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1.
BMC Biol ; 19(1): 43, 2021 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-33706787

RESUMO

BACKGROUND: Amyloids are ordered, insoluble protein aggregates, characterized by a cross-ß sheet quaternary structure in which molecules in a ß-strand conformation are stacked along the filament axis via intermolecular interactions. While amyloids are typically associated with pathological conditions, functional amyloids have also been identified and are present in a wide variety of organisms ranging from bacteria to humans. The cytoplasmic polyadenylation element-binding (CPEB) prion-like protein is an mRNA-binding translation regulator, whose neuronal isoforms undergo activity-dependent aggregation, a process that has emerged as a plausible biochemical substrate for memory maintenance. CPEB aggregation is driven by prion-like domains (PLD) that are divergent in sequence across species, and it remains unknown whether such divergent PLDs follow a similar aggregating assembly pathway. Here, we describe the amyloid-like features of the neuronal Aplysia CPEB (ApCPEB) PLD and compare them to those of the Drosophila ortholog, Orb2 PLD. RESULTS: Using in vitro single-molecule and bulk biophysical methods, we find transient oligomers and mature amyloid-like filaments that suggest similarities in the late stages of the assembly pathway for both ApCPEB and Orb2 PLDs. However, while prior to aggregation the Orb2 PLD monomer remains mainly as a random coil in solution, ApCPEB PLD adopts a diversity of conformations comprising α-helical structures that evolve to coiled-coil species, indicating structural differences at the beginning of their amyloid assembly pathways. CONCLUSION: Our results indicate that divergent PLDs of CPEB proteins from different species retain the ability to form a generic amyloid-like fold through different assembly mechanisms.


Assuntos
Amiloide/metabolismo , Aplysia/metabolismo , Príons/metabolismo , Animais , Aplysia/química , Poliadenilação , Príons/química
2.
Arch Biochem Biophys ; 698: 108731, 2021 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-33359563

RESUMO

Microbial pathogens, such as Trypanosoma brucei, have an enormous impact on global health and economic systems. Protein kinase A of T. brucei is an attractive drug target as it is an essential enzyme which differs significantly from its human homolog. The hinge region of this protein's regulatory domain is vital for enzymatic function, but its conformation is unknown. Here, the secondary structure of this region has been characterized using NMR and CD spectroscopies. More specifically, three overlapping peptides corresponding to residues T187-I211, G198-Y223 and V220-S245 called peptide 1, peptide 2 and peptide 3, respectively, were studied. The peptide 1 and peptide 2 are chiefly unfolded; only low populations (<10%) of α-helix were detected under the conditions studied. In contrast, the peptide 3 contains a long α-helix whose population is significantly higher; namely, 36% under the conditions studied. Utilizing the dihedral φ and ψ angles calculated on the basis of the NMR data, the conformation of the peptide 3 was calculated and revealed an α-helix spanning residues E230-N241. This α-helix showed amphiphilicity and reversible unfolding and refolding upon heating and cooling. Most fascinating, however, is its capacity to inhibit the activity of the catalytic domain of Trypanosoma equiperdum protein kinase A even though it is quite distinct from the canonical inhibitor motif. Based on this property, we advance that peptoids based on the peptide 3 α-helix could be novel leads for developing anti-trypanosomal therapeutics.


Assuntos
Proteínas Quinases Dependentes de AMP Cíclico/química , Fragmentos de Peptídeos/química , Inibidores de Proteínas Quinases/química , Trypanosoma brucei brucei/enzimologia , Sequência de Aminoácidos , Animais , Proteínas Quinases Dependentes de AMP Cíclico/antagonistas & inibidores , Ensaios Enzimáticos , Conformação Proteica em alfa-Hélice , Redobramento de Proteína , Desdobramento de Proteína , Proteínas de Protozoários/antagonistas & inibidores , Proteínas de Protozoários/química , Alinhamento de Sequência , Suínos
3.
Int J Mol Sci ; 21(21)2020 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-33143110

RESUMO

Activation of the cannabinoid CB1 receptor induces different cellular signaling cascades through coupling to different effector proteins (G-proteins and ß-arrestins), triggering numerous therapeutic effects. Conformational changes and rearrangements at the intracellular domain of this GPCR receptor that accompany ligand binding dictate the signaling pathways. The GPCR-binding interface for G proteins has been extensively studied, whereas ß-arrestin/GPCR complexes are still poorly understood. To gain knowledge in this direction, we designed peptides that mimic the motifs involved in the putative interacting region: ß-arrestin1 finger loop and the transmembrane helix 7-helix 8 (TMH7-H8) elbow located at the intracellular side of the CB1 receptor. According to circular dichroism and NMR data, these peptides form a native-like, helical conformation and interact with each other in aqueous solution, in the presence of trifluoroethanol, and using zwitterionic detergent micelles as membrane mimics. These results increase our understanding of the binding mode of ß-arrestin and CB1 receptor and validate minimalist approaches to structurally comprehend complex protein systems.


Assuntos
Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/metabolismo , Receptor CB1 de Canabinoide/química , Receptor CB1 de Canabinoide/metabolismo , beta-Arrestinas/química , beta-Arrestinas/metabolismo , Dicroísmo Circular/métodos , Humanos , Espectroscopia de Ressonância Magnética/métodos , Modelos Moleculares , Estrutura Secundária de Proteína , Transdução de Sinais
4.
PLoS Biol ; 14(1): e1002361, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26812143

RESUMO

Amyloids are ordered protein aggregates that are typically associated with neurodegenerative diseases and cognitive impairment. By contrast, the amyloid-like state of the neuronal RNA binding protein Orb2 in Drosophila was recently implicated in memory consolidation, but it remains unclear what features of this functional amyloid-like protein give rise to such diametrically opposed behaviour. Here, using an array of biophysical, cell biological and behavioural assays we have characterized the structural features of Orb2 from the monomer to the amyloid state. Surprisingly, we find that Orb2 shares many structural traits with pathological amyloids, including the intermediate toxic oligomeric species, which can be sequestered in vivo in hetero-oligomers by pathological amyloids. However, unlike pathological amyloids, Orb2 rapidly forms amyloids and its toxic intermediates are extremely transient, indicating that kinetic parameters differentiate this functional amyloid from pathological amyloids. We also observed that a well-known anti-amyloidogenic peptide interferes with long-term memory in Drosophila. These results provide structural insights into how the amyloid-like state of the Orb2 protein can stabilize memory and be nontoxic. They also provide insight into how amyloid-based diseases may affect memory processes.


Assuntos
Proteínas Amiloidogênicas/metabolismo , Proteínas de Drosophila/metabolismo , Consolidação da Memória , Fatores de Transcrição/metabolismo , Fatores de Poliadenilação e Clivagem de mRNA/metabolismo , Animais , Células COS , Chlorocebus aethiops , Proteínas de Drosophila/química , Proteínas de Drosophila/genética , Drosophila melanogaster , Feminino , Masculino , Mutação , Oligopeptídeos , Estrutura Terciária de Proteína , Fatores de Transcrição/química , Fatores de Transcrição/genética , Leveduras , Fatores de Poliadenilação e Clivagem de mRNA/química , Fatores de Poliadenilação e Clivagem de mRNA/genética
5.
J Biol Chem ; 292(9): 3591-3602, 2017 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-28100777

RESUMO

During sexual development ascomycete fungi produce two types of peptide pheromones termed a and α. The α pheromone from the budding yeast Saccharomyces cerevisiae, a 13-residue peptide that elicits cell cycle arrest and chemotropic growth, has served as paradigm for the interaction of small peptides with their cognate G protein-coupled receptors. However, no structural information is currently available for α pheromones from filamentous ascomycetes, which are significantly shorter and share almost no sequence similarity with the S. cerevisiae homolog. High resolution structure of synthetic α-pheromone from the plant pathogenic ascomycete Fusarium oxysporum revealed the presence of a central ß-turn resembling that of its yeast counterpart. Disruption of the-fold by d-alanine substitution of the conserved central Gly6-Gln7 residues or by random sequence scrambling demonstrated a crucial role for this structural determinant in chemoattractant activity. Unexpectedly, the growth inhibitory effect of F. oxysporum α-pheromone was independent of the cognate G protein-coupled receptors Ste2 and of the central ß-turn but instead required two conserved Trp1-Cys2 residues at the N terminus. These results indicate that, despite their reduced size, fungal α-pheromones contain discrete functional regions with a defined secondary structure that regulate diverse biological processes such as polarity reorientation and cell division.


Assuntos
Fatores Quimiotáticos/química , Proteínas Fúngicas/química , Fusarium/química , Feromônios/química , Ciclo Celular , Núcleo Celular/metabolismo , Cisteína/química , Genes Fúngicos Tipo Acasalamento , Peptídeos/química , Domínios Proteicos , Estrutura Secundária de Proteína , Receptores Acoplados a Proteínas G/metabolismo , Saccharomyces cerevisiae/química , Transdução de Sinais , Relação Estrutura-Atividade , Triptofano/química
6.
Biochem J ; 474(2): 231-246, 2017 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-28062839

RESUMO

The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e-/H+ coupling mechanisms to sustain cellular growth. This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome in the oxidized state. The comparison of oxidized and reduced structures revealed that the heme I axial ligand geometry changed and there were other significant changes in the segments near heme I. The pH-linked conformational rearrangements observed in the vicinity of the redox-Bohr center, both in the oxidized and reduced structures, constitute the structural basis for the differences observed in the pKa values of the redox-Bohr center, providing insights into the e-/H+ coupling molecular mechanisms driven by PpcA in G. sulfurreducens.


Assuntos
Proteínas de Bactérias/química , Citocromos c/química , Elétrons , Geobacter/química , Heme/química , Prótons , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Clonagem Molecular , Citocromos c/genética , Citocromos c/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Geobacter/enzimologia , Heme/metabolismo , Concentração de Íons de Hidrogênio , Marcação por Isótopo , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Oxirredução , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Termodinâmica
7.
Biochim Biophys Acta Bioenerg ; 1858(9): 733-741, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28377068

RESUMO

Gene knock-out studies on Geobacter sulfurreducens cells showed that the outer membrane-associated monoheme cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI). In addition, microarray analysis of an OmcF-deficient mutant revealed that many of the genes with decreased transcript level were those whose expression is up-regulated in cells grown with a graphite electrode as electron acceptor, suggesting that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electricity production by G. sulfurreducens in microbial fuel cells. 15N,13C-labeled OmcF was produced and NMR spectroscopy was used to determine the solution structure of the protein in the fully reduced state and the pH-dependent conformational changes. In addition, 15N relaxation NMR experiments were used to characterize the overall and internal backbone dynamics of OmcF. The structure obtained is well-defined, with an average pairwise root mean square deviation of 0.37Å for the backbone atoms and 0.98Å for all heavy atoms. For the first time a solution structure and the protein motions were determined for an outer membrane cytochrome from G. sulfurreducens, which constitutes an important step to understand the extracellular electron transfer mechanism in Geobacter cells.


Assuntos
Proteínas de Bactérias/química , Geobacter/química , Heme/química , Modelos Moleculares , Movimento (Física) , Ressonância Magnética Nuclear Biomolecular , Oxirredução , Fragmentos de Peptídeos/química , Conformação Proteica , Proteínas Recombinantes/química , Soluções
8.
J Biol Chem ; 291(40): 20962-20975, 2016 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-27502274

RESUMO

It has been suggested that DYNLT1, a dynein light chain known to bind to various cellular and viral proteins, can function both as a molecular clamp and as a microtubule-cargo adapter. Recent data have shown that the DYNLT1 homodimer binds to two dynein intermediate chains to subsequently link cargo proteins such as the guanine nucleotide exchange factor Lfc or the small GTPases RagA and Rab3D. Although over 20 DYNLT1-interacting proteins have been reported, the exact sequence requirements that enable their association to the canonical binding groove or to the secondary site within the DYNLT1 surface are unknown. We describe herein the sequence recognition properties of the hydrophobic groove of DYNLT1 known to accommodate dynein intermediate chain. Using a pepscan approach, we have substituted each amino acid within the interacting peptide for all 20 natural amino acids and identified novel binding sequences. Our data led us to propose activin receptor IIB as a novel DYNLT1 ligand and suggest that DYNLT1 functions as a molecular dimerization engine bringing together two receptor monomers in the cytoplasmic side of the membrane. In addition, we provide evidence regarding a dual binding mode adopted by certain interacting partners such as Lfc or the parathyroid hormone receptor. Finally, we have used NMR spectroscopy to obtain the solution structure of human DYNLT1 forming a complex with dynein intermediate chain of ∼74 kDa; it is the first mammalian structure available.


Assuntos
Dineínas/química , Dineínas/metabolismo , Multimerização Proteica/fisiologia , Receptores de Activinas Tipo II/genética , Receptores de Activinas Tipo II/metabolismo , Animais , Células COS , Chlorocebus aethiops , Dineínas/genética , Humanos , Interações Hidrofóbicas e Hidrofílicas , Camundongos , Ressonância Magnética Nuclear Biomolecular , Fatores de Troca de Nucleotídeo Guanina Rho/genética , Fatores de Troca de Nucleotídeo Guanina Rho/metabolismo
9.
Biochim Biophys Acta ; 1858(6): 1328-38, 2016 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-26975251

RESUMO

The short membrane-active peptide BP100 [KKLFKKILKYL-NH2] is known as an effective antimicrobial and cell penetrating agent. For a functional alanine scan each of the 11 amino acids was replaced with deuterated Ala-d3, one at a time. MIC assays showed that a substitution of Lys did not affect the antimicrobial activity, but it decreased when a hydrophobic residue was replaced. In most cases, a reduction in hydrophobicity led to a decrease in hemolysis, and some peptide analogues had an improved therapeutic index. Circular dichroism showed that BP100 folds as an amphiphilic α-helix in a bilayer. Its alignment was determined from (2)H NMR in oriented membranes of different composition. The azimuthal rotation angle was the same under all conditions, but the average helix tilt angle and the dynamical behavior of the peptide varied in a systematic manner. In POPC/POPG bilayers, with a negative spontaneous curvature, the peptide was found to lie flat on the bilayer surface, and with little wobble. In DMPC/DMPG, with a positive spontaneous curvature, BP100 at higher concentrations became tilted obliquely into the membrane, with the uncharged C-terminus inserted more deeply into the lipid bilayer, experiencing significant fluctuations in tilt angle. In DMPC/DMPG/lyso-MPC, with a pronounced positive spontaneous curvature, the helix tilted even further and became even more mobile. The 11-mer BP100 is obviously too short to form transmembrane pores. We conclude that BP100 operates via a carpet mechanism, whereby the C-terminus gets inserted into the hydrophobic core of the bilayer, which leads to membrane perturbation and induces transient permeability.


Assuntos
Proteínas de Membrana/química , Ressonância Magnética Nuclear Biomolecular/métodos , Oligopeptídeos/química , Sequência de Aminoácidos , Antibacterianos/química , Antibacterianos/farmacologia , Membrana Celular/efeitos dos fármacos , Dicroísmo Circular , Deutério , Hemólise/efeitos dos fármacos , Bicamadas Lipídicas , Testes de Sensibilidade Microbiana , Oligopeptídeos/farmacologia
10.
Invest New Drugs ; 35(3): 260-268, 2017 06.
Artigo em Inglês | MEDLINE | ID: mdl-28120180

RESUMO

Apoptin is a nonstructural protein encoded by one of the three open reading frames of the chicken anemia virus genome. It has attracted a great deal of interest due to its ability to induce apoptosis in multiple transformed and malignant mammalian cell lines without affecting primary and non-transformed cells. However, the use of Apoptin as an anticancer drug is restricted by its strong tendency to aggregate. A number of methods to overcome this problem have been proposed, including transduction techniques to deliver the Apoptin gene into tumor cells, but all such methods have certain drawbacks. Here we describe that a truncated variant of Apoptin, lacking residues 1 to 43, is a soluble, non-aggregating protein that maintains most of the biological properties of wild-type Apoptin when transfected into cells. We show that the cytotoxic effect of this variant is also present when it is added exogenously to cancer cells, but not to normal cells. In addition to the interest this protein has attracted as a promising therapeutic strategy, it is also an excellent model to study the structural properties of Apoptin and how they relate to its mechanism of action.


Assuntos
Antineoplásicos/farmacologia , Proteínas do Capsídeo/química , Proteínas do Capsídeo/farmacologia , Apoptose/efeitos dos fármacos , Proteínas do Capsídeo/genética , Linhagem Celular , Linhagem Celular Tumoral , DNA/metabolismo , Escherichia coli/genética , Humanos , Transfecção
11.
Arch Biochem Biophys ; 614: 53-64, 2017 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-28034642

RESUMO

Apoptin is a 121 residue protein which forms large, soluble aggregates and possesses an exceptionally selectively cytotoxic action on cancer cells. In the accompanying paper, we described the design, production and initial characterization of an Apoptin truncated variant called H6-ApopΔProΔLeu. Whereas both the variant and wild type protein possess similar selective cytotoxicity against cancer cells following transfection, only the variant is cytotoxic when added externally. Remarkably, as observed by gel filtration chromatography and dynamic light scattering, H6-ApopΔProΔLeu lacks the tendency of wild type Apoptin to form large aggregates, which greatly facilitated the study of its biological properties. Here, we characterize the conformation and dynamics of H6-ApopΔProΔLeu. Using a battery of 2D, 3D and (4,2)D NMR spectra, the essentially complete 1H, 13C and 15N resonance assignments of H6-ApopΔProΔLeu were obtained. The analysis of these data shows that the variant is an intrinsically disordered protein, which lacks a preferred conformation. This conclusion is corroborated by a lack of protection against proteolytic cleavage and hydrogen/deuterium exchange. Moreover, the CD spectra are dominated by random coil contributions. Finally, 1H-15N NOE ratios are low, which indicates flexibility on the ps-ns time scale. Interestingly, H6-ApopΔProΔLeu's intrinsically disordered ensemble is not significantly altered by the redox state of its Cys residues or by Thr phosphorylation, which has been proposed to play a key role in Apoptin's selective cytotoxicity. These results serve to better comprehend Apoptin's remarkably selective anticancer action and provide a framework for the future design of improved Apoptin variants.


Assuntos
Antineoplásicos/química , Proteínas do Capsídeo/química , Neoplasias/patologia , Neoplasias/terapia , Linhagem Celular Tumoral , Vírus da Anemia da Galinha , Cisteína/química , Ensaios de Seleção de Medicamentos Antitumorais , Endopeptidase K/química , Humanos , Espectroscopia de Ressonância Magnética , Fosforilação , Conformação Proteica , Dobramento de Proteína , Espectrometria de Fluorescência , Espectrofotometria Ultravioleta
12.
Biopolymers ; 107(11)2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28922450

RESUMO

TACC3 is a centrosomal adaptor protein that plays important roles during mitotic spindle assembly. It interacts with chTOG/XMAP215, which catalyzes the addition of tubulin dimers during microtubule growth. A 3D coiled-coil model for this interaction is available but the structural details are not well described. To characterize this interaction at atomic resolution, we have designed a simplified version of the system based on small peptides. Four different peptides have been studied by circular dichroism and nuclear magnetic resonance both singly and in all possible combinations; namely, five peptide pairs and two trios. In cosolvents, all single peptides tend to adopt helical conformations resembling those of the full-length protein. However, neither the single peptides nor pairs of peptides form coiled coils. We show that the simultaneous presence of all preformed helices is a prerequisite for binding. The simplest 3D model for the interaction, based on the NMR results, is proposed. Interestingly, the peptide's structure remains unaffected by mutations at essential positions for TACC3 activity. This suggests that the lack of interaction of this TACC3 mutant with XMAP does not correlate with changes in the protein structure and that specific interactions are likely responsible for the interaction and stability of the complex.


Assuntos
Proteínas Associadas aos Microtúbulos/química , Proteínas Associadas aos Microtúbulos/metabolismo , Ressonância Magnética Nuclear Biomolecular/métodos , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo , Proteínas de Xenopus/química , Proteínas de Xenopus/metabolismo , Dicroísmo Circular , Modelos Moleculares , Simulação de Acoplamento Molecular , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/metabolismo , Domínios e Motivos de Interação entre Proteínas
13.
Biochim Biophys Acta ; 1844(10): 1808-19, 2014 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-25091198

RESUMO

Human centrosomal proteins show a significant, 3.5 fold, bias to be both unstructured and coiled-coils with respect to generic human proteins, based on results from state of the art bioinformatics tools. We hypothesize that this bias means that these proteins adopt an ensemble of disordered and partially helical conformations, with the latter becoming stabilized when these proteins form complexes. Characterization of the structural properties of 13 peptides from 10 different centrosomal proteins ranging in size from 20 to 61 residues by biophysical methods led us to confirm our hypothesis in most cases. Interestingly, the secondary structure adopted by most of these peptides becomes stabilized at acidic pH and it is concentration dependent. For two of them, PIK3R1(453-513) and BRCA1(1253-1273), we observed not only the stabilization of helical structure through self-association, but also the presence of ß-structures linked to the formation of high molecular weight oligomers. These oligomers are the predominant forms detected by CD, but unobservable by liquid state NMR. BRCA1(1397-1424) and MAP3K11(396-441) populate helical structures that can also self-associate at pH3 through oligomeric species. Four peptides, derived from three proteins, namely CCNA2(103-123), BRCA1(1253-1273), BRCA1(1397-1424) and PIK3R1(453-513), can form intermolecular associations that are concomitant with alpha or beta structure stabilization. The self-phosphorylation previously described for the kinase NEK2 did not lead to any stabilization in the peptide's structure of NEK2(303-333), NEK2(341-361), and NEK2(410-430). Based on these results, obtained from a series of peptides derived from a significant number of different centrosomal proteins, we propose that conformational polymorphism, modulated by intermolecular interactions is a general property of centrosomal proteins.

14.
Arch Biochem Biophys ; 580: 93-101, 2015 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-26151774

RESUMO

Ole e 9 and Fra e 9 are two allergenic ß-1,3-glucanases from olive and ash tree pollens, respectively. Both proteins present a modular structure with a catalytic N-terminal domain and a carbohydrate-binding module (CBM) at the C-terminus. Despite their significant sequence resemblance, they differ in some functional properties, such as their catalytic activity and the carbohydrate-binding ability. Here, we have studied the different capability of the recombinant C-terminal domain of both allergens to bind laminarin by NMR titrations, binding assays and ultracentrifugation. We show that rCtD-Ole e 9 has a higher affinity for laminarin than rCtD-Fra e 9. The complexes have different exchange regimes on the NMR time scale in agreement with the different affinity for laminarin observed in the biochemical experiments. Utilising NMR chemical shift perturbation data, we show that only one side of the protein surface is affected by the interaction and that the binding site is located in the inter-helical region between α1 and α2, which is buttressed by aromatic side chains. The binding surface is larger in rCtD-Ole e 9 which may account for its higher affinity for laminarin relative to rCtD-Fra e 9.


Assuntos
Alérgenos/química , Antígenos de Plantas/química , Glucana 1,3-beta-Glucosidase/química , Glucanos/química , Proteínas de Plantas/química , beta-Glucosidase/química , Alérgenos/genética , Alérgenos/imunologia , Sequência de Aminoácidos , Antígenos de Plantas/genética , Antígenos de Plantas/imunologia , Sítios de Ligação , Fraxinus/química , Fraxinus/enzimologia , Expressão Gênica , Glucana 1,3-beta-Glucosidase/genética , Glucana 1,3-beta-Glucosidase/imunologia , Humanos , Modelos Moleculares , Dados de Sequência Molecular , Ressonância Magnética Nuclear Biomolecular , Olea/química , Olea/enzimologia , Pichia/genética , Pichia/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/imunologia , Pólen/química , Pólen/imunologia , Ligação Proteica , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/imunologia , Homologia de Sequência de Aminoácidos , beta-Glucosidase/genética , beta-Glucosidase/imunologia
15.
PLoS Biol ; 10(5): e1001335, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22666178

RESUMO

Amyloidogenic neurodegenerative diseases are incurable conditions with high social impact that are typically caused by specific, largely disordered proteins. However, the underlying molecular mechanism remains elusive to established techniques. A favored hypothesis postulates that a critical conformational change in the monomer (an ideal therapeutic target) in these "neurotoxic proteins" triggers the pathogenic cascade. We use force spectroscopy and a novel methodology for unequivocal single-molecule identification to demonstrate a rich conformational polymorphism in the monomer of four representative neurotoxic proteins. This polymorphism strongly correlates with amyloidogenesis and neurotoxicity: it is absent in a fibrillization-incompetent mutant, favored by familial-disease mutations and diminished by a surprisingly promiscuous inhibitor of the critical monomeric ß-conformational change, neurotoxicity, and neurodegeneration. Hence, we postulate that specific mechanostable conformers are the cause of these diseases, representing important new early-diagnostic and therapeutic targets. The demonstrated ability to inhibit the conformational heterogeneity of these proteins by a single pharmacological agent reveals common features in the monomer and suggests a common pathway to diagnose, prevent, halt, or reverse multiple neurodegenerative diseases.


Assuntos
Proteínas Amiloidogênicas/química , Doenças Neurodegenerativas/patologia , Neurotoxinas/química , Engenharia de Proteínas/métodos , Sequência de Aminoácidos , Animais , Fenômenos Biomecânicos , Proteínas de Transporte/química , Proteínas de Transporte/genética , Clonagem Molecular , Humanos , Dados de Sequência Molecular , Nanotecnologia , Nefelometria e Turbidimetria , Doenças Neurodegenerativas/genética , Neurotoxinas/genética , Fatores de Terminação de Peptídeos/química , Fatores de Terminação de Peptídeos/genética , Plasmídeos/química , Plasmídeos/genética , Poliproteínas/química , Estabilidade Proteica , Estrutura Secundária de Proteína , Desdobramento de Proteína , Ratos , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Análise Espectral/métodos , Termodinâmica , Proteína 2 Associada à Membrana da Vesícula/química , Proteína 2 Associada à Membrana da Vesícula/genética , alfa-Sinucleína/química , alfa-Sinucleína/genética
16.
J Am Chem Soc ; 135(7): 2667-75, 2013 Feb 20.
Artigo em Inglês | MEDLINE | ID: mdl-23360551

RESUMO

The current surge in defining glycobiomarkers by applying lectins rekindles interest in definition of the sugar-binding sites of lectins at high resolution. Natural complex-type N-glycans can present more than one potential binding motif, posing the question of the actual mode of interaction when interpreting, for example, lectin array data. By strategically combining N-glycan preparation with saturation-transfer difference NMR and modeling, we illustrate that epitope recognition depends on the structural context of both the sugar and the lectin (here, wheat germ agglutinin and a single hevein domain) and cannot always be predicted from simplified model systems studied in the solid state. We also monitor branch-end substitutions by this strategy and describe a three-dimensional structure that accounts for the accommodation of the α2,6-sialylated terminus of a biantennary N-glycan by viscumin. In addition, we provide a structural explanation for the role of terminal α2,6-sialylation in precluding the interaction of natural N-glycans with lectin from Maackia amurensis . The approach described is thus capable of pinpointing lectin-binding motifs in natural N-glycans and providing detailed structural explanations for lectin selectivity.


Assuntos
Epitopos/química , Polissacarídeos/química , Peptídeos Catiônicos Antimicrobianos/química , Sítios de Ligação , Epitopos/metabolismo , Ligantes , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Lectinas de Plantas/química , Polissacarídeos/metabolismo
17.
J Biomol NMR ; 55(3): 231-7, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23314728

RESUMO

Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of (13)C(α), is proposed.


Assuntos
Ressonância Magnética Nuclear Biomolecular/métodos , Proteínas/química , Humanos , Conformação Proteica
18.
Arch Biochem Biophys ; 532(1): 39-45, 2013 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-23376038

RESUMO

Actinoporins are water-soluble proteins with the ability to form pores upon insertion into biological membranes. They constitute a family of proteins with high degree of sequence identities but different hemolytic activities, suggesting that minor conformational arrangements result in major functional changes. A good example of this situation is the sea anemone Stichodactyla helianthus which produces two very similar actinoporins, sticholysins I (StnI) and II (StnII), but of very different hemolytic efficiency. Within this idea, given that the high resolution three-dimensional structure of StnII is already known, we have now solved that one corresponding to StnI in order to analyze the influence of particular residues on the conformation and activity of these proteins. In addition, random mutagenesis has been also used to produce five less hemolytic variants of StnI. All these mutations map to functionally relevant regions because they are probably involved in conformational changes associated with pore formation, which take place after membrane binding, and involve long-distance rearrangements of the polypeptide chain of actinoporins.


Assuntos
Proteínas Citotóxicas Formadoras de Poros/química , Anêmonas-do-Mar/química , Sequência de Aminoácidos , Animais , Hemólise/efeitos dos fármacos , Modelos Moleculares , Dados de Sequência Molecular , Ressonância Magnética Nuclear Biomolecular , Compostos Orgânicos/química , Compostos Orgânicos/metabolismo , Fosfolipídeos/metabolismo , Mutação Puntual , Proteínas Citotóxicas Formadoras de Poros/genética , Proteínas Citotóxicas Formadoras de Poros/metabolismo , Conformação Proteica , Anêmonas-do-Mar/genética , Anêmonas-do-Mar/metabolismo , Alinhamento de Sequência , Ovinos
19.
Biochem J ; 441(1): 179-87, 2012 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-21861844

RESUMO

Gs (Geobacter sulfurreducens) can transfer electrons to the exterior of its cells, a property that makes it a preferential candidate for the development of biotechnological applications. Its genome encodes over 100 cytochromes and, despite their abundance and key functional roles, to date there is no structural information for these proteins in solution. The trihaem cytochrome PpcA might have a crucial role in the conversion of electronic energy into protonmotive force, a fundamental step for ATP synthesis in the presence of extracellular electron acceptors. In the present study, 15N-labelled PpcA was produced and NMR spectroscopy was used to determine its solution structure in the fully reduced state, its backbone dynamics and the pH-dependent conformational changes. The structure obtained is well defined, with an average pairwise rmsd (root mean square deviation) of 0.25 Å (1 Å=0.1 nm) for the backbone atoms and 0.99 Å for all heavy atoms, and constitutes the first solution structure of a Gs cytochrome. The redox-Bohr centre responsible for controlling the electron/proton transfer was identified, as well as the putative interacting regions between PpcA and its redox partners. The solution structure of PpcA will constitute the foundation for studies aimed at mapping out in detail these interacting regions.


Assuntos
Proteínas de Bactérias/metabolismo , Citocromos/metabolismo , Regulação Bacteriana da Expressão Gênica/fisiologia , Geobacter/metabolismo , Proteínas de Bactérias/genética , Citocromos/química , Citocromos/genética , Concentração de Íons de Hidrogênio , Modelos Moleculares , Oxirredução , Conformação Proteica
20.
Biochim Biophys Acta ; 1808(9): 2275-88, 2011 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-21621507

RESUMO

Actinoporins constitute a group of small and basic α-pore forming toxins produced by sea anemones. They display high sequence identity and appear as multigene families. They show a singular behaviour at the water-membrane interface: In aqueous solution, actinoporins remain stably folded but, upon interaction with lipid bilayers, become integral membrane structures. These membranes contain sphingomyelin, display phase coexistence, or both. The water soluble structures of the actinoporins equinatoxin II (EqtII) and sticholysin II (StnII) are known in detail. The crystalline structure of a fragaceatoxin C (FraC) nonamer has been also determined. The three proteins fold as a ß-sandwich motif flanked by two α-helices, one of them at the N-terminal end. Four regions seem to be especially important: A cluster of aromatic residues, a phosphocholine binding site, an array of basic amino acids, and the N-terminal α-helix. Initial binding of the soluble monomers to the membrane is accomplished by the cluster of aromatic amino acids, the array of basic residues, and the phosphocholine binding site. Then, the N-terminal α-helix detaches from the ß-sandwich, extends, and lies parallel to the membrane. Simultaneously, oligomerization occurs. Finally, the extended N-terminal α-helix penetrates the membrane to build a toroidal pore. This model has been however recently challenged by the cryo-EM reconstruction of FraC bound to phospholipid vesicles. Actinoporins structural fold appears across all eukaryotic kingdoms in other functionally unrelated proteins. Many of these proteins neither bind to lipid membranes nor induce cell lysis. Finally, studies focusing on the therapeutic potential of actinoporins also abound.


Assuntos
Porinas/química , Água/química , Sequência de Aminoácidos , Animais , Venenos de Cnidários/química , Venenos de Cnidários/metabolismo , Microscopia Crioeletrônica/métodos , Bicamadas Lipídicas/química , Membranas Artificiais , Conformação Molecular , Dados de Sequência Molecular , Fosfolipídeos/química , Dobramento de Proteína , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Anêmonas-do-Mar , Homologia de Sequência de Aminoácidos
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