The pentameric ligand gated ion channel super family plays a central role in fast synaptic communication between neurons and at the neuromuscular junction. Extensive studies on the prototypic pLGIC, the Torpedo nicotinic acetylcholine receptor (nAChR) have revealed an exquisite lipid sensitivity, with the nAChR adopting a novel uncoupled conformation in membranes lacking activating anionic and neutral lipids. The lipid-exposed transmembrane alpha-helix, M4, in each homologous subunit likely acts as a lipid sensor. One model proposes that activating lipids promote M4 “binding” to the adjacent alpha-helices, M1 and M3, to enhance interactions between the M4 C-terminus and the Cys-loop of the agonist-binding domain, with such interactions promoting coupling between the agonist site and channel gate. The first part of my thesis indirectly tests this hypothesis by exploring the effects of membrane hydrophobic thickness on nAChR function. Specifically, I tested the hypothesis that thicker membranes, which should promote alignment of M4 parallel to M1/M3 and thus helix-helix interactions, favor a coupled conformation. Although I found that the nAChR is uncoupled in all membranes tested, regardless of hydrophobic thickness, thicker membranes promote transitions from uncoupled to ultimately the desensitized state over the minutes to hours time frame. In contrast to anionic lipids, which influence function primarily via a conformational selection mechanism, membrane hydrophobic thickness influences function via a kinetic mechanism - thick membranes lower the activation energy between uncoupled and coupled conformations to promote conformational transitions. In the second part of my thesis, I used the two prokaryotic homologs, GLIC and ELIC, to explore how amino acid interactions at the interface between M4 and M1/M3 influence channel activity. Alanine scanning mutagenesis of this interface shows that disruption of almost any interaction in GLIC leads to a loss of folding and/or function, while analogous mutations in ELIC typically lead to no change or produce gains in function. Sequence comparisons with other members of the pLGIC superfamily suggest that the transmembrane domains of GLIC and ELIC represent two distinct archetypes. Each archetype may strike a different balance between the need for strong M4 binding to M1/M3 to promote folding and pentamer assembly, and the need for weaker interactions that allow for greater conformational flexibility during function.

Investigations of structural and functional relationships of rat transient receptor potential cation channel, subfamily V, member 1 (TRPV1), also known as the capsaicin receptor, and human transient receptor potential cation channel, subfamily A, member 1, also known as TRPA1, are presented. Capsaicin induced Ca2+ -dependent desensitization of rat TRPV1 channel is studied and lead to the identification of key amino acid residues in the C- terminal domain of TRPV1 interacting with the membrane phospholipid PIP2 and an intradomain interaction that controls the open and desensitized state of the TRPV1 channel. Further the molecular basis of agonist AITC- and voltage-dependent gating on TRPA1 is explained. Hereby, residue P949 located near the center of the sixth transmembrane spanning helix (S6) is structurally required for normal functioning of the receptor and the distal bi-glycine G958XXXG962 motif controls its activation/deactivation properties. Furthermore, the gating region is extended towards the cytoplasmic part of the channel, putatively located near the inner mouth of the channel pore. A following series of experiments lead to the identification of a limited number of residues that appear important for allosteric regulation of the channel by chemical and voltage stimuli (K969, R975, K989, K1009, K1046, K1071, K1092 and K1099). In addition, three charge-neutralizing `gain-of- function{\crq} mutants (R975A, K988A, and K989A) which exhibited higher sensitivity to depolarizing voltages were characterized, indicating that these residues are directly involved in voltage-dependent modulation of TRPA1.

Pentameric ligand-gated ion channels (pLGICs) are membrane bound receptors found in the nervous system. They are responsible for detecting neurotransmitters released from neurons and subsequently mediating responses of the cells on which they are found. Thus, pLGICs play an invaluable role in communication between cells of the nervous system and understanding their function is pivotal to understanding how the nervous system works in general. One factor which is known to mediate pLGIC function is lipids found in the membrane environment in which pLGICs are embedded. This dissertation explores the various ways in which lipids interact with and modulate the function of pLGIC. Potential mechanisms and biological consequences of this modulation will be presented and discussed within the context of our current state of knowledge of pLGIC and nervous system function.

Pentameric ligand-gated ion channels (pLGICs) are membrane bound receptors found in the nervous system. They are responsible for detecting neurotransmitters released from neurons and subsequently mediating responses of the cells on which they are found. Thus, pLGICs play an invaluable role in communication between cells of the nervous system and understanding their function is pivotal to understanding how the nervous system works in general. One factor which is known to mediate pLGIC function is lipids found in the membrane environment in which pLGICs are embedded. This dissertation explores the various ways in which lipids interact with and modulate the function of pLGIC. Potential mechanisms and biological consequences of this modulation will be presented and discussed within the context of our current state of knowledge of pLGIC and nervous system function.

Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Genetic Algorithm (GA) to optimize the value of alpha, beta and Z-score. We obtain three energy scores libraries from a database of 4332 protein structures obtained from Protein Data Bank (PDB) server. Proposed energy function is found to outperform nearest competitor by 40.9% for the most challenging Rosetta decoy as well as better in terms of the Z-score based on Moulder and Rosetta decoy sets.

FGFs compreendem um grande família de 24 proteínas, participando de processos chaves nos mais variados tecidos, tendo funções parácrina, autócrina e intrácrina, regulando mitogênese, diferenciação celular, morfogênese e cicatrização. Mas, a relação estrutura-função dos FGFs é pobremente entendida. O membro protótipo desta família é o FGF-2, que apresenta quatro isoformas moleculares incluindo a forma de 18 kDa que é secretada e se liga aos receptores específicos (FGFRs) e dispara uma complexa sinalização. As outras isoformas, de alto peso molecular (21, 22 e 22,5 kDa) são expressas por códons alternativos (CUG) e permanecem no interior da célula interagindo com parceiros moleculares desconhecidos. Para antecipar mecanismos e parceiros do FGF-2 HMW foi realizada modelagem molecular desta isoforma que mostrou: uma estrutura do N-terminal da proteína com motivo β→α&#8594β e manutenção do barril β. A busca por parceiros intracelulares, foi realizada através da técnica do duplo hibrido de levedura, usando um biblioteca de cDNA de cérebro de rato. Foram encontrados 4 possíveis parceiros: BRD2, UBE2I, BRPF1, PC4. Todas essas interações foram confirmadas através do crescimento da levedura em meio sem histidina, produção de β-galactosidase e ensaios de \"pull-down\" com GST. Analises por FACS confirmam que FGF2 não causa apoptose em células adrenais tumorais Y1 de camundongo, mas promovem um acumulo de células na fase S com bloqueio do ciclo celular e da proliferação, configurando uma forma de senescência. Resultados com as células humanas HEK-ER:Ras permitem fazer a seguinte generalização: FGF2 induz senescência em células malignas transformadas pelos oncogenes raso A superexpressão da proteína de fusão FGF-2(18kDa):protA, mas não a da FGF-2(22,5 kDa):protA, protege a célula Y1 da senescência induzida por FGF-2. Por outro lado, a superexpressão destas mesmas isoformas de FGF-2 fusionadas à proteína A em células imortalizadas Balb3T3 não causou transformação celular e nem alterou a resposta mitogênica destas células ao FGF-2 recombinante adicionado ao meio de cultura. Células Y1 quando tratadas com FGF-2 recombinante produz ROS intracelular e libera anions superóxido no meio extracelular. Além disso, o anti-oxidante NAC protege estas células da indução de senescência induzida por FGF-2, sugerindo que ROS pode ser intermediário no disparo de senescência por FGF-2. / FGFs comprise a large fami1y of 24 proteins that play key roles in a number of tissues as local paracrine, autocrine and intracrine regulators of mitogenesis, cellular differentiation, organ morphogenesis and tissue repair. Structure-function relationship among FGFs is still poorly understood. FGF-2, the fami1y prototype member, exists as four molecular species. The 18 kDa form is released to the extracellular milieu and binds to specific receptors (FGFR), initiating a complex array of signals. Other isoforms of higher molecular weights (21, 22 and 22,5 kDa) are translated from alternative codons (CUG) and remain inside of the cell interacting with unknown partners. Aiming to anticipate mechanisms and partners, we modeled the FGF2-HMW molecule, showing that the protein displays β→α&#8594β motif in the N-terminal region and maintains the β-barrel structure common to ali FGFs. By the yeast two-hybrid method, using a cDNA rat brain library, we found four possible partners for FGF2-HMW: BRD2, UBE2I, BRP1 and PC4. Ali partners were confirmed by yeast growth without histidine, production of β-galactosidase and \"pull-down\" assays with GST. FACS analyses confirmed that FGF2 does not cause apoptosis in mouse Y1 adrenal tumor cells. But, FGF2 inhibited S phase progression blocking cell cycle and proliferation, characterizing a form of senescence. In addition, results obtained with the human HEK-ER:Ras cells support the following general statement: FGF2 triggers senescence in malignant cells transformed by ras oncogenes. Ectopic expression of the fusion protein FGF-2(18 kDa):protA, but not of FGF-2(22,s kDa):protA, protected Y1 cells senescence induced by FGF-2. On the other hand, ectopic expression of FGF-2 isoforms fusioned to protA in Balb3T3 immortalized cells did not cause transformation and neither modified the mitogenic response of this cell to recombinant FGF2. Recombinant FGF-2 stimules Y1 cells to produce intracellular ROS and to release superoxide anions into intracellular medium. Moreover, the ROS scavenger NAC protect Y1 cells from senescence induced by FGF-2, suggesting that ROS may be mediate senescence triggering induced by FGF-2.

A troponina (Tn) regula a contração do músculo estriado esquelético de vertebrados. Ela é composta de três subunidades: troponina I (TnI), troponina C (TnC) e troponina T (TnT). A TnI tem a função inibitória que é neutralizada pela ligação de Ca2+ nos sítios regulatórios do N-domínio da TnC, e a TnT posiciona o complexo no filamento fino. Para monitorar o sinal do Ca2+ sendo transmitido da TnC para a TnI as propriedades espectrais únicas do 5-hidroxitriptofano (5HW) foram utilizadas. O 5HW foi incorporado em mutantes pontuais de TnI com um único códon para triptofano. Foram identificadas duas sondas espectrais intrínsecas na TnI capazes de detectar a ligação de Ca2+ na Tn: as TnIs com 5HW nas posições 100 e 121. Complexos troponina reconstituídos com estes mutantes fluorescentes de TnI, Tn-TnIF100HW e Tn-TnIM121HW, apresentaram respectivamente 12 e 70 % de aumento na intensidade do espectro de emissão devido à ligação de Ca2+ na TnC. Nos complexos binários (TnC-TnI) as TnIs com 5HW nas posições 106 e 121 também captam a ligação do Ca2+ na TnC. A análise da fluorescência destas sondas demonstrou que: 1) as regiões da TnI que respondem ao N-domínio regulatório da TnC ocupado com Ca2+ são a região inibitória da TnI, resíduos 96 até 116, e a região vizinha que inclui a posição 121 da TnI; 2) mutações pontuais e a incorporação de 5HW na TnI podem afetar tanto a afinidade como a cooperatividade da ligação de Ca2+ na TnC, confirmando o papel da TnI em modular a afinidade da TnC por Ca2+; 3) as constantes de dissociação de Ca2+ surpreendentemente altas, Kd ~ 10-8 M, calculadas a partir dos sinais das sondas na região inibitória da TnI, sugerem a possibilidade de que os sítios do domínio N-terminal da TnC sejam os sítios de ligação de Ca2+ de maior afinidade no complexo troponina. / Vertebrate striated muscle contraction is regulated by troponin (Tn). Tn is composed of three subunits: troponin I (TnI), troponin C (TnC) and troponin T (TnT). TnI has an inhibitory role that is neutralized by calcium binding to the regulatory sites in the N-domain of TnC, and TnT positions the troponin complex on the thin filament. In order to follow the Ca2+ induced conformational change that is transmitted from TnC to TnI, the unique spectral properties of 5-hydroxytryptophan (5HW) incorporated as point-mutants of TnI were used. It was possible to identify two new TnI intrinsic spectral probes sensitive to Ca2+ binding to Tn: TnI with single 5HW at positions 100 and 121. Trimeric troponin complexes reconstituted with two fluorescent mutants of TnI, Tn-TnIF100HW and Tn-TnIM121HW, showed respectively 12 and 70 % increase in the emission spectra when Ca2+ bound to TnC. In the binary complexes (TnC-TnI) two TnIs with 5HW at positions 106 and 121 were also sensitive to Ca2+ binding to TnC. Fluorescence analysis of these probes showed: 1) the regions in TnI that respond to Ca2+ binding to the regulatory N-domain of TnC are the inhibitory region of TnI (residues 96 to 116), and a neighbor region that includes position 121; 2) point mutations and incorporation of 5HW in TnI can affect both the affinity and the cooperativity of Ca2+ binding to TnC, confirming the role of TnI as a modulator of the Ca2+ affinity of TnC; 3) the high dissociation constant for sites in the N-terminal domain of TnC (Kd ~ 10-8 M), derived from data using probes in the inhibitory region of TnI suggested the possibility that these sites are the high affinity Ca2+ binding sites in the troponin complex.

FGFs compreendem um grande família de 24 proteínas, participando de processos chaves nos mais variados tecidos, tendo funções parácrina, autócrina e intrácrina, regulando mitogênese, diferenciação celular, morfogênese e cicatrização. Mas, a relação estrutura-função dos FGFs é pobremente entendida. O membro protótipo desta família é o FGF-2, que apresenta quatro isoformas moleculares incluindo a forma de 18 kDa que é secretada e se liga aos receptores específicos (FGFRs) e dispara uma complexa sinalização. As outras isoformas, de alto peso molecular (21, 22 e 22,5 kDa) são expressas por códons alternativos (CUG) e permanecem no interior da célula interagindo com parceiros moleculares desconhecidos. Para antecipar mecanismos e parceiros do FGF-2 HMW foi realizada modelagem molecular desta isoforma que mostrou: uma estrutura do N-terminal da proteína com motivo β→α&#8594β e manutenção do barril β. A busca por parceiros intracelulares, foi realizada através da técnica do duplo hibrido de levedura, usando um biblioteca de cDNA de cérebro de rato. Foram encontrados 4 possíveis parceiros: BRD2, UBE2I, BRPF1, PC4. Todas essas interações foram confirmadas através do crescimento da levedura em meio sem histidina, produção de β-galactosidase e ensaios de \"pull-down\" com GST. Analises por FACS confirmam que FGF2 não causa apoptose em células adrenais tumorais Y1 de camundongo, mas promovem um acumulo de células na fase S com bloqueio do ciclo celular e da proliferação, configurando uma forma de senescência. Resultados com as células humanas HEK-ER:Ras permitem fazer a seguinte generalização: FGF2 induz senescência em células malignas transformadas pelos oncogenes raso A superexpressão da proteína de fusão FGF-2(18kDa):protA, mas não a da FGF-2(22,5 kDa):protA, protege a célula Y1 da senescência induzida por FGF-2. Por outro lado, a superexpressão destas mesmas isoformas de FGF-2 fusionadas à proteína A em células imortalizadas Balb3T3 não causou transformação celular e nem alterou a resposta mitogênica destas células ao FGF-2 recombinante adicionado ao meio de cultura. Células Y1 quando tratadas com FGF-2 recombinante produz ROS intracelular e libera anions superóxido no meio extracelular. Além disso, o anti-oxidante NAC protege estas células da indução de senescência induzida por FGF-2, sugerindo que ROS pode ser intermediário no disparo de senescência por FGF-2. / FGFs comprise a large fami1y of 24 proteins that play key roles in a number of tissues as local paracrine, autocrine and intracrine regulators of mitogenesis, cellular differentiation, organ morphogenesis and tissue repair. Structure-function relationship among FGFs is still poorly understood. FGF-2, the fami1y prototype member, exists as four molecular species. The 18 kDa form is released to the extracellular milieu and binds to specific receptors (FGFR), initiating a complex array of signals. Other isoforms of higher molecular weights (21, 22 and 22,5 kDa) are translated from alternative codons (CUG) and remain inside of the cell interacting with unknown partners. Aiming to anticipate mechanisms and partners, we modeled the FGF2-HMW molecule, showing that the protein displays β→α&#8594β motif in the N-terminal region and maintains the β-barrel structure common to ali FGFs. By the yeast two-hybrid method, using a cDNA rat brain library, we found four possible partners for FGF2-HMW: BRD2, UBE2I, BRP1 and PC4. Ali partners were confirmed by yeast growth without histidine, production of β-galactosidase and \"pull-down\" assays with GST. FACS analyses confirmed that FGF2 does not cause apoptosis in mouse Y1 adrenal tumor cells. But, FGF2 inhibited S phase progression blocking cell cycle and proliferation, characterizing a form of senescence. In addition, results obtained with the human HEK-ER:Ras cells support the following general statement: FGF2 triggers senescence in malignant cells transformed by ras oncogenes. Ectopic expression of the fusion protein FGF-2(18 kDa):protA, but not of FGF-2(22,s kDa):protA, protected Y1 cells senescence induced by FGF-2. On the other hand, ectopic expression of FGF-2 isoforms fusioned to protA in Balb3T3 immortalized cells did not cause transformation and neither modified the mitogenic response of this cell to recombinant FGF2. Recombinant FGF-2 stimules Y1 cells to produce intracellular ROS and to release superoxide anions into intracellular medium. Moreover, the ROS scavenger NAC protect Y1 cells from senescence induced by FGF-2, suggesting that ROS may be mediate senescence triggering induced by FGF-2.

A troponina (Tn) regula a contração do músculo estriado esquelético de vertebrados. Ela é composta de três subunidades: troponina I (TnI), troponina C (TnC) e troponina T (TnT). A TnI tem a função inibitória que é neutralizada pela ligação de Ca2+ nos sítios regulatórios do N-domínio da TnC, e a TnT posiciona o complexo no filamento fino. Para monitorar o sinal do Ca2+ sendo transmitido da TnC para a TnI as propriedades espectrais únicas do 5-hidroxitriptofano (5HW) foram utilizadas. O 5HW foi incorporado em mutantes pontuais de TnI com um único códon para triptofano. Foram identificadas duas sondas espectrais intrínsecas na TnI capazes de detectar a ligação de Ca2+ na Tn: as TnIs com 5HW nas posições 100 e 121. Complexos troponina reconstituídos com estes mutantes fluorescentes de TnI, Tn-TnIF100HW e Tn-TnIM121HW, apresentaram respectivamente 12 e 70 % de aumento na intensidade do espectro de emissão devido à ligação de Ca2+ na TnC. Nos complexos binários (TnC-TnI) as TnIs com 5HW nas posições 106 e 121 também captam a ligação do Ca2+ na TnC. A análise da fluorescência destas sondas demonstrou que: 1) as regiões da TnI que respondem ao N-domínio regulatório da TnC ocupado com Ca2+ são a região inibitória da TnI, resíduos 96 até 116, e a região vizinha que inclui a posição 121 da TnI; 2) mutações pontuais e a incorporação de 5HW na TnI podem afetar tanto a afinidade como a cooperatividade da ligação de Ca2+ na TnC, confirmando o papel da TnI em modular a afinidade da TnC por Ca2+; 3) as constantes de dissociação de Ca2+ surpreendentemente altas, Kd ~ 10-8 M, calculadas a partir dos sinais das sondas na região inibitória da TnI, sugerem a possibilidade de que os sítios do domínio N-terminal da TnC sejam os sítios de ligação de Ca2+ de maior afinidade no complexo troponina. / Vertebrate striated muscle contraction is regulated by troponin (Tn). Tn is composed of three subunits: troponin I (TnI), troponin C (TnC) and troponin T (TnT). TnI has an inhibitory role that is neutralized by calcium binding to the regulatory sites in the N-domain of TnC, and TnT positions the troponin complex on the thin filament. In order to follow the Ca2+ induced conformational change that is transmitted from TnC to TnI, the unique spectral properties of 5-hydroxytryptophan (5HW) incorporated as point-mutants of TnI were used. It was possible to identify two new TnI intrinsic spectral probes sensitive to Ca2+ binding to Tn: TnI with single 5HW at positions 100 and 121. Trimeric troponin complexes reconstituted with two fluorescent mutants of TnI, Tn-TnIF100HW and Tn-TnIM121HW, showed respectively 12 and 70 % increase in the emission spectra when Ca2+ bound to TnC. In the binary complexes (TnC-TnI) two TnIs with 5HW at positions 106 and 121 were also sensitive to Ca2+ binding to TnC. Fluorescence analysis of these probes showed: 1) the regions in TnI that respond to Ca2+ binding to the regulatory N-domain of TnC are the inhibitory region of TnI (residues 96 to 116), and a neighbor region that includes position 121; 2) point mutations and incorporation of 5HW in TnI can affect both the affinity and the cooperativity of Ca2+ binding to TnC, confirming the role of TnI as a modulator of the Ca2+ affinity of TnC; 3) the high dissociation constant for sites in the N-terminal domain of TnC (Kd ~ 10-8 M), derived from data using probes in the inhibitory region of TnI suggested the possibility that these sites are the high affinity Ca2+ binding sites in the troponin complex.

No description available.