Thesis advisor: Mary F. Roberts / Amphitropic proteins, such as the virulence factor phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus thuringiensis, often depend on lipid-specific recognition of target membranes. However, the recognition mechanisms for zwitterionic lipids such as phosphatidylcholine (PC), which is enriched in the outer leaflet of eukaryotic cell membranes, are not well understood. Molecular dynamics (MD) simulation and mutagenesis results strongly indicate that PI-PLC interacts with PC head groups via cation-π interactions with aromatic tyrosine residues, and suggest that cation-π interactions at the interface may be a mechanism for specific lipid recognition by amphitropic and membrane proteins. Aromatic amino acids can not only form cation-π interactions at the interface but also insert into membranes and have hydrophobic interactions with lipid tails. Heretofore there has been no facile way to differentiate these two types of interactions. We show that specific incorporation of fluorinated amino acids into proteins can experimentally distinguish cation-π interactions from membrane insertion of the aromatic side-chains. Fluorinated aromatic amino acids destabilize the cation-π interactions by altering electrostatics of the aromatic ring while their enhanced hydrophobicity enhances membrane insertion. Incorporation of pentafluorophenylalanine or difluorotyrosine into a Staphylococcus aureus phosphatidylinositol-specific phospholipase C (PI-PLC) variant engineered to contain a specific PC-binding site demonstrates the effectiveness of this methodology. Applying this methodology to the plethora of tyrosine residues in Bacillus thuringiensis PI-PLC identifies those involved in cation-π interactions with PC. Cation-π interactions provide a likely molecular mechanism for BtPI-PLC PC specificity but do not account for its preference for bilayers containing a small fraction of anionic lipids. MD simulations and fluorescence correlation spectroscopy (FCS) vesicle binding measurements of positively charged amino acids as well as surface tyrosine residues are used to formulate a complete model of BtPI-PLC specific binding to mixed anionic phospholipid/PC membrane. DNF2, a new plant protein with homology to bacterial PI-PLC, is confirmed to be the first plant small PI-PLC enzyme that can cleave both PI and glycosylphosphatidylinositol (GPI) anchored proteins. GPI-anchored protein cleavage also confirms that DNF2 plays an important role in symbiosome, the intracellular compartment formed by the plant that contains nitrogen fixing bacteria. / Thesis (PhD) — Boston College, 2015. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2016-10-05T14:03:37Z No. of bitstreams: 1 DissRFNS.pdf: 7648197 bytes, checksum: 76ec1475a7603115854bee2c6dc347a5 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2016-10-05T18:42:34Z (GMT) No. of bitstreams: 1 DissRFNS.pdf: 7648197 bytes, checksum: 76ec1475a7603115854bee2c6dc347a5 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2016-10-05T18:42:42Z (GMT) No. of bitstreams: 1 DissRFNS.pdf: 7648197 bytes, checksum: 76ec1475a7603115854bee2c6dc347a5 (MD5) / Made available in DSpace on 2016-10-05T19:07:51Z (GMT). No. of bitstreams: 1 DissRFNS.pdf: 7648197 bytes, checksum: 76ec1475a7603115854bee2c6dc347a5 (MD5) Previous issue date: 2015-08-11 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / In this work, oxidoreductases of the glutathione reductase (GR), trypanothione reductase (TR) and sulfhydryl oxidase (SOX) sub-subclasses that are FAD (flavin adenine dinucleotide) dependent enzymes and contain a group with sulfur as a charge acceptor/donor near the FAD isoalloxazine region were studied. Oxidoreductases are enzymes capable of catalyzing redox reactions, thus requiring donor groups and acceptor groups of charges. FAD is a cofactor of the oxidoreductases and participates in the enzymatic catalysis, brokering the transfer of charges between ligands and the polypeptide chain of the proteins. The thiol groups and disulfide bonds existing in the enzymes are, in many instances, involved in these transfer of protons and electrons together with the FAD. The conformation of the isoalloxazine region of the FAD and the π interactions between the sulfur atoms and the flavin region were studied. The crystal structures of 180 oxidoreductases with FAD and disulfide bonds retrieved from the Protein Data Bank (PDB) were analyzed, which allowed to set up some relationships between the bond lengths of the disulfide bridge in proteins and in small molecules, to determine the existence of deformations of the isoalloxazine moiety of the FAD, to measure the SG-π interaction distances and realize some FAD features that help differentiate the GR, TR and SOX sub-subclasses. / Neste trabalho foram estudadas oxidorredutases das sub-subclasses glutationa redutases (GR), tripanotiona redutases (TR) e sulfidril oxidases (SOX) que são enzimas dependentes de FAD (flavina adenina dinucleotídeo) e contêm um grupo com enxofre como aceitador/doador de cargas, próximo à região isoaloxazina do FAD. As oxidorredutases são enzimas capazes de catalisar reações redox, necessitando, para tal, de grupos doadores e grupos aceitadores de cargas. O FAD é um cofator das oxidorredutases e participa na catálise enzimática, intermediando a transferência de cargas entre ligantes e a cadeia polipeptídica das proteínas. Os grupos tiol e as ligações dissulfeto existentes nas enzimas estão, em muitos casos, envolvidos nessas transferências de prótons e elétrons em conjunto com o FAD. Foi realizado o estudo da conformação da região isoaloxazina do FAD e de interações π entre os átomos de enxofre e a flavina do FAD. Foram analisadas 180 estruturas cristalográficas de oxidorredutases com FAD e ligações dissulfeto obtidas do Protein Data Bank (PDB) o que permitiu relacionar os comprimentos da ligação dissulfeto em proteínas e em pequenas moléculas, classificar deformações da isoaloxazina do FAD, determinar distâncias de interação SG-π e perceber caraterísticas do FAD que permitem diferenciar as sub-subclasses de GR, TR e SOX. / CNPq: 166636/2013-4

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / In this dissertation were synthesized six compounds, of the which four are free triazene ligands and two are triazenido complex of Hg(II) and Ni(II). The compouns were characterized by melting point, infrared an UV/VIS spectroscopy, ray-X diffraction in single crystals. They were also made analyses of biological activity of the free ligands, where the potential bacteriostatic and bactericidal and of DNA cleavage plasmidial was tested. The compound 1 crystallizes in the triclinic crystal system, space group P(-1), with cell parameters a = 8,033(4) Å, b = 8,039(5) Å, c = 10,022(6) Å, α = 93,77(2)°, β = 96,86(2)°, γ = 97,98(2)°; Z=2; The final crystal structure refinement converged to the indices of disagreement R1 = 0,0741, wR2 = 0,2547. In the solid state compond 1 reveals one-dimensional infinite chains with the base vector [100] as result of intermolecular N−H···O classic hydrogen bonds. The compound 5 crystallizes in the monoclinic crystal system, space group C2/c, with cell parameters a = 21,455(5) Å, b = 5,538(10) Å, c = 23,228(10) Å, α =γ = 90°, β = 116,301(10)°; Z=4; The final crystal structure refinement converged to the indices of disagreement R1 = 0,0220, wR2 = 0,0799. The crystal structure of 5 reveals one-dimensional infinite chains along the [010] direction through Hg−η2, η2−arene π−interactions. These one-dimensional chains can be extended to the bi-dimensional (2D) through no-classic hydrogen interactions C - H···O along the crystallographic vector [100]. The compound 6 crystallizes in the ortorrombic crystal system, space group Pbcn. with cell parameters a = 16,3394(11) Å, b = 11,9953(8) Å, c = 17,6042(12) Å, α=β=γ=90°; Z=4; The final crystal structure refinement converged to the indices of disagreement R1 = 0,0466, wR2 = 0,0948. The mononuclear complex with Ni(II) showing a rhombic distorted coordination geometry. In the solid state complex 6 reveals one-dimensional infinite chains with the base vector [010] as result of intermolecular C−H···O no classic hydrogen bonds. The biological activity results show that for compound 3 a bacteriostatic action for the Micrococcus spp, Rhodococcus spp e Staphylococcus saprophyticus in the concentration 128 μg/mL. The compound 4 show bacteriostatic action only for the cell lines ATCC Staphylococcus aureus in the concentration 128 μg/mL. The compounds 2 e 4 didn't show effectiveness for cleavage of the plasmid of DNA. / Sintetizou-se o ligante 1-(2-fluorfenil)-3-(4-acetilfenil)triazeno (1) e a partir deste os complexos [HgII(C14H11N3OF)2] (5) e cis-NiII(C14H11N3OF)2(py)2 (6), com o propósito de observar a geometria de coordenação, interações intermoleculares e o arranjo cristalino destes compostos. Sintetizou-se também os ligantes 1-(fenil)-3-(4-acetilfenil)triazeno (2), bis-1,3(4- acetilfenil)triazeno (3) e bis-1,3(4-acetiloxima)triazeno (4) a fim de se investigar o potencial bacteriostático e de clivagem do DNA palsmidial pUC18. Os compostos 1, 2, 3 e 4 foram sintetizados a partir de uma reação de diazotação via nitrito de sódio de uma amina com posterior acoplamento da mesma ou de outra amina diferente gerando compostos triazenos simétricos e assimétricos, respectivamente. O composto 5 foi sintetizado a partir da reação entre o composto 1 desprotonado e acetato de mercúrio(II) em solução de tetraidrofurano na proporção de 2:1. O composto 6 foi sintetizado a partir da reação entre o composto 1 desprotonado e cloreto de níquel(II) hexahidratado em solução metanólica na proporção 2:1. Os compostos foram caracterizados por ponto de fusão, espectroscopia na região do ultravioleta-visível e inframermelho. Somente os compostos 1, 5, e 6 foram caracterizados por difração de raios-X em monocristal. O composto 1 cristaliza no sistema cristalino triclínico, grupo espacial P(-1). O refinamento da estrutura inclui os parâmetros principais: 2684 reflexões totais; 1885 reflexões independentes; a = 8,033(4) Å, b = 8,039(5) Å, c = 10,022(6) Å, α = 93,77(2)°, β = 96,86(2)°, γ = 97,98(2)°; Z=2; refinamento com matriz completa para F2 e parâmetros térmicos anisotrópicos para átomos não hidrogenóides, obtendo-se índices finais R1 = 0,0741, wR2 = 0,2547. As moléculas do composto 1 associam-se através de ligações de hidrogênio clássicas entre N H ··· O, formando um arranjo supramolecular unidimensional na direção cristalográfica [100]. O composto 5 cristaliza no sistema cristalino monoclínico, grupo espacial C2/c. O refinamento da estrutura inclui os parâmetros principais: 11325 reflexões totais; 2311 8 reflexões independentes; a = 21,455(5) Å, b = 5,538(10) Å, c = 23,228(10) Å, α =γ = 90°, β = 116,301(10)°; Z=4; refinamento com matriz completa para F2 e parâmetros térmicos anisotrópicos para átomos não hidrogenóides, obtendo-se índices finais R1 = 0,0220, wR2 = 0,0799. As moléculas do composto 5 associam-se através de interações Hg-areno-η2,η2 π entre o íon Hg(II) e os átomos de carbono dos anéis periféricos dos dois complexos vizinhos, formando um arranjo supramolecular unidimensional na direção cristalográfica [010]. As redes unidimencionais do [HgII(RPhNNNPhR´)2]n [R = CH3C(O), R´= F] podem ser estendidas à bidimencionais (2D) através de ligações de hidrogênio não-clássicas entre C H···O ao longo da direção cristalográfica [100]. O composto 6 cristaliza no sistema cristalino ortorrômbico, grupo espacial Pbcn. O refinamento da estrutura inclui os parâmetros principais: 16030 reflexões totais; 3214 reflexões independentes; a = 16,3394(11) Å, b = 11,9953(8) Å, c = 17,6042(12) Å, α=β=γ=90°; Z=4; refinamento com matriz completa para F2 e parâmetros térmicos anisotrópicos para átomos não hidrogenóides, obtendo-se índices finais R1 = 0,0466, wR2 = 0,0948. A geometria de coordenação do composto 6 é octaédrica com distorção rômbica ao centro metálico. As moléculas do composto 6 apresenta também ligações de hidrogênio nãoclássica entre C H···O, formando um arranjo supramolecular unidimensional na direção cristalográfica [010]. Os resultados da atividade biológica mostram que o composto 3 apresenta para as bactérias Micrococcus spp, Rhodococcus spp e Staphylococcus saprophyticus ação bacteriostática para a concentração de 128 μg/mL. O composto 4 apresentou atividade bacteriostática somente para a cepa ATCC Staphylococcus aureuS na concentração de 128 μg/mL. Os compostos 2 e 4 não mostraram eficácia para clivagem do DNA plasmidial.

A controllable self-assembly strategy of positively charged polycyclic aromatic hydrocarbons (PCPAH) towards the formation of rectangle sheets and ribbon-like nanostructures has been achieved by choosing divalent anions with different sizes. In contrast, only rod-like nanostructures are obtained from PCPAH with univalent anions. It is revealed that the divalent anions play a key role in guiding the packing of PCPAH, which provides an unprecedented route to fabricate two-dimensional nanostructures.

Le fullerène C60, une molécule sphérique, et le C70, un analogue ellisoïde, sont des composés aromatiques convexes constitués exclusivement d'atomes de carbone. La nature aromatique de la surface de ces cages de carbone rend possible leur association à l'état solide avec d'autres molécules aromatiques de topologie complémentaire. En particulier, l'association des fullerènes avec des composés présentant des motifs concaves aromatiques, via une association de type concave-convexe, est favorable. En effet, les interactions π•••π de type concave-convexe sont amplifiées grâce à la complémentarité topologique des partenaires impliqués. Le centrohexaindane est un hydrocarbure non planaire rigide qui a été synthétisé pour la première fois en 1988 par Kuck et collaborateurs. Cette molécule possède quatre surfaces aromatiques concaves orientées dans une géométrie tétraédrique qui sont susceptibles d'interagir favorablement avec les fullerènes. Nous avons ainsi avec succès cocristallisé le centrohexaindane avec les fullerènes C60 et C70. Puis, nous avons étudié les assemblages à l'état solide entre le centrohexaindane et les fullerènes par l'analyse des structures résolues via diffraction des rayons X. Les surfaces concaves aromatiques du centrohexaindane se sont révélées être propices à une association avec les fullerènes C60 et C70 via des interactions π•••π de type concave-convexe, tel que prévu. En outre, nous avons découvert que les liaisons C-H situées à la périphérie du centrohexaindane prennent part à une multitude de contacts C-H•••π avec les molécules de fullerène. Les échantillons de cocristaux composés de centrohexaindane et de fullerène ont aussi été caractérisés par diffraction de poudre des rayons X et par analyse thermogravimétrique dans le but d'en évaluer l'homogénéité. / Spherical fullerene C60 and C70, its ellipsoidal analogue, are convex aromatic compounds consisting exclusively of carbon atoms. The aromatic nature of the surface of these carbon cages enables their solid-state association with aromatic molecules that have complementary shapes. In particular, the association of fullerenes with compounds that have concave aromatic units, by a concave-convex type of association, is favored. Indeed, concave-convex π•••π interactions are enhanced because of the topological complementarity of the partners. Centrohexaindane is a rigid nonplanar hydrocardon that was first synthesized in 1988 by Kuck and coworkers. It contains four concave aromatic surfaces, oriented in a tetrahedral geometry, that are likely to interact favorably with fullerenes. To study this phenomenon, we successfully cocrystallized centrohexaindane with fullerenes C60 and C70. We then resolved the structure of the resulting solid-state assemblies by X-ray diffraction. The concave aromatic surfaces of centrohexaindane proved to be conducive for an association with fullerenes involving concave-convex π•••π interactions, as expected. In addition, we found that C-H bonds located at the periphery of centrohexaindane participate in a variety of C-H•••π contacts with the fullerene partners. Samples of cocrystals containing centrohexaindane and fullerene were also characterized using powder X-ray diffraction and thermogravimetric analysis in order to assess their homogeneity.

Le fullerène C60, une molécule sphérique, et le C70, un analogue ellisoïde, sont des composés aromatiques convexes constitués exclusivement d'atomes de carbone. La nature aromatique de la surface de ces cages de carbone rend possible leur association à l'état solide avec d'autres molécules aromatiques de topologie complémentaire. En particulier, l'association des fullerènes avec des composés présentant des motifs concaves aromatiques, via une association de type concave-convexe, est favorable. En effet, les interactions π•••π de type concave-convexe sont amplifiées grâce à la complémentarité topologique des partenaires impliqués. Le centrohexaindane est un hydrocarbure non planaire rigide qui a été synthétisé pour la première fois en 1988 par Kuck et collaborateurs. Cette molécule possède quatre surfaces aromatiques concaves orientées dans une géométrie tétraédrique qui sont susceptibles d'interagir favorablement avec les fullerènes. Nous avons ainsi avec succès cocristallisé le centrohexaindane avec les fullerènes C60 et C70. Puis, nous avons étudié les assemblages à l'état solide entre le centrohexaindane et les fullerènes par l'analyse des structures résolues via diffraction des rayons X. Les surfaces concaves aromatiques du centrohexaindane se sont révélées être propices à une association avec les fullerènes C60 et C70 via des interactions π•••π de type concave-convexe, tel que prévu. En outre, nous avons découvert que les liaisons C-H situées à la périphérie du centrohexaindane prennent part à une multitude de contacts C-H•••π avec les molécules de fullerène. Les échantillons de cocristaux composés de centrohexaindane et de fullerène ont aussi été caractérisés par diffraction de poudre des rayons X et par analyse thermogravimétrique dans le but d'en évaluer l'homogénéité. / Spherical fullerene C60 and C70, its ellipsoidal analogue, are convex aromatic compounds consisting exclusively of carbon atoms. The aromatic nature of the surface of these carbon cages enables their solid-state association with aromatic molecules that have complementary shapes. In particular, the association of fullerenes with compounds that have concave aromatic units, by a concave-convex type of association, is favored. Indeed, concave-convex π•••π interactions are enhanced because of the topological complementarity of the partners. Centrohexaindane is a rigid nonplanar hydrocardon that was first synthesized in 1988 by Kuck and coworkers. It contains four concave aromatic surfaces, oriented in a tetrahedral geometry, that are likely to interact favorably with fullerenes. To study this phenomenon, we successfully cocrystallized centrohexaindane with fullerenes C60 and C70. We then resolved the structure of the resulting solid-state assemblies by X-ray diffraction. The concave aromatic surfaces of centrohexaindane proved to be conducive for an association with fullerenes involving concave-convex π•••π interactions, as expected. In addition, we found that C-H bonds located at the periphery of centrohexaindane participate in a variety of C-H•••π contacts with the fullerene partners. Samples of cocrystals containing centrohexaindane and fullerene were also characterized using powder X-ray diffraction and thermogravimetric analysis in order to assess their homogeneity.

A controllable self-assembly strategy of positively charged polycyclic aromatic hydrocarbons (PCPAH) towards the formation of rectangle sheets and ribbon-like nanostructures has been achieved by choosing divalent anions with different sizes. In contrast, only rod-like nanostructures are obtained from PCPAH with univalent anions. It is revealed that the divalent anions play a key role in guiding the packing of PCPAH, which provides an unprecedented route to fabricate two-dimensional nanostructures.