Molecular basis of Celmer's rules: stereochemistry of catalysis by isolated ketoreductase domains from modular polyketide synthases

A system is reported for the recombinant expression of individual ketoreductase (KR) domains from modular polyketide synthases (PKSs) and scrutiny of their intrinsic specificity and stereospecificity toward surrogate diketide substrates. The eryKR(1) and the tylKR(1) domains, derived from the first extension module of the erythromycin PKS and the tylosin PKS, respectively, both catalyzed reduction of (2R, S)-2-methyl-3-oxopentanoic acid N-acetylcysteamine thioester, with complete stereoselectivity and stereospecificity, even though the substrate is not tethered to an acyl carrier protein or an intact PKS multienzyme. In contrast, and to varying degrees, the isolated enzymes eryKR(2), eryKR(5), and eryKR(6) exercised poorer control over substrate selection and the stereochemical course of ketoreduction. These data, together with modeling of diketide binding to KR(1) and KR(2), demonstrate the fine energetic balance between alternative modes of presentation of ketoacylthioester substrates to KR active sites.     

Molecular basis of Celmer's rules: the role of two ketoreductase domains in the control of chirality by the erythromycin modular polyketide synthase

BACKGROUND: Polyketides are compounds that possess medically significant activities. The modular nature of the polyketide synthase (PKS) multienzymes has generated interest in bioengineering new PKSs. Rational design of novel PKSs, however, requires a greater understanding of the stereocontrol mechanisms that operate in natural PKS modules. RESULTS: The N-acetyl cysteamine (NAC) thioester derivative of the natural beta-keto diketide intermediate was incubated with DEBS1-TE, a derivative of the erythromycin PKS that contains only modules 1 and 2. The reduction products of the two ketoreductase (KR) domains of DEBS1-TE were a mixture of the (2S, 3R) and (2R,3S) isomers of the corresponding beta-hydroxy diketide NAC thioesters. Repeating the incubation using a DEBS1-TE mutant that only contains KR1 produced only the (2S,3R) isomer. CONCLUSIONS: In contrast with earlier results, KR1 selects only the (2S) isomer and reduces it stereospecifically to the (2S, 3R)-3-hydroxy-2-methyl acyl product. The KR domain of module 1 controls the stereochemical outcome at both methyl-and hydroxyl-bearing chiral centres in the hydroxy diketide intermediate. Earlier work showed that the normal enzyme-bound ketoester generated in module 2 is not epimerised, however. The stereochemistry at C-2 is therefore established by a condensation reaction that exclusively gives the (2R)-ketoester, and the stereo-chemistry at C-3 by reduction of the keto group. Two different mechanisms of stereochemical control, therefore, operate in modules 1 and 2 of the erythromycin PKS. These results should provide a more rational basis for designing hybrid PKSs to generate altered stereochemistry in polyketide products.     

Compounding Selectivity in Reactions of Diastereoisomeric Radical Intermediates. An experimental demonstration that the yield of a product from a diastereotopic-group-selective reaction can significantly exceed the level of group selectivity

Reduction of a bis-radical precursor, 6-phenyl-1,1-bis[3-(phenylselanyl)propyl]-3a,4-dihydro-1H,3H-cyclopenta[c]furan-5-one ( 6 ), with 3 equiv. of Ph₃SnH provides mixtures of cis,cis- or cis,trans-angular triquinane products (3aα,5aβ,8β,8aR*)- and (3aα,5aα,8β,8aR*)-hexahydro-3a-propyl-8-phenyl-5H-dicyclopenta[b,c]furan-7(8H)-one (cis,cis- 12 /cis,trans- 12 ), in yields that vary from 50%/50% to 91%/6% depending on the reaction concentration. A mechanistic model for this process is proposed that involves a non-selective phenylselenium-group abstraction step followed by successive kinetic resolutions of diastereoisomeric radical intermediates. This reaction shows how yields in group-selective reactions can be compounded to levels above that ostensibly permitted by the level of the group-selective step.     

Fix L, a haemoglobin that acts as an oxygen sensor: signalling mechanism and structural basis of its homology with PAS domains

Fix L, which contains a haemoglobin domain homologous to the PAS family and a histidine kinase domain, forms, with Fix J, a two-component signalling complex that regulates expression of nitrogenase genes in Rhizobium. Spin transitions of its haem iron trigger stereochemical changes in and around the haem that, together with steric effects, control the activity of the kinase. Homology with the PAS family is based on a common core of about 20 structurally equivalent sites from which polar residues are excluded.     

How to choose one-dimensional basis functions so that a very efficient multidimensional basis may be extracted from a direct product of the one-dimensional functions: energy levels of coupled systems with as many as 16 coordinates

In this paper we propose a scheme for choosing basis functions for quantum dynamics calculations. Direct product bases are frequently used. The number of direct product functions required to converge a spectrum, compute a rate constant, etc., is so large that direct product calculations are impossible for molecules or reacting systems with more than four atoms. It is common to extract a smaller working basis from a huge direct product basis by removing some of the product functions. We advocate a build and prune strategy of this type. The one-dimensional (1D) functions from which we build the direct product basis are chosen to satisfy two conditions: (1) they nearly diagonalize the full Hamiltonian matrix; (2) they minimize off-diagonal matrix elements that couple basis functions with diagonal elements close to those of the energy levels we wish to compute. By imposing these conditions we increase the number of product functions that can be removed from the multidimensional basis without degrading the accuracy of computed energy levels. Two basic types of 1D basis functions are in common use: eigenfunctions of 1D Hamiltonians and discrete variable representation (DVR) functions. Both have advantages and disadvantages. The 1D functions we propose are intermediate between the 1D eigenfunction functions and the DVR functions. If the coupling is very weak, they are very nearly 1D eigenfunction functions. As the strength of the coupling is increased they resemble more closely DVR functions. We assess the usefulness of our basis by applying it to model 6D, 8D, and 16D Hamiltonians with various coupling strengths. We find approximately linear scaling.     

Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid and glutarate: insight into the basis of its substrate specificity.

BACKGROUND: Semisynthetic cephalosporins are primarily synthesized from 7-aminocephalosporanic acid (7-ACA), which is obtained by environmentally toxic chemical deacylation of cephalosporin C (CPC). Thus, the enzymatic conversion of CPC to 7-ACA by cephalosporin acylase (CA) would be of great interest. However, CAs use glutaryl-7-ACA (GL-7-ACA) as a primary substrate and the enzyme has low turnover rates for CPC. RESULTS: The binary complex structures of CA with GL-7-ACA and glutarate (the side-chain of GL-7-ACA) show extensive interactions between the glutaryl moiety of GL-7-ACA and the seven residues that form the side-chain pocket. These interactions explain why the D-alpha-aminoadipyl side-chain of CPC yields a poorer substrate than GL-7-ACA. CONCLUSIONS: This understanding of the nature of substrate specificity may be useful in the design of an enzyme with an improved performance for the conversion of CPC to 7-ACA. Additionally, the catalytic mechanism of the deacylation reaction was revealed by the ligand bound structures.     

Electron pairing and chemical bonds: pair localization in ELF domains from the analysis of domain averaged Fermi holes

This article reports the application of a recently proposed formalism of domain averaged Fermi holes to the problem of the localization of electron pairs in electron localization function (ELF) domains and its possible implications for the electron pair model of chemical bond. The main focus was on the systems, such as H2O or N2, in which the "unphysical" population of ELF domains makes the parallel between these domains and chemical bond questionable. On the basis of the results of the Fermi-hole analysis, we propose that the above problems could be due to the fact that in some cases the boundaries of the ELF domains need not be determined precisely enough.     

Ligand recognition by SH3 and WW domains: the role of N-alkylation in PPII helices.

SH3 and WW domains are involved in a variety of intracellular signaling pathways. Recent work has shed light on the mechanism whereby these signaling modules recognize prolines in polyproline ligands, which has implications in the design of ligands selectively targeting these interactions.     

Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures

Histone lysine methylation is emerging as an important mechanism to regulate chromatin structure and gene activity. To provide theoretical understanding of its reaction mechanism and product specificity, ab initio quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations and molecular dynamics simulations have been carried out to investigate the histone lysine methyltransferase SET7/9. It is found that the methyl-transfer reaction catalyzed by SET7/9 is a typical in-line S(N)2 nucleophilic substitution reaction with a transition state of 70% dissociative character. The calculated average free energy barrier at the MP2(6-31+G) QM/MM level is 20.4 +/- 1.1 kcal/mol, consistent with the activation barrier of 20.9 kcal/mol estimated from the experimental reaction rate. The barrier fluctuation has a strong correlation with the nucleophilic attack distance and angle in the reactant complex. The calculation results show that the product specificity of SET7/9 as a monomethyltransferase is achieved by disrupting the formation of near-attack conformations for the dimethylation reaction.     

Flavin photochemistry in the analysis of electron transfer reactions: role of charged and hydrophobic residues at the carboxyl terminus of ferredoxin-NADP(+) reductase in the interaction with its substrates

The enzyme Ferredoxin-NADP(+) reductase participates in the reductive side of the photosynthetic chain transferring electrons from reduced Ferredoxin (Fd) (or Flavodoxin (Fld)) to NADP(+), a process that yields NADPH that can be used in many biosynthetic dark reactions. The involvement of specific amino acids in the interaction between the two proteins has been studied using site-directed mutagenesis. In the present study, the participation of charged (H299), polar (T302) or hydrophobic (V300) amino acid residues that are in the NADP(+)-binding domain of the reductase have been examined by analyzing its C-terminal region, which is located close to the active site. Stopped-flow and laser flash photolysis results of the reaction in which these mutant proteins participate show very little differences with respect to the wild-type protein. These results suggest that the NADPH-binding domain of the reductase has little effect on the processes of recognition and electron transfer to (and from) Fd or Fld, according to the recently reported crystallographic structure of the FNR/Fd complex.     

Spatially resolved product formation in the reaction of formic acid with calcium carbonate (1014): the role of step density and adsorbed water-assisted ion mobility

The reaction of calcium carbonate (1014) single-crystal surfaces with formic acid (HCOOH) vapor was investigated using atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). AFM images indicate the reaction produces rather well-defined crystallites, preferentially at step edges and at distinct angles to one another and mirroring the rhombohedral structure of the calcite surface, while exposing unreacted carbonate surface. The size and surface density of the crystallites depend upon substrate step density, exposure time, and relative humidity. XPS data confirmed the crystallite composition as the expected calcium formate product. The AFM images show erosion and pit formation of the calcite surface in the vicinity of the product crystallites, clearly providing the spatially resolved characterization of the source of Ca ions. AFM experiments exploring the effects of water vapor on the reacted surface show that the calcium formate crystallites are mobile under conditions of high relative humidity, combining to form larger crystallites and nanometer-sized crystals with an orthorhombohedral habit consistent with the alpha form, as confirmed by X-ray diffraction. The implications for the reactions described here are discussed.     

Molecular rationale delineating the role of lycopene as a potent HMG-CoA reductase inhibitor: in vitro and in silico study

This study initially aimed to depict the molecular rationale evolving the role of lycopene in inhibiting the enzymatic activity of β-hydroxy-β-methylglutaryl-CoA (HMG-CoA) reductase via in vitro and in silico analysis. Our results illustrated that lycopene exhibited strong HMG-CoA reductase inhibitory activity (IC₅₀ value of 36 ng/ml) quite better than pravastatin (IC₅₀ = 42 ng/ml) and strong DPPH free radical scavenging activity (IC₅₀ value = 4.57 ± 0.23 μg/ml) as compared to ascorbic acid (IC₅₀ value = 9.82 ± 0.42 μg/ml). Moreover, the K_i value of lycopene (36 ng/ml) depicted via Dixon plot was well concurred with an IC₅₀ value of 36 ± 1.8 ng/ml. Moreover, molecular informatics study showed that lycopene exhibited binding energy of ?5.62 kcal/mol indicating high affinity for HMG-CoA reductase than HMG-CoA (ΔG: ?5.34 kcal/mol). Thus, in silico data clearly demonstrate and support the in vitro results that lycopene competitively inhibit HMG-CoA reductase activity by binding at the hydrophobic portion of HMG-CoA reductase.     

Chasing molecules that were never there: misassigned natural products and the role of chemical synthesis in modern structure elucidation

Over the course of the past half century, the structural elucidation of unknown natural products has undergone a tremendous revolution. Before World War II, a chemist would have relied almost exclusively on the art of chemical synthesis, primarily in the form of degradation and derivatization reactions, to develop and test structural hypotheses in a process that often took years to complete when grams of material were available. Today, a battery of advanced spectroscopic methods, such as multidimensional NMR spectroscopy and high-resolution mass spectrometry, not to mention X-ray crystallography, exist for the expeditious assignment of structures to highly complex molecules isolated from nature in milligram or sub-milligram quantities. In fact, it could be argued that the characterization of natural products has become a routine task, one which no longer even requires a reaction flask! This Review makes the case that imaginative detective work and chemical synthesis still have important roles to play in the process of solving nature's most intriguing molecular puzzles.     

A compelling experimental test of the hypothesis that enzymes have evolved to enhance quantum mechanical tunneling in hydrogen transfer reactions: the beta-neopentylcobalamin system combined with prior adocobalamin data

An intriguing but controversial hypothesis has appeared that "The optimization of enzyme catalysis may entail the evolutionary implementation of chemical strategies that increase the probability of tunneling and thereby accelerate the reaction rate" (Kohen, A.; Klinman, J. P. Acc. Chem. Res. 1998, 31, 397). Restated, enzymes may have evolved to enhance quantum mechanical tunneling by coupling to protein low nu modes that squeeze the reacting centers together in, for example, their H(*) atom abstraction reactions. Such a putative "protein squeezing" mechanism would enhance hydrogen quantum mechanical tunneling by reducing the barrier width. An alternative hypothesis is that enzymes do not enhance tunneling, but simply exploit the same amount of tunneling present in their enzyme-free solution reactions, if those reactions occur. A third, conceivable hypothesis is that enzymes might even inadvertently decrease the amount of tunneling as an undesired result of increasing the barrier width while reducing the barrier height. Testing these hypotheses experimentally requires the extremely rare event of being able to measure the amount of tunneling both in the enzyme system and in a very similar if not identical reaction in enzyme-free solution. This has been accomplished experimentally in only one prior case, our recent study of AdoCbl (coenzyme B(12)) and 8-Meo-AdoCbl undergoing enzyme-like H(*) abstraction reactions (Doll, K. M.; Bender, B. R.; Finke, R. G. to J. Am. Chem. Soc. 2003, in press). The data there reveal no change in the level of tunneling within or outside of the enzyme in comparison to the best literature data for an AdoCbl-dependent enzyme, methylmalonyl-CoA mutase. However, that first system suffers from two limitations: the measurement of the KIE (kinetic isotope effect) data in a nonenzymic 80-110 degrees C temperature range; and lower precision data than desired due to the HPLC-MS method required for one of the KIE analyses. These limitations have now been overcome by the synthesis, then thermolysis and KIE study vs temperature of the H(*) abstraction reaction of beta-neopentylcobalamin (beta-NpCbl) in ethylene glycol-d(0) and ethylene glycol-d(4). This is the first experimental test of Klinman's hypothesis using KIE data obtained at enzyme-relevant temperatures. The key data obtained are as follows: deuterium KIEs of 23.1 +/- 3.0 at 40 degrees C to 39.0 +/- 2.3 at 10 degrees C; an activation energy difference E(D) - E(H) of 3.1 +/- 0.3 kcal mol(-)(1); and a pre-exponential factor ratio A(H)/A(D) of 0.14 +/- 0.07. Moreover, our now three sets of data (NpCbl; AdoCbl; 8-MeOAdoCbl) are shown to lie on the same ln KIE vs 1/T linear plot yielding a set of enzyme-temperature-relevant, high-precision KIE, E(D) - E(H), and A(H)/A(D) data over a relatively large, 110 degrees C temperature range. Significantly, the enzyme-free solution KIE, E(D) - E(H), and A(H)/A(D) are identical within experimental error to those for methylmalonyl-CoA mutase. This finding leads to the conclusion that there is no enzymic enhancement of the tunneling in at least this B(12)-dependent enzyme. This B(12) enzyme does, however, exploit the same (unchanged) level of tunneling measured for the nonenzymic, Ado(*) solution H(*) abstraction reaction. A discussion is presented of the still open question of if this first experimental finding, of "no enzymic enhancement of tunneling" in one B(12)-dependent enzymic system, is likely to prove more general or not.     

Direct Spectroscopic Evidence that the Photochemical Outcome of Flutamide in a Protein Environment is Tuned by Modification of the Molecular Geometry: A Comparison with the Photobehavior in Cyclodextrin and Vesicles

The photoreactivity of the phototoxic anticancer drug flutamide (FM) in the presence of bovine serum albumin (BSA) has been investigated. The presence of BSA induces a remarkable modification of the photochemical outcome of the drug with respect to that observed in aqueous solution. Induced circular dichroism (ICD) measurements combined with theoretical calculations provide strong evidence that the new photochemical scenario is tuned by changes of the molecular geometry of FM when incorporated in the protein microenvironment. This behavior presents close analogies to that found in the presence of either cyclodextrin or phospholipid vesicles, chosen as models for biological systems, and delineates a quite general photochemical picture that can be useful for a more appropriate understanding of the adverse phototoxic effects induced by this drug.     

Computational study of the catalytic domain of human neutrophil collagenase. specific role of the S3 and S'3 subsites in the interaction with a phosphonate inhibitor

Human neutrophil collagenase (HNC, MMP-8) is one of the target enzymes for drug treatment of pathologic extracellular matrix degradation. Peptidomimetic inhibitors bind in the S-side of the enzyme active site occupying the S ₁primary specificity pocket by their large hydrophobic side-chains. The crystal structure of the complex between the catalytic domain of MMP-8 and Pro-Leu-l-Trp^P(OH)₂(PLTP) showed that this phosphonate inhibitor binds in the S side of the active site. This finding was unexpected since it represents the first example of accommodation of the bulky Trp indolyl chain in the S₁rather than in the S ₁subsite. Dynamical and structural factors favouring this uncommon mode of binding were therefore investigated.MD simulations performed on the uncomplexed enzyme show that its structure in aqueous solution is only slightly different from the crystal structure found in the complex with PLTP. ED analysis of the MD simulations, performed on PLTP alternatively interacting with the S- or S-side of the active site, shows that the enzyme fluctuation increases in both cases. The main contribution to the overall enzyme fluctuation is given by the loop 164–173. The fluctuation of this loop is spread over more degrees of freedom when PLTP interacts with the S-side. This dynamical factor can enhance the preference of PLTP for the S subsites of MMP-8. MD simulations also show that ligation of PLTP in the S subsites is further favoured by better zinc chelation, a cation- interaction at the S₃subsite and unstrained binding conformations. The role of the S₃, S ₃and S ₁subsites in determining the inhibitor binding is discussed.     

Conditions for the optimal analysis of volatile organic compounds in air with sorbent tube sampling and liquid standard calibration: demonstration of solvent effect

The combined use of sorbent tubes (ST) and thermal desorption (TD) has become the common practice for the trace-level analysis of gaseous volatile organic compounds (VOCs). In this research, the potential bias in VOC analysis due to the solvent introduced into the system as a liquid standard (LS) is examined in three stages by analyzing LSs of 19 VOCs in methanol solvent against a three-bed ST (Tenax TA, Carbopack B, and Carboxen 1000). In experimental stage 1, LS made at four concentration levels (between 10 and 150 ng μL^?1) were each analyzed at four injection volumes (1, 2, 5, and 10 μL) based on a vaporization method. In experimental stage 2, calibration was also conducted by direct injection over an extended concentration range at two volumes, 1 and 10 μL. In experimental stage 3, the response factors (RF) of a single analyte mass were compared across the four injection volumes and between two injection methods. These results were analyzed to explore the complex relationship between variables such as LS volume, target/solvent chemical type, sorbent strength, and prepurge condition. There was no change in the ST/TD performance up to 2 μL of LS. However, as the injection volume increased up to 5 μL, a notable shift in RF and retention time occurred (e.g., for benzene and methyl ethyl ketone). At the maximum injection volume (10 μL), a significant reduction in sensitivity is evident for all compounds, e.g., 50 % drops relative to 1 μL injection. As such, the TD performance tends to deteriorate with increasing volume of methanol initially loaded on the ST. Although the dominant fraction of solvent was removed by two prepurge steps, residue caught in the strong sorbent fraction is still found to exert an effect on the subsequent analysis, e.g., delayed retention, sensitivity reduction, or disappearance of certain compounds.     

Thermolysis of vic-dihydroxybacteriochlorins: effect of the nature of substrates in directing the formation of chlorin-chlorin dimers with fixed and flexible orientations and their preliminary in vitro photosensitizing efficacy

The thermolysis products obtained by refluxing a series of vic-dihydroxychlorins in o-dichlorobenzene are characterized. Depending on the nature of substrates, this methodology provides an access for novel carbon-carbon linked chlorin-chlorin dimers and chlorin-porphyrin dimers with fixed and flexible orientations. The configuration of the linkers in the symmetrical and unsymmetrical dimers was confirmed by extensive NMR (COSY, ROESY) and molecular modeling studies. The molecular modeling studies of the energy-optimized dimers with flexible orientation confirmed that one of the chlorin units of the dimeric structure is tilted toward the opposite ring as evident by the shielding effect in the resonances of some of the protons in the (1)H NMR spectroscopy. Among the dimers with fixed orientation, compared to the free-base analogues, the related mono- and di-Zn(II) complexes produced a decreased fluorescence intensity, suggesting a possibility of the faster energy transfer via intersystem crossing (ISC) in the metalated derivatives than the corresponding free-base analogues to produce the corresponding excited triplet states. The photosensitizing efficacy of the monomers and the related dimers was also compared in radiation-induced fibrosarcoma (RIF) tumor cells at variable drug/light doses. In preliminary screening, compared to monomers, the corresponding carbon-carbon linked dimers produced enhanced photosensitizing efficacy.