Mechanisms of chloroperoxidase-catalyzed enantioselective reactions as probed by site-directed mutagenesis and isotopic labeling

Chloroperoxidase (CPO) is a heme-containing glycoprotein secreted by the marine fungus Caldariomyces fumago. Chloroperoxidase contains one ferriprotoporphyrin IX prosthetic group per molecule and catalyzes a variety of reactions, such as halogenation, peroxidation and epoxidation. The versatile catalytic activities of CPO coupled with the increasing demands for chiral synthesis have attracted an escalating interest in understanding the mechanistic and structural properties of this enzyme. In order to better understand the mechanisms of CPO-catalyzed enantioselective reactions and to fine-tune the catalytic properties of chloroperoxidase, asparagine 74 (N74) located in the narrow substrate access channel of CPO was replaced by a bulky, nonpolar valine and a polar glutamine using site-directed mutagenesis. The CPO N74 mutants displayed significantly enhanced activity toward nonpolar substrates compared to wild-type CPO as a result of changes in space and polarity of the heme distal environment. More interestingly, N74 mutants showed dramatically decreased chlorination and catalase activity but significantly enhanced epoxidation activity as a consequence of improved kinetic perfection introduced by the mutation as reflected by the favorable changes in k cat and kcat/KM of these reactions. It is also noted that the N74V mutant is capable of decomposing cyanide, the most notorious poison for many hemoproteins, as judged by the unique binding behavior of N74V with potassium cyanide. Histidine 105 (H105) was replaced by a nonpolar amino acid alanine using site-directed mutagenesis. The CPO H105 mutant (H105A) displayed dramatically decreased chlorination and catalase activity possibly because of the decreased polarity in the heme distal environment and loss of the hydrogen bonds between histidine 105 and glutamic acid 183. However, significantly increased enantioselectivity was observed for the epoxidation of bulky styrene derivatives. Furthermore, my study provides strong evidence for the proposed histidine/cysteine ligand switch in chloroperoxidase, providing experimental support for the structure of the 420-nm absorption maximum for a number of carbon monoxide complexes of heme-thiolate proteins. For the NMR study, [dCPO(heme)] was produced using 90% deuterated growth medium with excess heme precursors and [dCPO(Phe)] was grown in the same highly deuterated medium that had been supplemented with excess natural phenylalanine. To make complete heme proton assignments, NMR spectroscopy has been performed for high-resolution structural characterization of [dCPO(heme)] and [dCPO(Phe)] to achieve unambiguous and complete heme proton assignments, which also allows important amino acids close to the heme active center to be determined.

Weak interactions in the crystal structures of two indole derivatives

Acknowledgements We thank the EPSRC National Crystallography Service (University of Southampton) for the data collections and the EPSRC National Mass Spectrometry Service (University of Swansea) for the HRMS data.

Different cation-protonation patterns in mol-ecular salts of unsymmetrical dimethyhydrazine : C2H9N2·Br and C2H9N2·H2PO3

Peer reviewed

Structural Basis of RNA Recognition by Mycobacterium tuberculosis MazF Homologues

The MazEF toxin-antitoxin (TA) system consists of the antitoxin MazE and the toxin MazF. MazF is a sequence-specific endoribonuclease that upon activation causes cellular growth arrest and increass the level of persisters. Moreover, MazF-induced cells are in a quasi-dormant state that cells remain metabolically active while stop dividing. The quasi-dormancy is similar to the nonreplicating state of M. tuberculosis during latent tuberculosis, thus suggesting the role of mazEF in M. tuberculosis dormancy and persistence. M. tuberculosis has nine mazEF TA modules, each with different RNA cleavage specificities and implicated in selective gene expression during stress conditions. To date only the Bacillus subtilis MazF-RNA complex structure has been determined. As M. tuberculosis MazF homologues recognize distinct RNA sequences, their molecular mechanisms of substrate specificity remain unclear. By taking advantage of X-ray crystallography, we have determined structures of two M. tuberculosis MazF-RNA complexes, MazF-mt1 (Rv2801c) and MazF-mt3 (Rv1991c) in complex with an uncleavable RNA substrate. These structures have provided the molecular basis of sequence-specific RNA recognition and cleavage by MazF toxins.

Both MazF-mt1-RNA and MazF-mt3-RNA complexes showed similar structural organization with one molecule of RNA bound to a MazF-mt1 or MazF-mt3 dimer and occupying the same pocket within the MazF dimer interface. Similar to B. subtilis MazF-RNA complex, MazF-mt1 and MazF-mt3 displayed a conserved active site architecture, where two highly conserved residues, Arg and Thr, form hydrogen bonds with the scissile phosphate group in the cleavage site of the bound RNA. The MazF-mt1-RNA complex also showed specific interactions with its three-base RNA recognition element. Compared with the B. subtilis MazF-RNA complex, our structures showed that residues involved in sequence-specific recognition of target RNA vary between the MazF homologues, therefore explaining the molecular basis for their different RNA recognition sequences. In addition, local conformational changes of the loops in the RNA binding site of MazF-mt1 appear to play a role in MazF targeting different RNA lengths and sequences. In contrast, the MazF-mt3-RNA complex is in a non-optimal RNA binding state with a symmetry-related MazF-mt3 molecule found to make interactions with the bound RNA in the crystal. The crystal-packing interactions were further examined by isothermal titration calorimetry (ITC) studies on selected MazF-mt3 mutants. Our attempts to utilize a MazF-mt3 mutant bearing mutations involved in crystal contacts all crystallized with few nucleotides, which are still found to interact with a symmetry mate. However, these different crystal forms revealed the conformational flexibility of loops in the RNA binding interface of MazF-mt3, suggesting their role in RNA binding and recognition, which will require further studies on additional MazF-mt3-RNA complex interactions.

In conclusion, the structures of the MazF-mt1-RNA and MazF-mt3-RNA complexes provide the first structural information on any M. tuberculosis MazF homologues. Supplemented with structure-guided mutational studies on MazF toxicity in vivo, this study has addressed the structural basis of different RNA cleavage specificities among MazF homologues. Our work will guide future studies on the function of other M. tuberculosis MazF and MazE-MazF homologues, and will help delineate their physiological roles in M. tuberculosis stress responses and pathogenesis.

Study of the relation between the shape of lacosamide crystals and the composition of crystallization medium

Crystallization is the critical process used by pharmaceutical industries to achieve the desired size, size distribution, shape and polymorphism of a product material. Control of these properties presents a major challenge since they influence considerably downstream processing factors. Experimental work aimed at finding ways to control the crystal shape of Lacosamide, an active pharmaceutical ingredient developed by UCB Pharma, during crystallization was carried out. It was found that the crystal lattice displayed a very strong unidirectional double hydrogen bonding, which was at the origin of the needle shape of the Lacosamide crystals. Two main strategies were followed to hinder the hydrogen bonding and compete with the addition of a Lacosamide molecule along the crystal length axis: changing the crystallization medium or weakening the hydrogen bonding. Various solvents were tested to check whether the solvent used to crystallize Lacosamide had an influence on the final crystal shape. Solvent molecules seemed to slow down the growth in the length axis by hindering the unidirectional hydrogen bonding of Lacosamide crystals, but not enough to promote the crystal growth in the width axis. Additives were also tested. Certain additives have shown to compete in a more efficient way than solvent molecules with the hydrogen bonding of Lacosamide. The additive effect has also shown to be compatible with the solvent effect. In parallel, hydrogen atoms in Lacosamide were changed into deuterium atoms in order to weaken the hydrogen bonds strength. Weakening the hydrogen bonds of Lacosamide allowed to let the crystal grow in the width axis. Deuteration was found to be combinable with solvent effect while being in competition with the additive effect. The Lacosamide molecule was eventually deemed an absolute needle by the terms of Lovette and Doherty. The results of this dissertation are aimed at contributing to this classification.

Solvation Structure of Uracil in Ionic Liquids

The local solvation environment of uracil dissolved in the ionic liquid 1-ethyl-3-methylimidazolium acetate has been studied using neutron diffraction techniques. At solvent:solute ratios of 3:1 and 2:1 ionic liquid:uracil, little perturbation of the ion-ion correlations compared to those of the neat ionic liquid are observed. We find that solvation of the uracil is driven predominantly by the acetate anion of the solvent. While short distance correlations exist between uracil and the imidazolium cation, the geometry of these contacts suggest that they cannot be considered as hydrogen bonds, in contrast to other studies by Araújo et al. (J. M. Araújo, A. B. Pereiro, J. N. Canongia-Lopes, L. P. Rebelo, I. M. Marrucho, J. Phys. Chem. B 2013, 117, 4109-4120). Nevertheless, this combination of interactions of the solute with both the cation and anion components of the solvents helps explain the high solubility of the nucleobase in this media. In addition, favorable uracil-uracil contacts are observed, of similar magnitude to those between cation and uracil, and are also likely to aid dissolution

Desenvolvimento de sensores químicos para aniões

O objectivo deste trabalho foi o desenvolvimento de sensores químicos para aniões em solução aquosa. Os sensores basearam-se em cristais piezoelétricos de quartzo revestidos com macrociclos pirrólicos. Sensores com porfirinas, hexafirinas, ftalocianinas e uma rede metalo-orgânica como filmes de reconhecimento foram avaliados no que respeita à reversibilidade, sensibilidade, seletividade e tempo de vida. A sensibilidade aos aniões presentes nas águas minerais destinadas ao consumo humano dos sensores com macrociclos pirrólicos dependia dos grupos substituintes na periferia do macrociclo. A presença de grupos substituintes NH potenciou a sensibilidade, sendo o valor mais elevado obtido com o grupo NH-tosilo. Técnicas espectroscópicas permitiram mostrar que a principal interação entre o anião e o composto se fazia por meio de pontes de hidrogénio entre o anião e o grupo NH. A sensibilidade destes compostos dependia ainda da quantidade do composto depositado sobre o cristal. Nenhum dos sensores era específico, mas apresentavam variações na seletividade com o composto pirrólico sobre o cristal. O sensor com uma membrana polimérica que incorporou uma rede metalo-orgânica construída com moléculas de uma ftalocianina de magnésio com grupos NH-tosilo ligados por iões cobre apresentou coeficientes de seletividade muito diferentes de todos os restantes sensores. Uma língua eletrónica construída com três dos novos sensores foi capaz de determinar simultaneamente as concentrações dos iões HCO3-, Cl- e SO42- em amostras de água mineral engarrafada, não tendo os valores obtidos sido estatisticamente diferentes (α=0,05) daqueles que foram obtidos por cromatografia iónica ou volumetria.

Estudo da intercalação de fontes de potássio em caulinita pura, com tratamento térmico e ativação ácida

The chemical changes in clay minerals has been widely studied in order to improve its properties for use in various applications. However kaolinite has strong hydrogen bonds between their adjacent layers hindering the process changes in its structure. With the objective to facilitate the process of intercalation monobasic potassium phosphate, bibasic potassium phosphate and potassium acetate we was performed on kaolinite heat treatment at 600 °C and activated acidic with phosphoric acid and 5 to 10 mol L-1. The samples they were characterized by energy dispersive spectroscopy (EDS), X-Ray Diffraction (XRD), Infrared Spectroscopy Fourier Transform (FTIR) and Thermogravimetric Analysis (TG) and Differential Thermal Analysis (DTG) and the superficial and textural changes the samples with heat treatment and acid activation they were characterized by scanning electron microscopy (SEM) and Textural Analysis of Adsorption/desorption N2. With the help of the techniques found that, the heat treatment becomes more susceptible to acid activation kaolinite making the samples with two treatments show larger amounts of phosphorus. It was also found that bibasic potassium phosphate binds more strongly the structure of kaolinite by having a structure with two-coordinating oxygens and intercalation with potassium acetate in acid-activated kaolin increases the interlayer distance of the kaolinite and the intercalation occurs with higher response index (RI) for samples with acid activation to 5 mol /L.

Síntese e caracterização de ligantes oximas e tiossemicarbazonas e seus complexos

Este trabalho apresenta a síntese e caracterização de cinco ligantes e quatro complexos derivados de oximas e tiossemicarbazonas. Entre essas, discutem-se as estruturas cristalinas/moleculares determinadas por difração de raios-X em monocristais: do ligante 4-feniltiossemicarbazida-isatina (Ligante 5), do complexo piridina-salicilaldeído-4- feniltiossemicarbazona de niquel (II) (Complexo 1), e do bis-4-feniltiossemicarbazonaisatina de chumbo(II) (Complexo 2). A estrutura do Ligante 5 cristaliza no sistema monoclínico, grupo espacial P21/c, com parâmetros de cela a = 6,3227(2) Å, b = 15,7973(7) Å, c = 14,4572(6) Å, β = 93,9330(10)°, V = 1440,61(10) Å3 , Z = 4. O refinamento da estrutura convergiu aos índices de discordância finais R1 = 0,0520, wR2 = 0,1471. Observa-se ainda a ocorrência de interações intermoleculares do tipo ligações de hidrogênio clássicas [N18−H3---O1′ 2,907(2)Å], com a formação de estruturas dímeras inter-relacionadas por simetria dentro da cela cristalina. Para a estrutura cristalina do Complexo 1, observa-se NC=4, e geometria de coordenação quadrada plana, onde o ligante saliciladeído-4-feniltiossemicarbazida comporta-se como quelante tridentado, e completando a esfera de coordenação do centro metálico temos uma molécula de piridina. A estrutura cristaliza no sistema monoclínico, grupo espacial P21/m, parâmetros de cela a = 12,8211(2) Å, b = 5,73370(10) Å, c = 23,9950(4) Å, β = 101,0910(10)°, V = 1730,98(5) Å3 , índices de discordância finais R1= 0,0320, wR2 = 0,0888, Z=3. O Complexo 1 apresenta ainda interações intermoleculares do tipo [N(3)-H(3)---S(1) = 3,5838(17)º, N(3)–H(3A)---S(1) = 160,91(19)º], formando estruturas dímeras e ligação de hidrogênio intramolecular não-clássica do tipo [C(10)-H(10)---N(2) = 2,838(2)º e C(10) – H(10)---N(2) = 122º]. A estrutura cristalina do complexo 2, apresenta duas formas independentes (uma com centro representado por Pb1 e outra por Pb2). Para a unidade com Pb1 temos o complexo composto por duas unidades do Ligante 5, que comportam-se como quelantes tridentados, e a esfera de coordenação é completada por interações intermoleculares do tipo η 2 areno π e através da ligação polarizada com o O1 da moléculas vizinha, o que confere ao íon Pb1 NC=9. A unidade Pb2 apresenta apenas as duas unidades do Ligante 5 coordenadas conferindo-lhe NC=6. A estrutura cristaliza no sistema monoclínico, grupo espacial C2/c, parâmetros de cela a = 37,9747(6) Å, b= 9,51280(10) Å, c = 31,4378(5) Å, β = 125,951(2)°, V= 9193,5(2) Å3 , Z = 4, índices de discordância finais= R1 = 0,0643, wR2 = 0,1227.

Síntese e caracterização de ligantes nitrogenados derivados de isatina, 4-benziltiossemicarbazida e seus complexos com metais d¹º

Neste trabalho são apresentadas e discutidas as estruturas cristalinas e moleculares do ligante (1), isatina-3-(toluilsulfono-hidrazona), dos complexos [bis(2-acetilpiridina-N4 - benziltiossemicarbazona-N,N,S)Cd(II)], (1), [bis (isatina-3-N4 -benziltiossemicarbazonaN,S)Hg(II)].Etanol, (2) e [bis (isatina-3-N4 -benziltiossemicarbazona-N,S,O)Zn(II)].DMF, (3). Cristais amarelos vítreos do ligante (1) foram obtidos a partir da evaporação lenta de etanol do ensaio de cristalização. Seus dados cristalográficos indicam que duas moléculas interagem através de ligações de hidrogênio do tipo N1-H···O1, formando unidades dímeras. A reação entre 2-acetilpiridina-N4 -benziltiossemicarbazona e Cd(CH3COO)2.2H2O, em presença de etanol, KOH, e após evaporação lenta da mistura de acetona e DMF(2:1), resultou em cristais amarelos do complexo (1). As interações do tipo C(10)-H(10)···S(1)···H(1)-N(4), e N(8)- H(29)⋅⋅⋅S(2) permitem a dimerização do complexo, e a formação de uma cadeia unidimensional. Os cristais laranja do complexo (2) foram obtidos da reação entre o ligante isatina-3-N4 -benziltiossemicarbazona e Hg(NO3)2.H2O, na presença de metanol, KOH, e após evaporação lenta de uma mistura de tolueno e acetona (2:1). As moléculas do complexo (2) estão associadas por ligações de hidrogênio do tipo N(63)-H(4)···O(21), essas interações centrossimétricas conduzem a formação de dímeros. A reação entre o ligante isatina-3-N4 - benziltiossemicarbazona e Zn(CH3COO)2.2H2O, em presença de etanol e KOH resultou em cristais de coloração laranja do complexo (3). A estrutura do complexo apresenta múltiplas ligações de hidrogênio, com formação de dímeros através das interações N1-H1···O1 e C3- H3···N(7). Os dímeros associam-se por interações N4-H4···O2 numa cadeia unidimensional ao longo da direção cristalográfica [100]. A polimerização bidimensional é observada 7 considerando-se as interações do tipo C20-H20···S1, N8-H8···S2 ao longo da direção cristalográfica [010], bem como das interações, N5-H5···O3DMF e C31-H31B···Car, que ocorrem através da molécula de solvente DMF.

Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface

The structure of hCx26 derived from the X-ray analysis was used to generate a homology model for hCx46. Interacting connexin molecules were used as starting model for the molecular dynamics (MD) simulation using NAMD and allowed us to predict the dynamic behavior of hCx46wt and the cataract related mutant hCx46N188T as well as two artificial mutants hCx46N188Q and hCx46N188D. Within the 50 ns simulation time the docked complex composed of the mutants dissociate while hCx46wt remains stable. The data indicates that one hCx46 molecule forms 5-7 hydrogen bonds (HBs) with the counterpart connexin of the opposing connexon. These HBs appear essential for a stable docking of the connexons as shown by the simulation of an entire gap junction channel and were lost for all the tested mutants. The data described here are related to the research article entitled "The cataract related mutation N188T in human connexin46 (hCx46) revealed a critical role for residue N188 in the docking process of gap junction channels" (Schadzek et al., 2015) [1].

Glutathione Transferases as Detoxification Agents: Structural and Functional Studies

Glutathione transferases (GSTs) are a diverse family of enzymes that catalyze the glutathione-dependent detoxification of toxic compounds. GSTs are responsible for the conjugation of the tripeptide glutathione (GSH) to a wide range of electrophilic substrates. These include industrial pollutants, drugs, genotoxic carcinogen metabolites, antibiotics, insecticides and herbicides. In light of applications in biomedicine and biotechnology as cellular detoxification agents, detailed structural and functional studies of GSTs are required. Plant tau class GSTs play crucial catalytic and non-catalytic roles in cellular xenobiotic detoxification process in agronomically important crops. The abundant existence of GSTs in Glycine max and their ability to provide resistance to abiotic and biotic stresses such as herbicide tolerance is of great interest in agriculture because they provide effective and suitable tools for selective weed control. Structural and catalytic studies on tau class GST isoenzymes from Glycine max (GmGSTU10-10, GmGSTU chimeric clone 14 (Sh14), and GmGSTU2-2) were performed. Crystal structures of GmGSTU10-10 in complex with glutathione sulfenic acid (GSOH) and Sh14 in complex with S-(p-nitrobenzyl)-glutathione (Nb-GSH) were determined by molecular replacement at 1.6 Å and 1.75 Å, respectively. Major structural variations that affect substrate recognition and catalytic mechanism were revealed in the upper part of helix H4 and helix H9 of GmGSTU10-10. Structural analysis of Sh14 showed that the Trp114Cys point mutation is responsible for the enhanced catalytic activity of the enzyme. Furthermore, two salt bridges that trigger an allosteric effect between the H-sites were identified at the dimer interface between Glu66 and Lys104. The 3D structure of GmGSTU2-2 was predicted using homology modeling. Structural and phylogenetic analysis suggested GmGSTU2-2 shares residues that are crucial for the catalytic activity of other tau class GSTs–Phe10, Trp11, Ser13, Arg20, Tyr30, Leu37, Lys40, Lys53, Ile54, Glu66 and Ser67. This indicates that the catalytic and ligand binding site in GmGSTU2-2 are well-conserved. Nevertheless, at the ligandin binding site a significant variation was observed. Tyr32 is replaced by Ser32 in GmGSTU2-2 and thismay affect the ligand recognition and binding properties of GmGSTU2-2. Moreover, docking studies revealed important amino acid residues in the hydrophobic binding site that can affect the substrate specificity of the enzyme. Phe10, Pro12, Phe15, Leu37, Phe107, Trp114, Trp163, Phe208, Ile212, and Phe216 could form the hydrophobic ligand binding site and bind fluorodifen. Additionally, side chains of Arg111 and Lys215 could stabilize the binding through hydrogen bonds with the –NO2 groups of fluorodifen. GST gene family from the pathogenic soil bacterium Agrobacterium tumefaciens C58 was characterized and eight GST-like proteins in A. tumefaciens (AtuGSTs) were identified. Phylogenetic analysis revealed that four members of AtuGSTs belong to a previously recognized bacterial beta GST class and one member to theta class. Nevertheless, three AtuGSTs do not belong to any previously known GST classes. The 3D structures of AtuGSTs were predicted using homology modeling. Comparative structural and sequence analysis of the AtuGSTs showed local sequence and structural characteristics between different GST isoenzymes and classes. Interactions at the G-site are conserved, however, significant variations were seen at the active site and the H5b helix at the C-terminal domain. H5b contributes to the formation of the hydrophobic ligand binding site and is responsible for recognition of the electrophilic moiety of the xenobiotic. It is noted that the position of H5b varies among models, thus providing different specificities. Moreover, AtuGSTs appear to form functional dimers through diverse modes. AtuGST1, AtuGST3, AtuGST4 and AtuGST8 use hydrophobic ‘lock–and–key’-like motifs whereas the dimer interface of AtuGST2, AtuGST5, AtuGST6 and AtuGST7 is dominated by polar interactions. These results suggested that AtuGSTs could be involved in a broad range of biological functions including stress tolerance and detoxification of toxic compounds.

Wysokociśnieniowe przemiany strukturalne kryształów węglowodanów

Wydział Chemii

Synteza i właściwości oksiranowych pochodnych estrów kwasów fosfonowych

Wydział Chemii

Computational and experimental study of the behavior of cyano-based ionic liquids in aqueous solution

The solvation of cyano- (CN-) based ionic liquids (ILs) and their capacity to establish hydrogen bonds (H-bonds) with water was studied by means of experimental and computational approaches. Experimentally, water activity data were measured for aqueous solutions of ILs based on 1-butyl-3-methylimidazolium ([BMIM](+)) cation combined with one of the following anions: thiocyanate ([SCN](-)), dicyanamide ([DCA](-)), or tricyanomethanide ([TCM](-)), and of 1-ethyl-3-methylimidazolium tetracyanoborate ([EMIM][TCB]). From the latter data, water activity coefficients were estimated showing that [BMIM][SCN] and [BMIM][DCA], unlike [BMIM][TCM] and [EMIM][TCB], are able to establish favorable interactions with water. Computationally, the conductor like screening model for real solvents (COSMO-RS) was used to estimate the water activity coefficients which compare well with the experimental ones. From the COSMO-RS results, it is suggested that the polarity of each ion composing the ILs has a strong effect on the solvation phenomena. Furthermore, classical molecular dynamics (MD) simulations were performed for obtaining an atomic level picture of the local molecular neighborhood of the different species. From the experimental and computational data it is showed that increasing the number of CN groups in the ILs' anions does not enhance their ability to establish H-bonds with water but decreases their polarities, being [BMIM][DCA] and [BMIM][SCN] the ones presenting higher propensity to interact.