Hydrogen bonding in enzymatic catalysis: analysis of energetic contributions

Modulating Hydrogen Shuttling in Ammonia by Neutral and Cationic Boron-Containing Frustrated Lewis Pairs (FLPs)

Xanthene-backbone FLPs featuring secondary borane functions -B(ArX)H (where ArX=C6F5 (ArF) or C6Cl5 (ArCl)) have been targeted through reactions of the dihydroboranes Me2S ⋅ BArXH2 with [4,5-xanth(PR2)Li]2 (R=Ph, iPr), and investigated in the synthesis of related cationic systems via hydride abstraction. The reactivity of these systems (both cationic and charge neutral) with ammonia have been probed, with a view to probing the potential for proton shuttling via N-H bond 'activation.' We find that in the case of four-coordinate boron systems (cationic or change neutral), the N-H linkage remains intact, supported by a NH⋅⋅⋅P hydrogen bond which is worth up to 17 kcal mol-1 thermodynamically, and enabled by planarization of the flexible xanthene scaffold. For cationic three coordinate systems, N-to-P proton transfer is viable, driven by the ability of the boron centre to stabilise the [NH2]- conjugate base through N-to-B π bonding. This proton transfer can be shown to be reversible in the presence of excess ammonia, depending on the nature of the B-bound ArX group. It is viable in the case of C6F5 substituents, but is prevented by the more sterically encumbering and secondary donor-stabilising capabilities of the C6Cl5 substituent.

Differing Effects of Nonlinearity around the Proton Acceptor on CH··O and NH··O H-Bond Strength within Proteins

The effects of deviations from nonlinearity around the carbonyl proton acceptor of an amide group are assessed by DFT quantum chemical calculations for both CH··O and NH··O H-bonds. The proton donors are the imidazole functional group of His and the indole of Trp, which are paired respectively with N-methylacetamide and acetamide. The displacement of either CH or NH group toward the carbonyl O sp2 lone pairs stabilizes the system and strengthens the H-bond. But the two donor groups differ in their response to a shift out of the amide plane. While the NH··O H-bond is weakened by this displacement, a substantial strengthening is observed when the CH donor is moved out of this plane, in one direction versus the other. This pattern is explained on the basis of simple Coulombic considerations.

Chalcone derivatives from licorice inhibit human and rat gonadal 3β-hydroxysteroid dehydrogenases as therapeutic uses

ETHNOPHARMACOLOGICAL RELEVANCE

In traditional Chinese medicine, licorice (the roots of Glycyrrhiza glabra and G. inflata) has been used to treat inflammation and sexual debility for over 1000 years. Pharmacological studies have identified many biologically active chalcone derivatives from licorice.

AIM OF THE STUDY

Human 3β-Hydroxysteroid dehydrogenase 2 (h3β-HSD2) catalyzes the formation of precursors for sex hormones and corticosteroids, which play critical roles in reproduction and metabolism. We explored inhibition and mode action of chalcones of inhibiting h3β-HSD2 and compared it with rat 3β-HSD1.

MATERIALS AND METHODS

We investigated the inhibition of 5 chalcones on h3β-HSD2 and compared species-dependent difference with 3β-HSD1.

RESULTS

The inhibitory strength on h3β-HSD2 was isoliquiritigenin (IC50, 0.391 μM) > licochalcone A (0.494 μM) > licochalcone B (1.485 μM) > echinatin (1.746 μM) >chalcone (100.3 μM). The inhibitory strength on r3β-HSD1 was isoliquiritigenin (IC50, 0.829 μM) > licochalcone A (1.165 μM) > licochalcone B (1.866 μM) > echinatin (2.593 μM) > chalcone (101.2 μM). Docking showed that all chemicals bind steroid and/or NAD+-binding site with the mixed mode. Structure-activity relationship analysis showed that strength was correlated with chemical's hydrogen bond acceptor.

CONCLUSION

Some chalcones are potent h3β-HSD2 and r3β-HSD1 inhibitors, possibly being potential drugs to treat Cushing's syndrome or polycystic ovarian syndrome.

The principle "like begets like" in algebra-matrix genetics and code biology

The article is devoted to analysis of emergent properties of the system of binary oppositions in the genetic code ensemble. The epochal model of the double helix of DNA by Watson and Crick showed that the multiple reproduction of genetic information on DNA strands uses the ancient principle "like begets like" based on the simple complementarity in pairs of nucleobases. Each of these pairs is built on the binary opposition "purine-pyrimidine". But the system of DNA n-plet alphabets and genetic coding is much richer in types of binary oppositions, which also have some coding meanings related to this principle. The article contains the results of the application of the author's "method of hierarchy binary stochastics" (HBS-method) to the analysis of the quasi-stochastic organization of binary sequences of hydrogen bonds in genomic single-stranded DNAs. This analysis revealed hidden probability rules related to dichotomous fractal-like probability trees. The relationship between inherited bodily dichotomies in living organisms and the discovered probability dichotomies in information sequences of genomic DNAs is discussed. The encoding properties of molecular binary oppositions in the DNA nucleotide system allows the algorithmic construction of (2n∗2n)-matrices of probabilities of n-plets in these binary sequences, which are matrix representations of 2n-dimensional hyperbolic numbers. Connections of these multidimensional numbers with some inherited physiological phenomena and deep neural networks are noted. A unified algebra-numeric certification of the DNAs of genomes and genes - based on these multidimensional numerical systems - is proposed.

Halogen atoms determine the inhibitory potency of halogenated bisphenol A derivatives on human and rat placental 11β-hydroxysteroid dehydrogenase 2

Some halogenated bisphenol A (BPA) derivatives (tetrabromobisphenol A, TBBPA, and tetrachlorobisphenol A, TCBPA) are produced in a high volume and exist in PM_2.5 after waste burning. 11β-Hydroxysteroid dehydrogenase 2 (11β-HSD2) is a critical enzyme for placental function. However, whether halogenated bisphenols inhibit 11β-HSD2 and the mode of action remains unclear. The objective of this study was to investigate BPA derivatives on human and rat placental 11β-HSD2. The inhibitory strength on human 11β-HSD2 was TBBPA (IC₅₀, 0.665 μM)>TCBPA (2.22 μM)>trichloro BPA (TrCBPA, 19.87 μM)>tetrabromobisphenol S (TBBPS, 36.76 μM)>monochloro BPA (MCBPA, 104.0 μM)>BPA (144.9 μM)>bisphenol S. All chemicals are mixed and competitive inhibitors. Rat 11β-HSD2 was less sensitive to BPA derivatives, with TBBPA (IC₅₀, 96.63 μM)>TCBPA (99.69 μM)>TrCBPA (104.1 μM)>BPA (117.1 μM)>others. Docking analysis showed that BPA derivatives bind steroid active sites. Structure-activity relationship revealed that halogen atoms and LogP were inversely correlated with inhibitory strength on human 11β-HSD2, while LogS and polar desolvation energy were positively correlated with the inhibitory strength. In conclusion, halogenated BPA derivatives are mostly potent inhibitors on human 11β-HSD2 and there is structure-dependent inhibition.

Anion-Coordination-Driven Assembly: From Discrete Supramolecular Self-Assemblies to Functional Soft Materials

Anion templated assembly of supramolecular systems has been extensively explored in previous reports, whereas anions serve only as an auxiliary and spectator role. With the development of anion coordination chemistry in recent years, anion coordination-driven assembly (ACDA) has emerged as a new strategy for the construction of supramolecular self-assemblies. Anions are proved to exist as the main actors in the construction of supramolecular architectures, i. e., serve as the coordination center. This Review will focus on the recent progress in anion-coordination-driven assembly of discrete supramolecular architectures, such as helicates, polyhedrons and polygons, and the various applications of 'aniono'-systems. At the end of this Review, we highlight current challenges and opportunities for future research of anion-coordination-driven self-assembly.

Ensemble-function relationships to dissect mechanisms of enzyme catalysis

Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.

Parallel molecular mechanisms for enzyme temperature adaptation

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

Hydrogen Bonds: Simple after All?

Hydrogen bonds play integral roles in biological structure, function, and conformational dynamics and are fundamental to life as it has evolved on Earth. However, our understanding of these fundamental and ubiquitous interactions has seemed fractured and incomplete, and it has been difficult to extract generalities and principles about hydrogen bonds despite thousands of papers published on this topic, perhaps in part because of the expanse of this subject and the density of studies. Fortunately, recent hydrogen bond proposals, discussions, and debates have stimulated new tests and models and have led to a remarkably simple picture of the structure of hydrogen bonds. This knowledge also provides clarity concerning hydrogen bond energetics, limiting and simplifying the factors that need be considered. Herein we recount the advances that have led to this simpler view of hydrogen bond structure, dynamics, and energetics. A quantitative predictive model for hydrogen bond length can now be broadly and deeply applied to evaluate current proposals and to uncover structural features of proteins, their conformational restraints, and their correlated motions. In contrast, a quantitative energetic description of molecular recognition and catalysis by proteins remains an important ongoing challenge, although our improved understanding of hydrogen bonds may aid in testing predictions from current and future models. We close by codifying our current state of understanding into five "Rules for Hydrogen Bonding" that may provide a foundation for understanding and teaching about these vital interactions and for building toward a deeper understanding of hydrogen bond energetics.

Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP)

Short hydrogen bonds and specifically low-barrier hydrogen bonds (LBHBs) have been the focus of much attention and controversy for their possible role in enzymatic catalysis. The green fluorescent protein (GFP) mutant S65T, H148D has been found to form a very short hydrogen bond between Asp148 and the chromophore resulting in significant spectral perturbations. Leveraging the unique autocatalytically formed chromophore and its sensitivity to this interaction we explore the consequences of proton affinity matching across this putative LBHB. Through the use of noncanonical amino acids introduced through nonsense suppression or global incorporation, we systematically modify the acidity of the GFP chromophore with halogen substituents. X-ray crystal structures indicated that the length of the interaction with Asp148 is unchanged at ∼2.45 Å while the absorbance spectra demonstrate an unprecedented degree of color tuning with increasing acidity. We utilized spectral isotope effects, isotope fractionation factors, and a simple 1D model of the hydrogen bond coordinate in order to gain insight into the potential energy surface and particularly the role that proton delocalization may play in this putative short hydrogen bond. The data and model suggest that even with the short donor-acceptor distance (∼2.45 Å) and near perfect affinity matching there is not a LBHB, that is, the barrier to proton transfer exceeds the H zero-point energy.

Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability

Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (ΔGf) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to ΔGf, but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H···O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite ΔGf differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond ΔGf are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.

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.

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol-Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations.

Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes

Enzymes are remarkable catalysts that lie at the heart of biology, accelerating chemical reactions to an astounding extent with extraordinary specificity. Enormous progress in understanding the chemical basis of enzymatic transformations and the basic mechanisms underlying rate enhancements over the past decades is apparent. Nevertheless, it has been difficult to achieve a quantitative understanding of how the underlying mechanisms account for the energetics of catalysis, because of the complexity of enzyme systems and the absence of underlying energetic additivity. We review case studies from our own work that illustrate the power of precisely defined and clearly articulated questions when dealing with such complex and multifaceted systems, and we also use this approach to evaluate our current ability to design enzymes. We close by highlighting a series of questions that help frame some of what remains to be understood, and we encourage the reader to define additional questions and directions that will deepen and broaden our understanding of enzymes and their catalysis.

Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase

Prior site-directed mutagenesis studies in bacterial ketosteroid isomerase (KSI) reported that substitution of both oxyanion hole hydrogen bond donors gives a 10(5)- to 10(8)-fold rate reduction, suggesting that the oxyanion hole may provide the major contribution to KSI catalysis. But these seemingly conservative mutations replaced the oxyanion hole hydrogen bond donors with hydrophobic side chains that could lead to suboptimal solvation of the incipient oxyanion in the mutants, thereby potentially exaggerating the apparent energetic benefit of the hydrogen bonds relative to water-mediated hydrogen bonds in solution. We determined the functional and structural consequences of substituting the oxyanion hole hydrogen bond donors and several residues surrounding the oxyanion hole with smaller residues in an attempt to create a local site that would provide interactions more analogous to those in aqueous solution. These more drastic mutations created an active-site cavity estimated to be ~650 Å(3) and sufficient for occupancy by 15-17 water molecules and led to a rate decrease of only ~10(3)-fold for KSI from two different species, a much smaller effect than that observed from more traditional conservative mutations. The results underscore the strong context dependence of hydrogen bond energetics and suggest that the oxyanion hole provides an important, but moderate, catalytic contribution relative to the interactions in the corresponding solution reaction.

Membrane protein folding: how important are hydrogen bonds?

Water is an inhospitable environment for protein hydrogen bonds because it is polarizable and capable of forming competitive hydrogen bonds. In contrast, the apolar core of a biological membrane seems like an ideal environment for hydrogen bonds, and it has long been assumed that hydrogen bonding should be a powerful force driving membrane protein folding. Nevertheless, while backbone hydrogen bonds may be much stronger in membrane proteins, experimental measurements indicate that side chain hydrogen bond strengths are not strikingly different in membrane and water soluble proteins. How is this possible? I argue that model compounds in apolar solvents do not adequately describe the system because the protein itself is ignored. The protein chain provides a rich source of competitive hydrogen bonds and a polarizable environment that can weaken hydrogen bonds. Thus, just like water soluble proteins, evolution can drive the creation of potent hydrogen bonds in membrane proteins where necessary, but mitigating forces in their environment must still be overcome.

A computational analysis of intramolecularity in proton transfer reactions

Hydrogen bonds along which most proton transfers take place are analyzed regarding their contribution to the efficiency of intramolecular processes through the assessment of effective molarities by DFT calculations on rigid intra-molecular model systems in comparison with their intermolecular counterparts. A few cyclic systems in which there is no possibility of hydrogen bonding between reactants neither in the ground state nor in the product are identified by theoretical calculations as leading to important rate increases in intramolecular general-base catalysis constituting a new exception to the rule of low effective molarities (EMs) for proton transfers. The recovery of high efficiency in these systems is attributed to the absence of special features facilitating the corresponding intermolecular reactions. This work confirms that any explanation of EMs found in intramolecular systems also requires a careful analysis of the corresponding bimolecular systems.

The thiolase reaction mechanism: the importance of Asn316 and His348 for stabilizing the enolate intermediate of the Claisen condensation

The biosynthetic thiolase catalyzes a Claisen condensation reaction between acetyl-CoA and the enzyme acetylated at Cys89. Two oxyanion holes facilitate this catalysis: oxyanion hole I stabilizes the enolate intermediate generated from acetyl-CoA, whereas oxyanion hole II stabilizes the tetrahedral intermediate of the acetylated enzyme. The latter intermediate is formed when the alpha-carbanion of acetyl-CoA enolate reacts with the carbonyl carbon of acetyl-Cys89, after which C-C bond formation is completed. Oxyanion hole II is made of two main chain peptide NH groups, whereas oxyanion hole I is formed by a water molecule (Wat82) and NE2(His348). Wat82 is anchored in the active site by an optimal set of hydrogen bonding interactions, including a hydrogen bond to ND2(Asn316). Here, the importance of Asn316 and His348 for catalysis has been studied; in particular, the properties of the N316D, N316A, N316H, H348A, and H348N variants have been determined. For the N316D variant, no activity could be detected. For each of the remaining variants, the k(cat)/K(m) value for the Claisen condensation catalysis is reduced by a factor of several hundred, whereas the thiolytic degradation catalysis is much less affected. The crystal structures of the variants show that the structural changes in the active site are minimal. Our studies confirm that oxyanion hole I is critically important for the condensation catalysis. Removing either one of the hydrogen bond donors causes the loss of at least 3.4 kcal/mol of transition state stabilization. It appears that in the thiolytic degradation direction, oxyanion hole I is not involved in stabilizing the transition state of its rate limiting step. However, His348 has a dual role in the catalytic cycle, contributing to oxyanion hole I and activating Cys89. The analysis of the hydrogen bonding interactions in the very polar catalytic cavity shows the importance of two conserved water molecules, Wat82 and Wat49, for the formation of oxyanion hole I and for influencing the reactivity of the catalytic base, Cys378, respectively. Cys89, Asn316, and His348 form the CNH-catalytic triad of the thiolase superfamily. Our findings are also discussed in the context of the importance of this triad for the catalytic mechanism of other enzymes of the thiolase superfamily.

Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase

A fundamental difference between enzymes and small chemical catalysts is the ability of enzymes to use binding interactions with nonreactive portions of substrates to accelerate chemical reactions. Remote binding interactions can localize substrates to the active site, position substrates relative to enzymatic functional groups and other substrates, trigger conformational changes, induce local destabilization, and modulate an active site environment by solvent exclusion. We investigated the role of remote substrate binding interactions in the reaction catalyzed by the enzyme ketosteroid isomerase (KSI), which catalyzes a double bond migration of steroid substrates through a dienolate intermediate that is stabilized in an oxyanion hole. Comparison of a single-ring and multiple-ring substrate allowed the catalytic contribution of binding interactions with the distal substrate rings to be determined. The value of k(cat)/K(M) for a single-ring substrate is reduced 27,000-fold relative to a multiple-ring steroid substrate, suggesting that remote binding interactions with the steroid substrate contribute substantially to the KSI reaction. Nevertheless, the reaction rates for KSI-bound single- and multiple-ring substrates (k(cat)) are within 2-fold. Further, oxyanion hole mutations have the same effect on reactions of the single- and multiple-ring substrates. These results suggest that remote binding interactions contribute >5 kcal/mol to catalysis by KSI but that local rather than remote interactions dictate the catalytic contributions from KSI's general base and oxyanion hole.

Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins

Understanding the energetics of molecular interactions is fundamental to all of the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water. Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins. Because of limited structural information and technical challenges, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is only 0.6 kcal mol(-1). In agreement with these experiments, we find that 4% of polar atoms in the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. Our results indicate that most hydrogen-bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.

Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole

A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing p K_a models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50–0.76 ppm/p K_a unit, suggesting a bond shortening of ˜0.02 Å/p K_a unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (ΔΔG = −0.2 kcal/mol/p K_a unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (ΔΔH = −2.0 kcal/mol/p K_a unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of ˜300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.

Enzymatic reactions require exquisitely detailed molecular interactions. Here the authors show that geometric complementarity is likely more important than electrostatic charge in contributing to the binding necessary for catalytic reactions.

Changes in the structural properties and rate of hydrolysis of cotton fibers during extended enzymatic hydrolysis

An extended enzymatic hydrolysis of cotton fibers by crude cellulase from Trichoderma pseudokoningii S-38 is described with characterization of both the enzyme changes of activities and cellulose structure. The hydrolysis rates declined drastically during the early stage and then slowly and steadily throughout the whole hydrolysis process the same trend could be seen during the following re-hydrolysis process. Morphological and structural changes to the fibers, such as swelling, frequent surface erosion, and variation in the packing and orientation of microfibrils, were investigated by scanning electron microscopy (SEM) and atomic force microscopy (AFM). Observation of X-ray diffraction and IR spectra suggests that the hydrolysis process results in a gradual increase in the relative intensity of the hydrogen bond network, and a gradual decrease in the apparent crystal size of cellulose. The I(alpha) crystal phase was hydrolyzed more easily than was the I(beta) crystal phase. Apart from the inactivation of CBHs activity, changes in the packing and arrangement of microfibrils and the structural heterogeneity of cellulose during hydrolysis could be responsible for the reduction in the rate of reaction, especially in its later stages. The results indicate that the enzymatic hydrolysis of cellulose occurs on the outer layer of the fiber surface and that, following this, the process continues in a sub-layer manner.

Thiourea-catalyzed enantioselective cyanosilylation of ketones

The new chiral amino thiourea catalyst 3d promotes the highly enantioselective cyanosilylation of a wide variety of ketones. The hindered tertiary amine substituent plays a crucial role with regard to both stereoinduction and reactivity, suggesting a cooperative mechanism involving electrophile activation by thiourea and nucleophile activation by the amine.

Challenges in enzyme mechanism and energetics

Since the discovery of enzymes as biological catalysts, study of their enormous catalytic power and exquisite specificity has been central to biochemistry. Nevertheless, there is no universally accepted comprehensive description. Rather, numerous proposals have been presented over the past half century. The difficulty in developing a comprehensive description for the catalytic power of enzymes derives from the highly cooperative nature of their energetics, which renders impossible a simple division of mechanistic features and an absolute partitioning of catalytic contributions into independent and energetically additive components. Site-directed mutagenesis has emerged as an enormously powerful approach to probe enzymatic catalysis, illuminating many basic features of enzyme function and behavior. The emphasis of site-directed mutagenesis on the role of individual residues has also, inadvertently, limited experimental and conceptual attention to the fundamentally cooperative nature of enzyme function and energetics. The first part of this review highlights the structural and functional interconnectivity central to enzymatic catalysis. In the second part we ask: What are the features of enzymes that distinguish them from simple chemical catalysts? The answers are presented in conceptual models that, while simplified, help illustrate the vast amount known about how enzymes achieve catalysis. In the last section, we highlight the molecular and energetic questions that remain for future investigation and describe experimental approaches that will be necessary to answer these questions. The promise of advancing and integrating cutting edge conceptual, experimental, and computational tools brings mechanistic enzymology to a new era, one poised for novel fundamental insights into biological catalysis.

Closed Conformation of the Active Site Loop of Rabbit Muscle Triosephosphate Isomerase in the Absence of Substrate: Evidence of Conformational Heterogeneity

The active site loop of triosephosphate isomerase (TIM) exhibits a hinged-lid motion, alternating between the two well defined "open" and "closed" conformations. Until now the closed conformation had only been observed in protein complexes with substrate analogues. Here, we present the first rabbit muscle apo TIM structure, refined to 1.5A resolution, in which the active site loop is either in the open or in the closed conformation in different subunits of the enzyme. In the closed conformation described here, the lid loop residues participate in stabilizing hydrogen bonds characteristic of holo TIM structures, whereas chemical interactions observed in the open loop conformation are similar to those found in the apo structures of TIM. In the closed conformation, a number of water molecules are observed at the projected ligand atom positions that are hydrogen bonded to the active site residues. Additives used during crystallization (DMSO and Tris molecules and magnesium atoms) were modeled in the electron density maps. However, no specific binding of these molecules is observed at, or close to, the active site and the lid loop. To further investigate this unusual closed conformation of the apo enzyme, two more rabbit muscle TIM structures, one in the same and another in a different crystal form, were determined. These structures present the open lid conformation only, indicating that the closed conformation cannot be explained by crystal contact effects. To rationalize why the active site loop is closed in the absence of ligand in one of the subunits, extensive comparison with previously solved TIM structures was carried out, supported by the bulk of available experimental information about enzyme kinetics and reaction mechanism of TIM. The observation of both open and closed lid conformations in TIM crystals might be related to a persistent conformational heterogeneity of this protein in solution.

Transition state stabilization by a catalytic RNA

The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of the 2.2 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor and product complexes reveals a rigid active site that makes more hydrogen bonds to the transition state than to the precursor or product. Because of the paucity of RNA functional groups capable of general acid-base or electrostatic catalysis, transition state stabilization is likely to be an important catalytic strategy for ribozymes.

Tanford-Kirkwood electrostatics for protein modeling

Solvent plays a significant role in determining the electrostatic potential energy of proteins, most notably through its favorable interactions with charged residues and its screening of electrostatic interactions. These energetic contributions are frequently ignored in computational protein design and protein modeling methodologies because they are difficult to evaluate rapidly and accurately. To address this deficiency, we report a revised form of the original Tanford-Kirkwood continuum electrostatic model [Tanford, C. & Kirkwood, J. G. (1957) J. Am. Chem. Soc. 79, 5333-5339], which accounts for the effects of solvent polarization on charged atoms in proteins. The Tanford-Kirkwood model was modified to increase its speed and to improve its sensitivity to the details of protein structure. For the 37 electrostatic self-energies of the polar side-chains in bovine pancreatic trypsin inhibitor, and their 666 interaction energies, the modified Tanford-Kirkwood potential of mean force differs from a computationally intensive numerical potential (DelPhi) by root-mean-square errors of 0.6 kcal/mol and 0.08 kcal/mol, respectively. The Tanford-Kirkwood approach makes possible a realistic treatment of electrostatics in computationally demanding protein modeling calculations. For example, pH titration calculations for ovomucoid third domain that model polar side-chain relaxation (including >2 x 10(23) rotamer conformations of the protein) provide pKa values of unprecedented accuracy.