformational energy of the zwitterion reacting in the intramolecular mechanism is taken into account, both mechanisms are observed to compete. The various conformers of the neutral glycine may form via multiple proton transfer reactions through several water molecules instead of a conformational rearrangement.     

Excited state dynamics and catalytic mechanism of the light-driven enzyme protochlorophyllide oxidoreductase

The reduction of protochlorophyllide (Pchlide) to chlorophyllide, catalysed by the enzyme protochlorophyllide oxidoreductase (POR), is the penultimate step in the chlorophyll biosynthetic pathway and is a key light-driven reaction that triggers a profound transformation in plant development. As POR is light-activated it can provide new information on the way in which light energy can be harnessed to power enzyme reactions. Consequently, POR presents a unique opportunity to study catalysis at low temperatures and on ultrafast timescales, which are not usually accessible for the majority of enzymes. Recent advances in our understanding of the catalytic mechanism of POR illustrate why it is an important model for studying enzyme catalysis and reaction dynamics. The reaction involves the addition of one hydride and one proton, and catalysis is initiated by the absorption of light by the Pchlide substrate. As the reaction involves the Pchlide excited state, a variety of ultrafast spectroscopic measurements have shown that significant parts of the reaction occur on the picosecond timescale. A number of excited state Pchlide species, including an intramolecular charge transfer complex and a hydrogen bonded intermediate, are proposed to be required for the subsequent hydride and proton transfers, which occur on the microsecond timescale. Herein, we review spectroscopic investigations, with a particular focus on time-resolved transient absorption and fluorescence experiments that have been used to study the excited state dynamics and catalytic mechanism of POR.     

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

The mechanism for the reaction catalyzed by the 4-oxalocrotonate tautomerase (4-OT) enzyme has been studied using a quantum mechanical/molecular mechanical (QM/MM) method developed in our laboratory. Total free energy barriers were obtained for the two steps involved in this reaction. In the first step, Pro-1 acts as a general base to abstract a proton from the third carbon of the substrate, 2-oxo-4-hexenedioate, creating a negative charge on the oxygen at C-2 of this substrate. In the second step, the same hydrogen abstracted by the N-terminal Pro-1 is shuttled back to the fifth carbon of the substrate to form the product, 2-oxo-3-hexenedioate. The calculated total free energy barriers are 14.54 and 16.45 kcal/mol for the first and second steps, respectively. Our calculations clearly show that there is no general acid in the reaction. Arg-39' ', which is hydrogen bonded to the carboxylate group of the substrate, and an ordered water, which moves closer to the site of the charge formed in the transition state and intermediate, play the main role in transition state/intermediate stabilization without acting as general acids in the reaction.     

Intramolecular H-Bond Dynamics of Catechol Investigated by THz High-Resolution Spectroscopy of Its Low-Frequency Modes

Catechol is an oxygenated aromatic volatile organic compound and a biogenic precursor of secondary organic aerosols. Monitoring this compound in the gas phase is desirable due to its appreciable reactivity with tropospheric ozone. From a molecular point of view, this molecule is attractive since the two adjacent hydroxy groups can interchangeably act as donor and acceptor in an intramolecular hydrogen bonding due to the tunnelling between two symmetrically equivalent structures. Using synchrotron radiation, we recorded a rotationally-resolved Fourier Transform far-infrared (IR) spectrum of the torsional modes of the free and bonded -OH groups forming the intramolecular hydrogen bond. Additionally, the room temperature, pure rotational spectrum was measured in the 70–220 GHz frequency range using a millimeter-wave spectrometer. The assignment of these molecular transitions was assisted by anharmonic high-level quantum-chemical calculations. In particular, pure rotational lines belonging to the ground and the four lowest energy, vibrationally excited states were assigned. Splitting due to the tunnelling was resolved for the free -OH torsional state. A global fit combining the far-IR and millimeter-wave data provided the spectroscopic parameters of the low-energy far-IR modes, in particular those characterizing the intramolecular hydrogen bond dynamics.     

Intramolecular dimers: a new design strategy for fluorescence-quenched probes

Fluorogenic probes dual-labeled with reporter and quencher dyes use a change in fluorescence to monitor biochemical events (e.g., substrate binding or enzyme digestion). Such events change the reporter-quencher distance, which affects fluorescence. Recently, it is has been shown that static quenching through intramolecular dimers is an important mechanism that can sometimes be more efficient than F?rster resonance energy transfer (FRET).     

Theoretical calculation of the OH vibrational overtone spectra of 1,5-pentanediol and 1,6-hexanediol

It is well-known that intramolecular hydrogen bonding affects the relative energetics of conformers, as well as the OH stretching peak positions, intensities, and width. In this study we simulated the Δv(OH) = 3, 4 overtone spectra of 1,5-pentanediol (PeD) and 1,6-hexanediol (HD) using the peak positions, intensities, and width calculated from the B3LYP/6-31+G(d,p) method. Furthermore, room temperature free energy calculations were performed using B3LYP/6-31+G(d,p) MP2/6-31+G(d,p), and MP2/6-311++G(3df,3pd) to obtain the relative population of the conformers. From the calculation of 109 and 381 distinct conformers for PeD and HD, respectively, we find that for these long chain diols the intramolecular hydrogen bonded conformers are not the most dominant conformation at room temperature. This is in stark contrast with shorter chain diols such as ethylene glycol for which the hydrogen bonded conformer dominates the population at room temperature. On the other hand, we found that the correlation between the hydrogen bonded OH red shift versus the homogeneous width, Γ = 0.0155(Δω)(1.36), which was derived for shorter chain diols, is valid even for these longer chain diols. We also showed that the intramolecular hydrogen bonded OH initially decays through the CCOH torsion and COH bending mode no matter how long the alkanediol chain length is for 1,n-alkanediols for n up to 6.     

A computational study of substituent effects on the stability and geometry of carbazole‐pyridine complexes

Hydrogen bonding between carbazole and pyridine is known to quench fluorescence emission of carbazole. Three carbazolopyridinophanes—compounds composed of carbazole and pyridine subunits such that an intramolecular hydrogen bond may exist between them—have been pursued as reversible fluorescent sensors that detect given analytes through fluorescence restoration. However, these sensors exhibit background fluorescence believed to be related to the proportion of non‐hydrogen‐bonded conformers present. In this computational investigation, the potential energy surfaces of various hydrogen‐bonded carbazole:pyridine complexes are investigated using density functional theory with the intent of explaining the observed background fluorescence for the carbazolopyridinophanes. The results indicate carbazolopyridinophane conformers most resembling the geometry of their corresponding free carbazole:pyridine complexes exhibit the least background fluorescence.     

Photophysics of a sulfonated 2-hydroxyphenylbenzotriazole UV absorber in solution and in polymer substrates

The total absorption spectrum of the UV absorber sodium 2-(2′-hydroxy-5′-methylphenyl) benzotriazole sulfonate (TINS) has been resolved into contributions by two ground-state forms in acetonitrile-water solvent mixtures and hydrogen bonding polymer and protein substrates. These two ground-state species can be assigned to (i) a planar intramolecularly hydrogen bonded form which can undergo the efficient nonradiative energy dissipation process of excited-state intramolecular proton transfer (ESIPT), and (ii) a fluorescent nonplanar species in which ESIPT is effectively prevented. The mole fractions of each contributing conformer in the polymeric substrates have been estimated. In all the polymer systems studied, a significant proportion of the TINS molecules exist in the nonplanar form and thus may not contribute to photostabilization of the substrate. The proportion of nonplanar molecules varied from 11 to 86% in synthetic polymers and 20 to 41% in protein substrates.     

Potential-energy and free-energy surfaces of glycyl-phenylalanyl-alanine (GFA) tripeptide: experiment and theory

The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA) tripeptide was explored by molecular dynamics (MD) simulations in combination with high-level correlated ab initio quantum chemical calculations and metadynamics. Both the MD and metadynamics employed the tight-binding DFT-D method instead of the AMBER force field, which yielded inaccurate results. We classified the minima localised in the FESs as follows: a) the backbone-conformational arrangement; and b) the existence of a COOH...OC intramolecular H-bond (families CO(2)H(free) and CO(2)H(bonded)). Comparison with experimental results showed that the most stable minima in the FES correspond to the experimentally observed structures. Remarkably, however, we did not observe experimentally the CO(2)H(bonded) family (also predicted by metadynamics), although its stability is comparable to that of the CO(2)H(free) structures. This fact was explained by the former's short excited-state lifetime. We also carried out ab initio calculations using DFT-D and the M06-2X functional. The importance of the dispersion energy in stabilising peptide conformers is well reflected by our pioneer analysis using the DFT-SAPT method to explore the nature of the backbone/side-chain interactions.     

Computational exploration of rearrangements related to the vitamin B12-dependent ethanolamine ammonia lyase catalyzed transformation

DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ) are used to investigate several possible mechanisms involving free radical intermediates as well as their protonated forms for processes related to the coenzyme B(12)-dependent rearrangement catalyzed by ethanolamine ammonia lyase. Two major types of rearrangements are discussed in detail, intramolecular migration and dissociation of the amine/ammonia groups, for both of which several scenarios are considered. According to the calculations, the complete dissociation of the migrating group and its subsequent association constitute an unlikely route for both the protonated and the unprotonated reactant because of the high-energy barriers (more than 23 kcal/mol) involved in these steps. Direct migration of the protonated amine group is far more favorable (10.4 kcal/mol) and therefore presents the most likely candidate for the actual enzymatic reaction. The calculations further imply that the direct loss of an ammonium cation (10.6 kcal/mol) represents a feasible pathway as well. Comparing the rearrangements for the aminoethanol radical and its protonated counterpart, in line with previous findings reported by Golding, Radom, and co-workers, we find that the migration of a protonated group is in general associated with lower energy barriers, suggesting that the actual enzyme substrate quite likely corresponds to (partially) protonated aminoethanol. As the extent of the substrate protonation/deprotonation by the active site of the enzyme may vary, the actual energy barriers are expected to range between the values calculated for the two extreme cases of a substrate, that is, the aminoethanol radical 2 and its fully protonated form 6.     

On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

Stereoselection in the diels–alderase ribozyme: A molecular dynamics study

The Diels‐Alderase ribozyme is an in vitro‐evolved ribonucleic acid enzyme that catalyzes a [4 + 2] cycloaddition reaction between an anthracene diene and a maleimide dienophile. The ribozyme can in principle be used to selectively synthesize only one product enantiomer, depending on which of the two entrances to the catalytic pocket, “front” or “back”, the substrate is permitted to use. Here, we investigate stereoselection and substrate recognition in the ribozyme by means of multiple molecular dynamics simulations, performed on each of the two substrates individually in the pocket, on the reactant state, and on the product state. The results are consistent with a binding mechanism in which the maleimide likely binds first followed by the anthracene, which enters preferentially through the front door. The free energy profiles for anthracene binding indicate that the pre‐(R,R)‐enantiomer conformation is slightly preferred, in agreement with the experimentally observed small enantiomeric excess of the (R,R)‐enantiomer of the product. The reactant state is stabilized by the simultaneous presence of both substrates bound to their binding sites in the hydrophobic pocket as well as by stacking interactions between them. © 2012 Wiley Periodicals, Inc.     

Ultrafast Relaxation Dynamics of the Excited States of 1‐Amino‐ and 1‐(N,N‐Dimethylamino)‐fluoren‐9‐ones

The dynamics of the excited states of 1‐aminofluoren‐9‐one (1AF) and 1‐(N,N‐dimethylamino)‐fluoren‐9‐one (1DMAF) are investigated by using steady‐state absorption and fluorescence as well as subpicosecond time‐resolved absorption spectroscopic techniques. Following photoexcitation of 1AF, which exists in the intramolecular hydrogen‐bonded form in aprotic solvents, the excited‐state intramolecular proton‐transfer reaction is the only relaxation process observed in the excited singlet (S₁) state. However, in protic solvents, the intramolecular hydrogen bond is disrupted in the excited state and an intermolecular hydrogen bond is formed with the solvent leading to reorganization of the hydrogen‐bond network structure of the solvent. The latter takes place in the timescale of the process of solvation dynamics. In the case of 1DMAF, the main relaxation pathway for the locally excited singlet, S₁(LE), or S₁(ICT) state is the configurational relaxation, via nearly barrierless twisting of the dimethylamino group to form the twisted intramolecular charge‐transfer, S₁(TICT), state. A crossing between the excited‐state and ground‐state potential energy curves is responsible for the fast, radiationless deactivation and nonemissive character of the S₁(TICT) state in polar solvents, both aprotic and protic. However, in viscous but strong hydrogen‐bond‐donating solvents, such as ethylene glycol and glycerol, crossing between the potential energy surfaces for the ground electronic state and the hydrogen‐bonded complex formed between the S₁(TICT) state and the solvent is possibly avoided and the hydrogen‐bonded complex is weakly emissive.     

Solvent dependent excited state spectral properties of 4-hydroxyacridine: Evidence for only water mediated excited state proton transfer process

The possibility of ground and excited state proton transfer reaction across the five member intramolecular hydrogen bonded ring in 4-hydroxyacridine (4-HA) has been investigated spectroscopically and the experimental results have been correlated with quantum chemical calculations. The difference in the emissive behaviour of 4-HA in different types of solvents is due to the presence of different species in the excited state. In non-polar solvents, the species present is non-fluorescing in nature, whereas 4-HA molecule shows normal emission from intramolecularly hydrogen bonded closed conformer in polar aprotic solvents. In polar protic solvents like MeOH, EtOH, etc. (except water), a single broad emission band is attributed to the hydrogen bonded solvated form of 4-HA. However, in case of water, fluorescence from the tautomeric form of 4-HA is observed apart from emission from the solvated form. Emission from the tautomeric form may arise due to double proton transfer via a single water molecule bonded to 4-HA. Evaluation of the potential energy surfaces by quantum chemical calculations using density functional theory (DFT) and time dependent density functional theory (TDDFT), however, points towards the possibility of proton transfer—both intrinsic intramolecular as well as water mediated in the first excited state of 4-HA.     

A Process Theory of Enzyme Catalytic Power – the Interplay of Science and Metaphysics

Enzymes are protein catalysts of extraordinary efficiency, capable of bringing about rate enhancements of their biochemical reactions that can approach factors of 10²⁰. Theories of enzyme catalysis, which seek to explain the means by which enzymes effect catalytic transformation of the substrate molecules on which they work, have evolved over the past century from the “lock-and-key” model proposed by Emil Fischer in 1894 to models that explicitly rely on transition state theory to the most recent theories that strive to provide accounts that stress the essential role of protein dynamics. In this paper, I attempt to construct a metaphysical framework within which these new models of enzyme catalysis can be developed. This framework is constructed from key doctrines of process thought, which gives ontologic priority to becoming over being, as well as tenets of a process philosophy of chemistry, which stresses environmentally responsive molecular transformation. Enzyme catalysis can now be seen not as enzyme acting on its substrate, but rather as enzyme and substrate entering into a relation which allows them to traverse the reaction coordinate as an ontologic unity.     

Influence of strong bonding with impenetrable substrate on swelling of elastomers in low-molecular-weight liquids

Swelling in various liquids was studied for a wide variety of free and bonded cross-linked polyurethane materials with different structures and densities of three-dimensional network. A calculational method was proposed for predicting the equilibrium swelling in liquids of elastic polymeric coatings bonded with a nonswelling substrate.     

Intramolecularity and enzyme modelling: a critique

A critical reappraisal of the concept of intramolecularity is attempted, but particulary focussed on the effective molarity (EM) criterion and the relationship of intramolecularity to enzymic reactivity. The prevalent ambiguities in the EM concept are addressed and a revised definition (EM_rev) is suggested. It is argued that there are fundamental limitations to the use of intramolecular reactions as enzyme models. Although the simplest mechanism for enzymic reactivity is based on transition state stabilisation, an alternative (although complex) possibility is based on the stabilisation of the enzyme. Possible mechanisms for the utilisation of the enzymic free energy for effecting catalysis are discussed.