Felipe E. Zilly

Regio- and stereoselectivity of P450-catalysed hydroxylation of steroids controlled by laboratory evolution

A current challenge in synthetic organic chemistry is the development of methods that allow the regio- and stereoselective oxidative C–H activation of natural or synthetic compounds with formation of the corresponding alcohols. Cytochrome P450 enzymes enable C–H activation at non-activated positions, but the simultaneous control of both regio- and stereoselectivity is problematic. Here, we demonstrate that directed evolution using iterative saturation mutagenesis provides a means to solve synthetic problems of this kind. Using P450 BM3(F87A) as the starting enzyme and testosterone as the substrate, which results in a 1:1 mixture of the 2β- and 15β-alcohols, mutants were obtained that are 96–97% selective for either of the two regioisomers, each with complete diastereoselectivity. The mutants can be used for selective oxidative hydroxylation of other steroids without performing additional mutagenesis experiments. Molecular dynamics simulations and docking experiments shed light on the origin of regio- and stereoselectivity. Selective reaction of one C–H bond among many in complex organic molecules is a grand challenge for organic chemistry. Here, starting from an enzyme that oxidizes two positions in a steroid without bias, laboratory evolution is used to prepare mutants that can regio- and stereoselectively oxidize either position.

Munc18-Bound Syntaxin Readily Forms SNARE Complexes with Synaptobrevin in Native Plasma Membranes

Munc18–1, a protein essential for regulated exocytosis in neurons and neuroendocrine cells, belongs to the family of Sec1/Munc18-like (SM) proteins. In vitro, Munc18–1 forms a tight complex with the SNARE syntaxin 1, in which syntaxin is stabilized in a closed conformation. Since closed syntaxin is unable to interact with its partner SNAREs SNAP-25 and synaptobrevin as required for membrane fusion, it has hitherto not been possible to reconcile binding of Munc18–1 to syntaxin 1 with its biological function. We now show that in intact and exocytosis-competent lawns of plasma membrane, Munc18–1 forms a complex with syntaxin that allows formation of SNARE complexes. Munc18–1 associated with membrane-bound syntaxin 1 can be effectively displaced by adding recombinant synaptobrevin but not syntaxin 1 or SNAP-25. Displacement requires the presence of endogenous SNAP-25 since no displacement is observed when chromaffin cell membranes from SNAP-25–deficient mice are used. We conclude that Munc18–1 allows for the formation of a complex between syntaxin and SNAP-25 that serves as an acceptor for vesicle-bound synaptobrevin and that thus represents an intermediate in the pathway towards exocytosis.

Tuning a P450 Enzyme for Methane Oxidation

Cytochrome P450 (CYP) enzymes are heme-dependent monooxygenases that catalyze the oxidation of C H bonds of endogenous and exogenous organic compounds with formation of the respective alcohols. The mechanism involves the intermediacy of a high-spin oxyferryl porphyrin radical cation which abstracts a hydrogen atom from the substrate, and the short-lived alkyl radical then undergoes C Obond formation. The binding pockets of CYPs are relatively large, therefore small compounds do not have a statistically high enough probability of being properly oriented near the oxyferryl moiety for rapid oxidation to occur; additionally there are other effects that slow down or prevent catalysis. A notorious challenge is the oxidation of methane to methanol by chemical catalysis or using enzymes of the type methane monooxygenases (MMOs). It is not only the smallest alkane, but also has the strongest C H bond (104 kcalmol ). Although CYPs represent a superfamily of monooxygenases, none have been shown to accept methane, whereas MMOs are complex enzymes (many membrane bound) that have not been expressed in heterologous hosts in any significant quantities, among other problems. Herein we show that chemical tuning of a CYP, which is based on guest/host activation using perfluoro carboxylic acids as chemically inert guests, activates the enzyme for oxidation of not only medium-sized alkanes such as n-hexane, but also of small gaseous molecules such as propane and even methane as the ultimate challenge. In the present study we chose, for practical reasons, the enzyme P450 BM3 (CYP102A1) from Bacillus megaterium, which is a self-sufficient fusion protein composed of a P450 monooxygenase and an NADPH diflavin reductase. Several crystal structures of this CYP harboring a fatty acid or fatty acid derived inhibitors, as well in the absence of such compounds have been published. To engineer mutants of P450 BM3 and of other CYPs for enhanced activity and selectivity toward a variety of different compounds, including such difficult substrates as small alkanes, rational design as well as directed evolution have proven to be successful to some extent. For example, P450 BM3 variants characterized by numerous point mutations were obtained in extensive laboratory evolution, and showed for the first time notable activity toward propane by formation of the respective alcohols (2-propanol/1-propanol= 9:1); however, the ethane to ethanol conversion remains problematic and methane oxidation has not been achieved to date. Higher activity in ethane oxidation was accomplished using mutants of P450cam, but here again methane oxidation was not reported. Our chemical approach involves a chemically inert compound that serves as a guest in the binding pocket of P450 BM3, thereby filling the space and reducing the translational freedom of small alkanes or of any other substrate. On the basis of previous reports involving CYPs harboring various substrates, such guest/host interactions can be expected to induce other modes of activation effects as well, specifically water displacement at the Fe/heme site accompanied by a change in the electronic state from the inactive low-spin state to the catalytically active high-spin states. Moreover, many studies have shown that P450 enzymes and mutants thereof can harbor two different substrates simultaneously, thus leading to cooperative effects; one example is lauric acid and palmitic acid in which cooperativity has been demonstrated by isotope labeling experiments. In yet another study regarding the metabolism of bilirubin, the addition of lauric acid or the perfluorinated analogue was reported to facilitate NADPH oxidation and substrate degradation, a finding that has implications for the treatment of jaundice, uroporphyria, and possibly cancer. It has also been shown for the case of a distantly related H2O2dependent P450 enzyme that its peroxidase activity can be influenced by the addition of fatty acids, wherein increased or decreased activity is observed depending upon their chain length. In our endeavor we were guided by the binding mode of the natural substrates, fatty acids, of P450 BM3. The binding includes H-bonds originating from their carboxy function and residues Arg 47 and Tyr 51, as well as hydrophobic interactions. The use of perfluoro carboxylic acids such as 1a–h as chemically inert, yet activating guests was therefore envisioned, because perfluoro alkyl groups are known to be resistant to oxidation while having a hydrophobic character. Moreover, it is known that a CF3 residue is sterically comparable to a CH(CH3)2 group, [11a] which means that a perfluoro fatty acid fills much more space in a P450 binding pocket than a traditional fatty acid, and can additionally induce the crucial low-spin to high-spin conversion of Fe/heme. In exploratory studies, the oxidation of n-octane and n-hexane as well as isomers thereof was studied using P450 [*] Dr. F. E. Zilly, Dr. J. P. Acevedo, Dr. W. Augustyniak, A. Deege, U. W. H usig, Prof. M. T. Reetz Max-Planck-Institut f r Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470 M lheim an der Ruhr (Germany) reetz@mpiso-muelheim.mpg.de

Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates

Saturation mutagenesis constitutes a powerful method in the directed evolution of enzymes. Traditional protocols of whole plasmid amplification such as Stratagene’s QuikChange™ sometimes fail when the templates are difficult to amplify. In order to overcome such restrictions, we have devised a simple two-primer, two-stage polymerase chain reaction (PCR) method which constitutes an improvement over existing protocols. In the first stage of the PCR, both the mutagenic primer and the antiprimer that are not complementary anneal to the template. In the second stage, the amplified sequence is used as a megaprimer. Sites composed of one or more residues can be randomized in a single PCR reaction, irrespective of their location in the gene sequence.The method has been applied to several enzymes successfully, including P450-BM3 from Bacillus megaterium, the lipases from Pseudomonas aeruginosa and Candida antarctica and the epoxide hydrolase from Aspergillus niger. Here, we show that megaprimer size as well as the direction and design of the antiprimer are determining factors in the amplification of the plasmid. Comparison of the results with the performances of previous protocols reveals the efficiency of the improved method.

A dual function for Munc-18 in exocytosis of PC12 cells

Munc‐18 interacts with the SNARE protein syntaxin and is supposed to influence transmitter release by controlling the formation of exocytosis‐relevant SNARE complexes. Here, we used combined biochemical and physiological analyses to study the role of the Munc‐18/syntaxin interaction in large dense core vesicle (LDCV) exocytosis of neuroendocrine PC12 cells. We compared two Munc‐18 mutants carrying mutations in the syntaxin‐binding region and show that Munc‐18s membrane association depends on direct binding to syntaxin. The data suggest that perturbation of syntaxin binding inhibits neurotransmitter release upstream of the individual fusion event implying an essential role of the Munc‐18/syntaxin complex leading to exocytosis. Furthermore, we show that a Munc‐18 mutant lacking any syntaxin binding has a stimulatory effect on secretion, and provide evidence that the Munc‐18/Mint1 interaction may constitute a second pathway for Munc‐18 to regulate exocytosis. We propose that Munc‐18 represents a dynamic link between syntaxin‐related and Mint1‐related mechanisms, both involved in the control of LDCV exocytosis in neuroendocrine cells.

Deazaflavins as mediators in light-driven cytochrome P450 catalyzed hydroxylations

A light-driven deazaflavin-dependent direct enzyme regeneration system has been developed for a P450-BM3 catalyzed CH-activating hydroxylation, thereby avoiding the need for the expensive NADPH cofactor.

Ca2+ induces clustering of membrane proteins in the plasma membrane via electrostatic interactions.

Membrane proteins and membrane lipids are frequently organized in submicron‐sized domains within cellular membranes. Factors thought to be responsible for domain formation include lipid–lipid interactions, lipid–protein interactions and protein–protein interactions. However, it is unclear whether the domain structure is regulated by other factors such as divalent cations. Here, we have examined in native plasma membranes and intact cells the role of the second messenger Ca2+ in membrane protein organization. We find that Ca2+ at low micromolar concentrations directly redistributes a structurally diverse array of membrane proteins via electrostatic effects. Redistribution results in a more clustered pattern, can be rapid and triggered by Ca2+ influx through voltage‐gated calcium channels and is reversible. In summary, the data demonstrate that the second messenger Ca2+ strongly influences the organization of membrane proteins, thus adding a novel and unexpected factor that may control the domain structure of biological membranes.

Speeding up Directed Evolution: Combining the Advantages of Solid-Phase Combinatorial Gene Synthesis with Statistically Guided Reduction of Screening Effort

Efficient and economic methods in directed evolution at the protein, metabolic, and genome level are needed for biocatalyst development and the success of synthetic biology. In contrast to random strategies, semirational approaches such as saturation mutagenesis explore the sequence space in a focused manner. Although several combinatorial libraries based on saturation mutagenesis have been reported using solid-phase gene synthesis, direct comparison with traditional PCR-based methods is currently lacking. In this work, we compare combinatorial protein libraries created in-house via PCR versus those generated by commercial solid-phase gene synthesis. Using descriptive statistics and probabilistic distributions on amino acid occurrence frequencies, the quality of the libraries was assessed and compared, revealing that the outsourced libraries are characterized by less bias and outliers than the PCR-based ones. Afterward, we screened all libraries following a traditional algorithm for almost complete library coverage and compared this approach with an emergent statistical concept suggesting screening a lower portion of the protein sequence space. Upon analyzing the biocatalytic landscapes and best hits of all combinatorial libraries, we show that the screening effort could have been reduced in all cases by more than 50%, while still finding at least one of the best mutants.