Kemp Eliminase Activity of Ketosteroid Isomerase.

Kemp eliminases represent the most successful class of computationally designed enzymes, with rate accelerations of up to 109-fold relative to the rate of the same reaction in aqueous solution. Nevertheless, several other systems such as micelles, catalytic antibodies, and cavitands are known to accelerate the Kemp elimination by several orders of magnitude. We found that the naturally occurring enzyme ketosteroid isomerase (KSI) also catalyzes the Kemp elimination. Surprisingly, mutations of D38, the residue that acts as a general base for its natural substrate, produced variants that catalyze the Kemp elimination up to 7000-fold better than wild-type KSI does, and some of these variants accelerate the Kemp elimination more than the computationally designed Kemp eliminases. Analysis of the D38N general base KSI variant suggests that a different active site carboxylate residue, D99, performs the proton abstraction. Docking simulations and analysis of inhibition by active site binders suggest that the Kemp elimination takes place in the active site of KSI and that KSI uses the same catalytic strategies of the computationally designed enzymes. In agreement with prior observations, our results strengthen the conclusion that significant rate accelerations of the Kemp elimination can be achieved with very few, nonspecific interactions with the substrate if a suitable catalytic base is present in a hydrophobic environment. Computational design can fulfill these requirements, and the design of more complex and precise environments represents the next level of challenges for protein design.

The eukaryotic enzyme Bds1 is an alkyl but not an aryl sulfohydrolase.

The eukaryotic enzyme Bds1 in Saccharomyces cerevisiae is a metallo-ß-lactamase-related enzyme evolutionarily originating from bacterial horizontal gene transfer that serves an unknown biological role. Previously, Bds1 was reported to be an alkyl and aryl sulfatase. However, we demonstrate here that Bds1 acts on primary alkyl sulfates (of 6-12 carbon atoms) but not the aryl sulfates p-nitrophenyl sulfate and p-nitrocatechol sulfate. The apparent catalytic rate constant for hydrolysis of the substrate 1-hexyl sulfate by Bds1 is over 100 times lower than that of the reaction catalyzed by its bacterial homolog SdsA1. We show that Bds1 shares a catalytic mechanism with SdsA1 in which the carbon atom of the sulfate ester is the subject of nucleophilic attack, rather than the sulfur atom, resulting in C-O bond lysis. In contrast to SdsA1 and another bacterial homolog with selectivity for secondary alkyl sulfates named Pisa1, Bds1 does not show any substantial activity towards secondary alkyl sulfates. Neither Bds1 nor SdsA1 have any significant activity towards a branched primary alkyl sulfate, primary and secondary steroid sulfates, or phosphate diesters. Therefore, the enzymes homologous to SdsA1 that have been identified and characterized thus far vary in their selectivity towards primary and secondary alkyl sulfates but do not exhibit aryl sulfatase activity.

Exploring purine N7 interactions via atomic mutagenesis: the group I ribozyme as a case study.

Atomic mutagenesis has emerged as a powerful tool to unravel specific interactions in complex RNA molecules. An early extensive study of analogs of the exogenous guanosine nucleophile in group I intron self-splicing by Bass and Cech demonstrated structure-function relationships analogous to those seen for protein ligands and provided strong evidence for a well-formed substrate binding site made of RNA. Subsequent functional and structural studies have confirmed these interacting sites and extended our understanding of them, with one notable exception. Whereas 7-methyl guanosine did not affect reactivity in the original study, a subsequent study revealed a deleterious effect of the seemingly more conservative 7-deaza substitution. Here we investigate this paradox, studying these and other analogs with the more thoroughly characterized ribozyme derived from the Tetrahymena group I intron. We found that the 7-deaza substitution lowers binding by ~20-fold, relative to the cognate exogenous guanosine nucleophile, whereas binding and reaction with 7-methyl and 8-aza-7-deaza substitutions have no effect. These and additional results suggest that there is no functionally important contact between the N7 atom of the exogenous guanosine and the ribozyme. Rather, they are consistent with indirect effects introduced by the N7 substitution on stacking interactions and/or solvation that are important for binding. The set of analogs used herein should be valuable in deciphering nucleic acid interactions and how they change through reaction cycles for other RNAs and RNA/protein complexes.

The effect of the hydrophobic environment on the retro-aldol reaction: comparison to a computationally-designed enzyme.

Recent work on a computationally-designed retroaldolase RA-61 suggested that most of the rate-acceleration brought about by this enzyme was due to non-specific interactions with the aromatic substrate. To provide a benchmark for the role of non-specific interactions in this system, we measured the second-order rate constant for the amine-catalysed retro-aldol reaction of methodol in the presence of non-specific hydrophobic pockets such as micelles. We found that a simple micellar system, that consists of a positively-charged surfactant and a long-chain amine, can accelerate the retro-aldol reaction of methodol by 9500-fold. This effect rivals the 10(5)-fold rate acceleration of RA-61. Similar results were obtained with BSA used as the catalyst, implying that the retro-aldol reaction of methodol can be greatly accelerated by non-specific hydrophobic pockets that contain an amino group.

HAMLET in human milk is resistant to digestion and carries essential free long chain polyunsaturated fatty acids and oleic acid.

The oleic acid/alpha-lactalbumin complex HAMLET (human alpha-lactalbumin made lethal to tumors) is cytotoxic to various cancerous cell lines and is assembled from alpha-lactalbumin (ALA) and free oleic acid (OA). HAMLET is also cytotoxic to normal immature intestinal cells. It remains unclear if HAMLET, experimentally assembled with OA and heat, can spontaneously assemble in frozen human milk over time. To approach this issue, we used a set of timed proteolytic experiments to evaluate the digestibility of HAMLET and native ALA. The purity of HAMLET in human milk was confirmed by ultra high performance liquid chromatography coupled to tandem mass spectrometry and western blot to resolve the ALA and OA components. Timed proteolytic experiments were used to identify HAMLET in whole milk samples. Structural characterization of HAMLET was performed by Fournier transformed infrared spectroscopy and indicated a transformation of secondary structure with increased alpha-helical character of ALA upon binding to OA.

Significant Enhancement of Two-Photon Excited Fluorescence in Water-Soluble Triphenylamine-Based All-Organic Compounds.

Understanding water-soluble and environmentally friendly two-photon absorption (TPA) molecules benefits the design of superior organic complexes for biomedical, illumination, and display applications. In this work, we designed two triphenylamine-based all-organic compounds and explored the mechanism of enhanced TP fluorescence in water solutions for potential applications. Experimentally, we showed that adding protein into our TPA molecule solution can drastically boost the TP fluorescence. Numerical simulations reveal that the TPA molecules prefer to dock inside the protein complex. We hypothesize that the interaction between our triphenylamine-based all-organic compounds and water molecules lead to non-radiative decay processes, which prevent strong TP fluorescence in the water solution. Therefore, the protection by, for example, protein molecules from such interactions can be a universal strategy for superior functioning of organic TPA molecules. Further experiments and numerical simulations support our hypothesis. The present study may facilitate the design of superior water-soluble and environmentally friendly superior organic complexes.

Tightening of active site interactions en route to the transition state revealed by single-atom substitution in the guanosine-binding site of the Tetrahymena group I ribozyme.

Protein enzymes establish intricate networks of interactions to bind and position substrates and catalytic groups within active sites, enabling stabilization of the chemical transition state. Crystal structures of several RNA enzymes also suggest extensive interaction networks, despite RNA's structural limitations, but there is little information on the functional and the energetic properties of these inferred networks. We used double mutant cycles and presteady-state kinetic analyses to probe the putative interaction between the exocyclic amino group of the guanosine nucleophile and the N7 atom of residue G264 of the Tetrahymena group I ribozyme. As expected, the results supported the presence of this interaction, but remarkably, the energetic penalty for introducing a CH group at the 7-position of residue G264 accumulates as the reaction proceeds toward the chemical transition state to a total of 6.2 kcal/mol. Functional tests of neighboring interactions revealed that the presence of the CH group compromises multiple contacts within the interaction network that encompass the reactive elements, apparently forcing the nucleophile to bind and attack from an altered, suboptimal orientation. The energetic consequences of this indirect disruption of neighboring interactions as the reaction proceeds demonstrate that linkage between binding interactions and catalysis hinges critically on the precise structural integrity of a network of interacting groups.

A rearrangement of the guanosine-binding site establishes an extended network of functional interactions in the Tetrahymena group I ribozyme active site.

Protein enzymes appear to use extensive packing and hydrogen bonding interactions to precisely position catalytic groups within active sites. Because of their inherent backbone flexibility and limited side chain repertoire, RNA enzymes face additional challenges relative to proteins in precisely positioning substrates and catalytic groups. Here, we use the group I ribozyme to probe the existence, establishment, and functional consequences of an extended network of interactions in an RNA active site. The group I ribozyme catalyzes a site-specific attack of guanosine on an oligonucleotide substrate. We previously determined that the hydrogen bond between the exocyclic amino group of guanosine and the 2'-hydroxyl group at position A261 of the Tetrahymena group I ribozyme contributes to overall catalysis. We now use functional data, aided by double mutant cycles, to probe this hydrogen bond in the individual reaction steps of the catalytic cycle. Our results indicate that this hydrogen bond is not formed upon guanosine binding to the ribozyme but instead forms at a later stage of the catalytic cycle. Formation of this hydrogen bond is correlated with other structural rearrangements in the ribozyme's active site that are promoted by docking of the oligonucleotide substrate into the ribozyme's active site, and disruption of this interaction has deleterious consequences for the chemical transformation within the ternary complex. These results, combined with earlier results, provide insight into the nature of the multiple conformational steps used by the Tetrahymena group I ribozyme to achieve its active structure and reveal an intricate, extended network of interactions that is used to establish catalytic interactions within this RNA's active site.

Kemp Eliminases of the AlleyCat Family Possess High Substrate Promiscuity.

Minimalist enzymes designed to catalyze model reactions provide useful starting points for creating catalysts for practically important chemical transformations. We have shown that Kemp eliminases of the AlleyCat family facilitate conversion of leflunomide (an immunosupressor pro-drug) to its active form teriflunomide with outstanding rate enhancement (nearly four orders of magnitude) and catalytic proficiency (more than seven orders of magnitude) without any additional optimization. This remarkable activity is achieved by properly positioning the substrate in close proximity to the catalytic glutamate with very high pKa.

Functional identification of ligands for a catalytic metal ion in group I introns.

Many enzymes use metal ions within their active sites to achieve enormous rate acceleration. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s). The three-dimensional arrangement determined by X-ray crystallography provides a powerful starting point for identifying ground state interactions, but only functional studies can establish and interrogate transition state interactions. The Tetrahymena group I ribozyme is a paradigm for the study of RNA catalysis, and previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified catalytic metal ions making five contacts with the substrate atoms. Here, we have combined atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to establish transition state ligands on the ribozyme for one of the catalytic metal ions, referred to as M A. We identified the pro-S P oxygen atoms at nucleotides C208, A304, and A306 as ground state ligands for M A, verifying interactions suggested by the Azoarcus crystal structures. We further established that these interactions are present in the chemical transition state, a conclusion that requires functional studies, such as those carried out herein. Elucidating these active site connections is a crucial step toward an in-depth understanding of how specific structural features of the group I intron lead to catalysis.

Kemp Elimination in Cationic Micelles: Designed Enzyme-Like Rates Achieved through the Addition of Long-Chain Bases.

The Kemp elimination is prototypical reaction used to study proton abstraction from carbon. Several hydrophobic systems are known to accelerate this reaction, including two classes of computationally-designed enzymes. However, it is unclear whether these computationally-designed enzymes establish specific interactions with their substrates, as natural enzymes do, or if most of the rate acceleration is due to the hydrophobicity of the substrate. We used a simple system composed of cationic micelles and a long chain base (such as lauryl phosphate or lauric acid) to measure the rate acceleration for the Kemp elimination. Remarkably, we found that this simple system can accelerate the reaction by 4 orders of magnitude, approaching the rates of more complex designed systems. Use of different substrates suggests that the reaction takes place at the interface between the micellar head and water (the Stern layer) with the long-chain base embedded in the micelle and the substrate in the aqueous solution. Thus, we suggest that significant rate accelerations can be achieved regardless of the precise positioning of substrates. Because natural enzymes use specific interactions to position their substrates, we propose that acceleration of the Kemp elimination is not a suitable benchmark for the success of the design process, and we suggest that more complex reactions should be used.

2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA.

The ability of fluorine in a C-F bond to act as a hydrogen bond acceptor is controversial. To test such ability in complex RNA macromolecules, we have replaced native 2'-OH groups with 2'-F and 2'-H groups in two related systems, the Tetrahymena group I ribozyme and the ΔC209 P4-P6 RNA domain. In three cases the introduced 2'-F mimics the native 2'-OH group, suggesting that the fluorine atom can accept a hydrogen bond. In each of these cases the native hydroxyl group interacts with a purine exocyclic amine. Our results give insight about the properties of organofluorine and suggest a possible general biochemical signature for tertiary interactions between 2'-hydroxyl groups and exocyclic amino groups within RNA.

Metal ion-based RNA cleavage as a structural probe.

It is well established that many metal ions accelerate the spontaneous degradation of RNA. This property has been exploited in several ways to garner information about RNA structure, especially in regards to the location of site-specifically bound metal ions, the presence of defined structural motifs, and the occurrence of conformational changes in structured RNAs. In this chapter, we review this information, briefly giving strengths and limitations for each of these approaches. Finally, we provide a general protocol to perform metal ion-mediated cleavage of RNA.

Use of phosphorothioates to identify sites of metal-ion binding in RNA.

Single atom substitutions provide an exceptional opportunity to investigate RNA structure and function. Replacing a phosphoryl oxygen with a sulfur represents one of the most common and powerful single atom substitutions and can be used to determine the sites of metal-ion binding. Using functional assays of ribozyme catalysis, based on pre-steady-state kinetics, it is possible to extend this analysis to the transition state, capturing ligands for catalytic metal ions in this fleeting state. In conjunction with data determined from X-ray crystallography, this technique can provide a picture of the environment surrounding catalytic metal ions in both the ground state and the transition state at atomic resolution. Here, we describe the principles of such analysis, explain limitations of the method, and provide a practical example based on our results with the Tetrahymena group I ribozyme.

Modulation of individual steps in group I intron catalysis by a peripheral metal ion.

Enzymes are complex macromolecules that catalyze chemical reactions at their active sites. Important information about catalytic interactions is commonly gathered by perturbation or mutation of active site residues that directly contact substrates. However, active sites are engaged in intricate networks of interactions within the overall structure of the macromolecule, and there is a growing body of evidence about the importance of peripheral interactions in the precise structural organization of the active site. Here, we use functional studies, in conjunction with published structural information, to determine the effect of perturbation of a peripheral metal ion binding site on catalysis in a well-characterized catalytic RNA, the Tetrahymena thermophila group I ribozyme. We perturbed the metal ion binding site by site-specifically introducing a phosphorothioate substitution in the ribozyme's backbone, replacing the native ligands (the pro-R (P) oxygen atoms at positions 307 and 308) with sulfur atoms. Our data reveal that these perturbations affect several reaction steps, including the chemical step, despite the absence of direct contacts of this metal ion with the atoms involved in the chemical transformation. As structural probing with hydroxyl radicals did not reveal significant change in the three-dimensional structure upon phosphorothioate substitution, the effects are likely transmitted through local, rather subtle conformational rearrangements. Addition of Cd(2+), a thiophilic metal ion, rescues some reaction steps but has deleterious effects on other steps. These results suggest that native interactions in the active site may have been aligned by the naturally occurring peripheral residues and interactions to optimize the overall catalytic cycle.

Promiscuous catalysis by the tetrahymena group I ribozyme.

Catalytic promiscuity, the ability of an enzyme to catalyze alternative reactions, has been suggested to have played an important role in the evolution of new catalytic activities in protein enzymes. Similarly, promiscuous activities may have been advantageous in an earlier RNA world. The Tetrahymena Group I ribozyme naturally catalyzes the site-specific guanosine attack on an anionic phosphate diester and has been shown to also catalyze aminoacyl transfer to water, albeit with a small rate acceleration (<10-fold). This inefficient catalysis could be due to the differences in charge and/or geometry requirements for the two reactions. Herein, we describe a new promiscuous activity of this ribozyme, the site-specific guanosine attack on a neutral phosphonate diester. This alternative substrate lacks the negative charge at the reaction center but, in contrast to the aminoacyl substrate, can undergo nucleophilic attack with the same geometry as the natural substrate. Our results show that the neutral phosphonate reaction is catalyzed about 1 x 106-fold, substantially better than the acyl transfer but far below the normal anionic substrate. We conclude that both charge and geometry are important factors for catalysis of the normal reaction and that promiscuous catalytic activities of ribozymes could have been created or enhanced by reorienting and swapping RNA domains.

An altered mechanism of hydrolysis for a metal-complexed phosphate diester.

Isotope effects in the nucleophile and in the leaving group were measured to gain information about the mechanism and transition state of the hydrolysis of methyl p-nitrophenyl phosphate complexed to a dinuclear cobalt complex. The complexed diester undergoes hydrolysis about 1011 times faster than the corresponding uncomplexed diester. The kinetic isotope effects indicate that this rate acceleration is accompanied by a change in mechanism. A large inverse 18O isotope effect in the bridging hydroxide nucleophile (0.937 +/- 0.002) suggests that nucleophilic attack occurs before the rate-determining step. Large isotope effects in the nitrophenyl leaving group (18Olg = 1.029 +/- 0.002, 15N = 1.0026 +/- 0.0002) indicate significant fission of the P-O ester bond in the transition state of the rate-determining step. The data indicate that in contrast to uncomplexed diesters, which undergo hydrolysis by a concerted mechanism, the reaction of the complexed diester likely proceeds via an addition-elimination mechanism. The rate-limiting step is expulsion of the p-nitrophenyl leaving group from the intermediate, which proceeds by a late transition state with extensive bond fission to the leaving group. This represents a substantial change in mechanism from the hydrolysis of uncomplexed aryl phosphate diesters.