SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses.

Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content

Introduction to crystal structure determination methods by X-ray diffraction: ruthenium complexes.

Esta dissertação consiste de duas partes: Parte I: Descrição teórica suscinta dos fundamentos da cristalografia de raios-X. Parte II: Resolução de quatro estruturas cristalinas, três complexos de rutênio (capítulos V, VI, VII) e um ligante comumente encontrado em complexos de rutênio, o C28H28O2P2. As estruturas resolvidas foram: 1) C28H28O2P2, Mr= 458.48, triclínico, PI a= 5.826(1), b= 8.862(1), c= 12.517(2)&#197, &#945= 100.29(1), &#946= 102.67(1), &#933= 104.22(1)&#176, V= 592.5(3)&#1973, Z=1, Dx=1.285g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 2.00cm-1, F(000)=242, T=296K, Rint=0.01, R=0.031, Rw=0.030 para 1390 reflexões independentes observadas [I&#62 3 &#959 (I)]. Os átomos P estão a 0.126(1)&#197 do plano formado pelo grupo (CH2)4-. Os anéis fenil são planares dentro da margem de erro experimental. Os átomos P têm uma configuração tetraédrica distorcida. 2) PyH[RuCl4(CO)Py], Mr=430.11, monoclínico, P21/n, a= 7.821(1), b= 10.337(3), c= 19.763(3)&#197, &#946=93.07(1)&#176, V= 1595.5(5)&#1973, Z=4, Dx=1.791g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 14.86cm-1, F(000)=843.9, T=296K, Rint=0.03, R=0.062, Rw=0.063 para 1478 reflexões independentes observadas [I&#62 3&#959 (I)]. A estrutura é composta essencialmente por dois planos perpendiculares entre si; um formado pelos quatro átomos de cloro (com ângulo de aproximadamente 90&#176 entre si), o outro pelos grupos Py e carbonila e o átomo de Ru na intersecção destes. O complexo tem carga líquida negativa, sendo necessário a presença do grupo PyH (com carga líquida positiva), para a estabilização do cristal. 3) PyH(RuCl4Py2), Mr= 481.20, monoclínico, P21/n, a= 8.080(7), b= 22.503(7), c= 10.125(6)&#197, &#946= 93.19(6)&#176, V= 1838(2)&#1973, Z=4, Dx= 1.739g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 13.06cm-1, F(000)=959.9, T=296K, Rint=0.03, R=0.038, Rw=0.039 para 1553 reflexões independentes observadas [I&#62 3&#959 (I)]. Esta estrutura é bastante similar com a 2) descrita acima, ou seja, é composta essencialmente por dois planos perpendiculares entre si; um formado pelos quatro átomos de cloro (com ângulo de aproximadamente 90&#176 entre si), o outro pelos dois grupos Py e o átomo de Ru na intersecção destes. Pelo mesmo argumento usado acima, há um grupo PyH (com carga líquida positiva) no cristal. 4) [RuCl2(MeIm)2(CH3OH)(CO)], Mr= 396.24, triclínico, PI, a= 8.609(3), b= 8.060(3), c= 10.581(4)&#197, &#945= 77.78(3), &#946= 88.43(3), &#933= 66.88(3)&#176, V= 740.4(5)&#1973, Z=2, Dx= 1.777g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 12.80cm-1, F(000)=386, T=296K, Rint=0.004, R=0.025, Rw=0.027 para 2489 reflexões independentes observadas [I&#62 3&#959 (I)]. As distâncias e ângulos médios das ligações dos quatro complexos aqui descritos são comparados entre si e com mais quatro complexos no capítulo VII.This work consists of two parts: Part I: A brief theoretical description of the basic principles of X-ray crystallography. Part II: Resolution of the four crystal structures; three ruthenium compounds (chapter V, VI, VII) and a ligand commonly found in ruthenium complexes, C28H28O2P2. The structures resolved were: 1) C28H28O2P2, Mr= 458.48, triclinic, PI a= 5.826(1), b= 8.862(1), c= 12.517(2)&#197, &#945= 100.29(1), &#946= 102.67(1), &#933= 104.22(1)&#176, V= 592.5(3)&#1973, Z=1, Dx=1.285g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 2.00cm-1, F(000)=242, T=296K, final R=0.031 for 1390 independent observed reflections. The P atoms 0.126(1)&#197 away from plane formed by (CH2)4-. Both phenyl rings are planar to within experimental accuracy. The P atom has a distorced tetrahedral configuration. 2) PyH[RuCl4(CO)Py], Mr=430.11, monoclinic, P21/n, a= 7.821(1), b= 10.337(3), c= 19.763(3)&#197, &#946=93.07(1)&#176, V= 1595.5(5)&#1973, Z=4, Dx=1.791g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 14.86cm-1, F(000)=843.9, T=296K, Rint=0.03, final R=0.062, Rw=0.063 for 1478 independent observed reflections [I&#62 3&#959 (I)]. The structure is essentially composed of two perpendicular planes; one consisting of four chlorine atoms (in a square-planar arrangement), and a second plane composed of Py and carbonyl groups, with the ruthenium atom at intersection of them. The molecules have a net negative charge and the presence of the PyH group (with net positive charge), is necessary for crystal stabilization. 3) PyH(RuCl4Py2), Mr= 481.20, monoclinic, P21/n, a= 8.080(7), b= 22.503(7), c= 10.125(6)&#197, &#946= 93.19(6)&#176, V= 1838(2)&#1973, Z=4, Dx= 1.739g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 13.06cm-1, F(000)=959.9, T=296K, Rint=0.03, final R=0.038, Rw=0.039 for 1553 independent observed reflections [I&#62 3&#959 (I)]. This structures is very similar to that described in 2) above, being essentially composed of two perpendicular planes; one composed of four chlorine atoms (in a square-planar arrangement), and the other composed of two Py groups, with the ruthenium atom at the intersection of them. For the reason given above, there is one PyH group (with positive liquid charge) in the crystal. 4) [RuCl2(MeIm)2(CH3OH)(CO)], Mr= 396.24, triclinic, PI, a= 8.609(3), b= 8.060(3), c= 10.581(4)&#197, &#945= 77.78(3), &#946= 88.43(3), &#933= 66.88(3)&#176, V= 740.4(5)&#1973, Z=2, Dx= 1.777g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 12.80cm-1, F(000)=386, T=296K, Rint=0.004, final R=0.025, Rw=0.027 for 2489 independent observed reflections [I&#62 3&#959 (I)]. In chapter VII, the average inter-atomic distances and angles for the four compounds are compare one with another and with four previously determinate structures

Crystal structure of enzyme glucosamine-6-phosphate deaminase de E. coli K12 and its complexes with allosteric activator and inhibitor

A enzima Glucosamina-6-fosfato desaminase (GlcN6P desaminase) é envolvida na conversão reversível da D-glucosamina-6-fosfato (GlcN6P) em Fru6P e amônia, como parte do caminho metabólico de aminoaçúcares como fonte de energia celular. A enzima hexamérica (peso mol. 178200) exibe uma cooperatividade homotrópica intensa em direção à GlcN6P a qual é modulada alostericamente pelo ativador N-acetil-D-glucosamina 6-fosfato (GlcNAc6P). A GlcN6P desaminase foi cristalizada no grupo espacial R32, com parâmetros de rede a = b = 125.9 &#197 e c = 223.2 &#197 e um conjunto de dados à 2.1 &#197 de resolução foi coletado usando radiação de luz síncrotron (Horjales et ai., 1992). A procura no banco de dados de seqüências OWL não mostrou homologia significante com qualquer outra família de proteína, desta maneira a determinação da estrutura foi feita pela técnica de substituição isomórfica múltipla (MIR) a partir de dois derivados, um composto de platina, o K2PtCl4 e um complexo de mercúrio, o ácido mersálico. O mapa MIR a 3 &#197 de resolução mostrou contornos claros e utilizando técnicas de nivelamento de solvente (solvent flattening) estendeu-se as fases até 2.5 &#197. A enzima cristaliza-se com dois monômeros na unidade assimétrica. A densidade eletrônica final foi interpretada com o auxílio do programa gráfico \'O\', sendo possível determinar sem ambigüidade 230 dos 266 resíduos de cada monômero; a partir daí foram usados subseqüentes mapas de Fourier diferença para a localização de todos os outros resíduos. O refinamento do modelo foi feito utilizando o programa X-PLOR (Brünger, 1993), usando a rotina simulated annealing, obtendo o fator R final de 17.4% com 348 moléculas de água e quatro íons inorgânicos de fosfato. O enovelamento do monômero tem uma estrutura do tipo &#945/&#946 com uma folha-&#946 pregueada paralela central com sete fitas com topologia 4x, 1x, 1x, -3x, -1x, -1x, envolvida por ambos os lados por oito hélices-&#945 e uma hélice 310 com duas voltas. A sexta fita da folha-&#946 central tem um prolongamento no C-terminal que faz parte de uma segunda folha-&#946 antiparalela de três fitas com topologia 2, -1. O hexâmero tem uma simetria local 32, com dois trímeros empacotados frente-a-frente com uma rotação relativa de 15&#176 em tomo do eixo de ordem 3 e ligados por pontes salinas e algumas interações hidrofóbicas em tomo do eixo não cristalográfico de ordem 2. As moléculas de cada trímero formam um contato não usual de três resíduos Cis 219 próximo ao eixo de ordem três. Os complexos com ativador alostérico (GlcNAc6P) e inibidor competitivo (2-desoxi 2-amino glucitol 6-fosfato) foram co-cristalizados isomorficamente com a estrutura nativa. Os mapas Fourier diferença mostram claramente densidades para os ligantes, definindo sem ambigüidade o sítio ativo e alostérico. O refinamento dos complexos produziu a mesma conformação da proteína nativa, na margem de erro experimental. Os sítios alostéricos (seis) estão localizados na interface adjacente dos monômeros de cada trímero e os sítios ativos (ou catalíticos) no lado externo de cada monômero, no C-terminal da folha-&#946 central. O monômero tem uma topologia com enovelamento similar a um domínio de ligação de NAD, excluindo os segmentos de aminoácidos 1-35, 145-188 e 243-266. As estruturas dos complexos e da nativa estão em um estado alostérico R em concordância com o modelo MWC para um sistema do tipo K (Monod et al, 1965). Um mecanismo alostérico similar ao da GlcN6P desaminase é encontrado na enzima fosfofrutoquinase (Evans, 1981). Um mecanismo catalítico é proposto para a reação de isomerisação-desaminação da enzima GlcN6P desaminase a partir do mecanismo geral para aldose-cetona isomerases.The enzyme Glucosamine-6-phosphate deaminase (GlcN6P deaminase) is involved in the reversible conversion of D-glucosamine-6-phosphate (GlcN6P) into Fru6P and ammonia. The hexameric enzyme (mol.wt.=178200) exhibits an intense homotropic co-operativity towards GlcN6P which is allosterically modulated by the activator N-acetyl-D-glucosamine 6-phosphate (GlcNAc6P). The GlcN6P deaminase was crystallized in space group R32, with cell parameters a=b= 125.9 &#197 and c = 223.2 &#197 and a native dataset was collected to 2.1 &#197 resolution at a synchrotron source (Horjales et al, 1992). A search of the OWL sequences database has shown no significant homology with any other known protein family. Therefore, the structure determination will have to be achieved through the Multiple Isomorphous Replacement technique from two isomorphous derivatives, a platinum compound K2PtCl4 and a mercury complex, mersalyl acid. The MIR map at 3 &#197 resolution showed clear molecular boundaries and solvent flattening techniques (Wang, 1985) were used to extend the phase set to 2.5 &#197. The final electron density map was interpreted with the aid of the graphic program \'O\'. The enzyme crystallizes with a dimmer in the asymmetric unit and 230 out of the total 266 residues of each crystallographically independent monomer could be unambiguously identified in the map. The remaining residues were located after subsequent difference Fourier maps. The refinement was made with program X-PLOR (Brunger, 1993), using the simulated annealing routine, obtained R=17.4 % with 348 water molecules and four inorganic phosphate ions. The monomer fold shows an &#945/&#946 structure with a central 7-stranded &#946-sheet with topology 4x, 1x, 1x, -3x, -1x, -1x, surrounded on both sides by eight &#945-helices and 2-turn 310 -helix. The sixth strand of the central &#946-sheet is common to a second 3-stranded anti-parallel &#946-sheet with topology 2, -1. The hexamer has local 32 symmetry, with two trimmers packed in a face-to-face arrangement with a relative rotation of 15&#176 around the 3-fold axis, and linked together by salt-bridge and some hydrophobic contacts. The molecules of each trimmer have extensive contacts and show an unusual feature of the three Cys219 residues closely clustered around the 3-fold axis. The complexes with allosteric activator (GlcNAc6P) and inhibitor (2-deoxy-2-amino glucitol 6-phosphate) were co-crystallized isomorphously with the native structure. The difference Fourier maps shows clear density for the ligands, unambiguously defining the active and allosteric sites. The complexes refinement produced the same conformation of the native, within experimental error. The allosteric sites are located at the interfaces of adjacent monomers from each trimer and the active sites (or catalytic) lie at the external side of each monomer, at the C-terminal end of the central parallel &#946-sheet. The monomer has a similar folding topology as a typical NAD binding domain, excluding the segments of aminoacids 135, 145-188 and 243-266. The native and complexes structures are at the allosteric state R concerted with MWC model for a K-system (Monod et al, 1965). A similar allosteric mechanism is found in the enzyme phosphofructokinase (Evans, 1981). A catalytic mechanism is proposed for the isomerisation-deamination reaction of the enzyme from general mechanism for aldo-keto isomerases

Crystal structure of enzyme glucosamine-6-phosphate deaminase de E. coli K12 and its complexes with allosteric activator and inhibitor

A enzima Glucosamina-6-fosfato desaminase (GlcN6P desaminase) é envolvida na conversão reversível da D-glucosamina-6-fosfato (GlcN6P) em Fru6P e amônia, como parte do caminho metabólico de aminoaçúcares como fonte de energia celular. A enzima hexamérica (peso mol. 178200) exibe uma cooperatividade homotrópica intensa em direção à GlcN6P a qual é modulada alostericamente pelo ativador N-acetil-D-glucosamina 6-fosfato (GlcNAc6P). A GlcN6P desaminase foi cristalizada no grupo espacial R32, com parâmetros de rede a = b = 125.9 &#197 e c = 223.2 &#197 e um conjunto de dados à 2.1 &#197 de resolução foi coletado usando radiação de luz síncrotron (Horjales et ai., 1992). A procura no banco de dados de seqüências OWL não mostrou homologia significante com qualquer outra família de proteína, desta maneira a determinação da estrutura foi feita pela técnica de substituição isomórfica múltipla (MIR) a partir de dois derivados, um composto de platina, o K2PtCl4 e um complexo de mercúrio, o ácido mersálico. O mapa MIR a 3 &#197 de resolução mostrou contornos claros e utilizando técnicas de nivelamento de solvente (solvent flattening) estendeu-se as fases até 2.5 &#197. A enzima cristaliza-se com dois monômeros na unidade assimétrica. A densidade eletrônica final foi interpretada com o auxílio do programa gráfico \'O\', sendo possível determinar sem ambigüidade 230 dos 266 resíduos de cada monômero; a partir daí foram usados subseqüentes mapas de Fourier diferença para a localização de todos os outros resíduos. O refinamento do modelo foi feito utilizando o programa X-PLOR (Brünger, 1993), usando a rotina simulated annealing, obtendo o fator R final de 17.4% com 348 moléculas de água e quatro íons inorgânicos de fosfato. O enovelamento do monômero tem uma estrutura do tipo &#945/&#946 com uma folha-&#946 pregueada paralela central com sete fitas com topologia 4x, 1x, 1x, -3x, -1x, -1x, envolvida por ambos os lados por oito hélices-&#945 e uma hélice 310 com duas voltas. A sexta fita da folha-&#946 central tem um prolongamento no C-terminal que faz parte de uma segunda folha-&#946 antiparalela de três fitas com topologia 2, -1. O hexâmero tem uma simetria local 32, com dois trímeros empacotados frente-a-frente com uma rotação relativa de 15&#176 em tomo do eixo de ordem 3 e ligados por pontes salinas e algumas interações hidrofóbicas em tomo do eixo não cristalográfico de ordem 2. As moléculas de cada trímero formam um contato não usual de três resíduos Cis 219 próximo ao eixo de ordem três. Os complexos com ativador alostérico (GlcNAc6P) e inibidor competitivo (2-desoxi 2-amino glucitol 6-fosfato) foram co-cristalizados isomorficamente com a estrutura nativa. Os mapas Fourier diferença mostram claramente densidades para os ligantes, definindo sem ambigüidade o sítio ativo e alostérico. O refinamento dos complexos produziu a mesma conformação da proteína nativa, na margem de erro experimental. Os sítios alostéricos (seis) estão localizados na interface adjacente dos monômeros de cada trímero e os sítios ativos (ou catalíticos) no lado externo de cada monômero, no C-terminal da folha-&#946 central. O monômero tem uma topologia com enovelamento similar a um domínio de ligação de NAD, excluindo os segmentos de aminoácidos 1-35, 145-188 e 243-266. As estruturas dos complexos e da nativa estão em um estado alostérico R em concordância com o modelo MWC para um sistema do tipo K (Monod et al, 1965). Um mecanismo alostérico similar ao da GlcN6P desaminase é encontrado na enzima fosfofrutoquinase (Evans, 1981). Um mecanismo catalítico é proposto para a reação de isomerisação-desaminação da enzima GlcN6P desaminase a partir do mecanismo geral para aldose-cetona isomerases.The enzyme Glucosamine-6-phosphate deaminase (GlcN6P deaminase) is involved in the reversible conversion of D-glucosamine-6-phosphate (GlcN6P) into Fru6P and ammonia. The hexameric enzyme (mol.wt.=178200) exhibits an intense homotropic co-operativity towards GlcN6P which is allosterically modulated by the activator N-acetyl-D-glucosamine 6-phosphate (GlcNAc6P). The GlcN6P deaminase was crystallized in space group R32, with cell parameters a=b= 125.9 &#197 and c = 223.2 &#197 and a native dataset was collected to 2.1 &#197 resolution at a synchrotron source (Horjales et al, 1992). A search of the OWL sequences database has shown no significant homology with any other known protein family. Therefore, the structure determination will have to be achieved through the Multiple Isomorphous Replacement technique from two isomorphous derivatives, a platinum compound K2PtCl4 and a mercury complex, mersalyl acid. The MIR map at 3 &#197 resolution showed clear molecular boundaries and solvent flattening techniques (Wang, 1985) were used to extend the phase set to 2.5 &#197. The final electron density map was interpreted with the aid of the graphic program \'O\'. The enzyme crystallizes with a dimmer in the asymmetric unit and 230 out of the total 266 residues of each crystallographically independent monomer could be unambiguously identified in the map. The remaining residues were located after subsequent difference Fourier maps. The refinement was made with program X-PLOR (Brunger, 1993), using the simulated annealing routine, obtained R=17.4 % with 348 water molecules and four inorganic phosphate ions. The monomer fold shows an &#945/&#946 structure with a central 7-stranded &#946-sheet with topology 4x, 1x, 1x, -3x, -1x, -1x, surrounded on both sides by eight &#945-helices and 2-turn 310 -helix. The sixth strand of the central &#946-sheet is common to a second 3-stranded anti-parallel &#946-sheet with topology 2, -1. The hexamer has local 32 symmetry, with two trimmers packed in a face-to-face arrangement with a relative rotation of 15&#176 around the 3-fold axis, and linked together by salt-bridge and some hydrophobic contacts. The molecules of each trimmer have extensive contacts and show an unusual feature of the three Cys219 residues closely clustered around the 3-fold axis. The complexes with allosteric activator (GlcNAc6P) and inhibitor (2-deoxy-2-amino glucitol 6-phosphate) were co-crystallized isomorphously with the native structure. The difference Fourier maps shows clear density for the ligands, unambiguously defining the active and allosteric sites. The complexes refinement produced the same conformation of the native, within experimental error. The allosteric sites are located at the interfaces of adjacent monomers from each trimer and the active sites (or catalytic) lie at the external side of each monomer, at the C-terminal end of the central parallel &#946-sheet. The monomer has a similar folding topology as a typical NAD binding domain, excluding the segments of aminoacids 135, 145-188 and 243-266. The native and complexes structures are at the allosteric state R concerted with MWC model for a K-system (Monod et al, 1965). A similar allosteric mechanism is found in the enzyme phosphofructokinase (Evans, 1981). A catalytic mechanism is proposed for the isomerisation-deamination reaction of the enzyme from general mechanism for aldo-keto isomerases

Introduction to crystal structure determination methods by X-ray diffraction: ruthenium complexes.

Esta dissertação consiste de duas partes: Parte I: Descrição teórica suscinta dos fundamentos da cristalografia de raios-X. Parte II: Resolução de quatro estruturas cristalinas, três complexos de rutênio (capítulos V, VI, VII) e um ligante comumente encontrado em complexos de rutênio, o C28H28O2P2. As estruturas resolvidas foram: 1) C28H28O2P2, Mr= 458.48, triclínico, PI a= 5.826(1), b= 8.862(1), c= 12.517(2)&#197, &#945= 100.29(1), &#946= 102.67(1), &#933= 104.22(1)&#176, V= 592.5(3)&#1973, Z=1, Dx=1.285g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 2.00cm-1, F(000)=242, T=296K, Rint=0.01, R=0.031, Rw=0.030 para 1390 reflexões independentes observadas [I&#62 3 &#959 (I)]. Os átomos P estão a 0.126(1)&#197 do plano formado pelo grupo (CH2)4-. Os anéis fenil são planares dentro da margem de erro experimental. Os átomos P têm uma configuração tetraédrica distorcida. 2) PyH[RuCl4(CO)Py], Mr=430.11, monoclínico, P21/n, a= 7.821(1), b= 10.337(3), c= 19.763(3)&#197, &#946=93.07(1)&#176, V= 1595.5(5)&#1973, Z=4, Dx=1.791g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 14.86cm-1, F(000)=843.9, T=296K, Rint=0.03, R=0.062, Rw=0.063 para 1478 reflexões independentes observadas [I&#62 3&#959 (I)]. A estrutura é composta essencialmente por dois planos perpendiculares entre si; um formado pelos quatro átomos de cloro (com ângulo de aproximadamente 90&#176 entre si), o outro pelos grupos Py e carbonila e o átomo de Ru na intersecção destes. O complexo tem carga líquida negativa, sendo necessário a presença do grupo PyH (com carga líquida positiva), para a estabilização do cristal. 3) PyH(RuCl4Py2), Mr= 481.20, monoclínico, P21/n, a= 8.080(7), b= 22.503(7), c= 10.125(6)&#197, &#946= 93.19(6)&#176, V= 1838(2)&#1973, Z=4, Dx= 1.739g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 13.06cm-1, F(000)=959.9, T=296K, Rint=0.03, R=0.038, Rw=0.039 para 1553 reflexões independentes observadas [I&#62 3&#959 (I)]. Esta estrutura é bastante similar com a 2) descrita acima, ou seja, é composta essencialmente por dois planos perpendiculares entre si; um formado pelos quatro átomos de cloro (com ângulo de aproximadamente 90&#176 entre si), o outro pelos dois grupos Py e o átomo de Ru na intersecção destes. Pelo mesmo argumento usado acima, há um grupo PyH (com carga líquida positiva) no cristal. 4) [RuCl2(MeIm)2(CH3OH)(CO)], Mr= 396.24, triclínico, PI, a= 8.609(3), b= 8.060(3), c= 10.581(4)&#197, &#945= 77.78(3), &#946= 88.43(3), &#933= 66.88(3)&#176, V= 740.4(5)&#1973, Z=2, Dx= 1.777g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 12.80cm-1, F(000)=386, T=296K, Rint=0.004, R=0.025, Rw=0.027 para 2489 reflexões independentes observadas [I&#62 3&#959 (I)]. As distâncias e ângulos médios das ligações dos quatro complexos aqui descritos são comparados entre si e com mais quatro complexos no capítulo VII.This work consists of two parts: Part I: A brief theoretical description of the basic principles of X-ray crystallography. Part II: Resolution of the four crystal structures; three ruthenium compounds (chapter V, VI, VII) and a ligand commonly found in ruthenium complexes, C28H28O2P2. The structures resolved were: 1) C28H28O2P2, Mr= 458.48, triclinic, PI a= 5.826(1), b= 8.862(1), c= 12.517(2)&#197, &#945= 100.29(1), &#946= 102.67(1), &#933= 104.22(1)&#176, V= 592.5(3)&#1973, Z=1, Dx=1.285g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 2.00cm-1, F(000)=242, T=296K, final R=0.031 for 1390 independent observed reflections. The P atoms 0.126(1)&#197 away from plane formed by (CH2)4-. Both phenyl rings are planar to within experimental accuracy. The P atom has a distorced tetrahedral configuration. 2) PyH[RuCl4(CO)Py], Mr=430.11, monoclinic, P21/n, a= 7.821(1), b= 10.337(3), c= 19.763(3)&#197, &#946=93.07(1)&#176, V= 1595.5(5)&#1973, Z=4, Dx=1.791g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 14.86cm-1, F(000)=843.9, T=296K, Rint=0.03, final R=0.062, Rw=0.063 for 1478 independent observed reflections [I&#62 3&#959 (I)]. The structure is essentially composed of two perpendicular planes; one consisting of four chlorine atoms (in a square-planar arrangement), and a second plane composed of Py and carbonyl groups, with the ruthenium atom at intersection of them. The molecules have a net negative charge and the presence of the PyH group (with net positive charge), is necessary for crystal stabilization. 3) PyH(RuCl4Py2), Mr= 481.20, monoclinic, P21/n, a= 8.080(7), b= 22.503(7), c= 10.125(6)&#197, &#946= 93.19(6)&#176, V= 1838(2)&#1973, Z=4, Dx= 1.739g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 13.06cm-1, F(000)=959.9, T=296K, Rint=0.03, final R=0.038, Rw=0.039 for 1553 independent observed reflections [I&#62 3&#959 (I)]. This structures is very similar to that described in 2) above, being essentially composed of two perpendicular planes; one composed of four chlorine atoms (in a square-planar arrangement), and the other composed of two Py groups, with the ruthenium atom at the intersection of them. For the reason given above, there is one PyH group (with positive liquid charge) in the crystal. 4) [RuCl2(MeIm)2(CH3OH)(CO)], Mr= 396.24, triclinic, PI, a= 8.609(3), b= 8.060(3), c= 10.581(4)&#197, &#945= 77.78(3), &#946= 88.43(3), &#933= 66.88(3)&#176, V= 740.4(5)&#1973, Z=2, Dx= 1.777g.cm-3, &#955(M&#959K&#945)=0,71073&#197, &#956= 12.80cm-1, F(000)=386, T=296K, Rint=0.004, final R=0.025, Rw=0.027 for 2489 independent observed reflections [I&#62 3&#959 (I)]. In chapter VII, the average inter-atomic distances and angles for the four compounds are compare one with another and with four previously determinate structures

Crystal structure of a phospholipase A2 from Bothrops asper venom: Insights into a new putative “myotoxic cluster”

Snake venoms from the Viperidae and Elapidae families often have several phospholipases A2 (PLA2s), which may display different functions despite having a similar structural scaffold. These proteins are considered an important target for the development of drugs against local myotoxic damage because they are not efficiently neutralized by conventional serum therapy. PLA2s from these venoms are generally divided into two classes: (i) catalytic PLA2s (or Asp49-PLA2s) and (ii) non-catalytic PLA2-like toxins (or Lys49-PLA2s). In many Viperidae venoms, a subset of the basic Asp49-PLA2s displays some functional and structural characteristics of PLA2-like proteins and group within the same phylogenetic clade, but their myotoxic mechanism is still largely unknown. In the present study, we have crystallized and solved the structure of myotoxin I (MT-I), a basic myotoxic Asp49-PLA2 isolated from Bothrops asper venom. The structure presents a dimeric conformation that is compatible with that of previous dimers found for basic myotoxic Asp49-PLA2s and Lys49-PLA2s and has been confirmed by other biophysical and bioinformatics techniques. This arrangement suggests a possible cooperative action between both monomers to exert myotoxicity via two different sites forming a putative membrane-docking site (MDoS) and a putative membrane disruption site (MDiS). This mechanism would resemble that proposed for Lys49-PLA2s, but the sites involved appear to be situated in a different region. Thus, as both sites are close to one another, they form a “myotoxic cluster”, which is also found in two other basic myotoxic Asp49-PLA2s from Viperidae venoms. Such arrangement may represent a novel structural strategy for the mechanism of muscle damage exerted by the group of basic, Asp49-PLA2s found in viperid snake venoms.Fundação de Amparo à Pesquisa do Estado de São Paulo/[2015/17286-0]/FAPESP/BrasilFundação de Amparo à Pesquisa do Estado de São Paulo/[2015/24167-7]/FAPESP/BrasilConselho Nacional de Desenvolvimento Científico e Tecnológico/[300596/2013-8]/CNPq/BrasilCoordenação de Aperfeiçoamento de Pessoal de Nivel Superior/[23038.006271/2011-16]/CAPES/BrasilUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Instituto Clodomiro Picado (ICP

The synthetic Varespladib molecule is a multi-functional inhibitor for PLA2 and PLA2-like ophidic toxins

The treatment for snakebites is early administration of antivenom, which can be highly effective in inhibiting the systemic effects of snake venoms, but is less effective in the treatment of extra-circulatory and local effects. To complement standard-of-care treatments such as antibody-based antivenoms, natural and synthetic small molecules have been proposed for the inhibition of key venom components such as phospholipase A2 (PLA2) and PLA2-like toxins. Varespladib (compound LY315920) is a synthetic molecule developed and clinically tested aiming to block inflammatory cascades of several diseases associated with high PLA2s. Recent studies have demonstrated this molecule is able to potently inhibit snake venom catalytic PLA2 and PLA2-like toxins. In vivo and in vitro techniques were used to evaluate the inhibitory effect of varespladib against MjTX-I. X-ray crystallography was used to reveal details of the interaction between these molecules. A new methodology that combines crystallography, mass spectroscopy and phylogenetic data was used to review its primary sequence. Varespladib was able to inhibit the myotoxic and cytotoxic effects of MjTX-I. Structural analysis revealed a particular inhibitory mechanism of MjTX-I when compared to other PLA2-like myotoxin, presenting an oligomeric-independent function. Results suggest the effectiveness of varespladib for the inhibition of MjTX-I, in similarity with other PLA2 and PLA2-like toxins. Varespladib appears to be a promissory molecule in the treatment of local effects led by PLA2 and PLA2-like toxins (oligomeric dependent and independent), indicating that this is a multifunctional or broadly specific inhibitor for different toxins within this superfamily.Fundação de Amparo à Pesquisa do Estado de São Paulo/[2015/17286-0]/FAPESP/BrasilFundação de Amparo à Pesquisa do Estado de São Paulo/[2016/24191-8]/FAPESP/BrasilConselho Nacional de Desenvolvimento Científico e Tecnológico/[302883/2017-7]/CNPq/BrasilCoordenação de Aperfeiçoamento de Pessoal de Nível Superior/[]/CAPES/BrasilUniversidad de Costa Rica/[]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Instituto Clodomiro Picado (ICP