RESUMO
Endogenous inhibitors of angiogenesis, such as thrombospondin-1 (TSP-1), are promising sources of therapeutic agents to treat angiogenesis-driven diseases, including cancer. TSP-1 regulates angiogenesis through different mechanisms, including binding and sequestration of the angiogenic factor fibroblast growth factor-2 (FGF-2), through a site located in the calcium binding type III repeats. We hypothesized that the FGF-2 binding sequence of TSP-1 might serve as a template for the development of inhibitors of angiogenesis. Using a peptide array approach followed by binding assays with synthetic peptides and recombinant proteins, we identified a FGF-2 binding sequence of TSP-1 in the 15-mer sequence DDDDDNDKIPDDRDN. Molecular dynamics simulations, taking the full flexibility of the ligand and receptor into account, and nuclear magnetic resonance identified the relevant residues and conformational determinants for the peptide-FGF interaction. This information was translated into a pharmacophore model used to screen the NCI2003 small molecule databases, leading to the identification of three small molecules that bound FGF-2 with affinity in the submicromolar range. The lead compounds inhibited FGF-2-induced endothelial cell proliferation in vitro and affected angiogenesis induced by FGF-2 in the chicken chorioallantoic membrane assay. These small molecules, therefore, represent promising leads for the development of antiangiogenic agents. Altogether, this study demonstrates that new biological insights obtained by integrated multidisciplinary approaches can be used to develop small molecule mimics of endogenous proteins as therapeutic agents.
Assuntos
Inibidores da Angiogênese/farmacologia , Fator 2 de Crescimento de Fibroblastos/antagonistas & inibidores , Trombospondina 1/fisiologia , Animais , Proliferação de Células , Galinhas , Membrana Corioalantoide/metabolismo , Córion/metabolismo , Humanos , Cinética , Espectroscopia de Ressonância Magnética , Peptídeos/química , Ligação Proteica , Conformação Proteica , Proteínas Recombinantes/química , Trombospondina 1/químicaRESUMO
Fibroblast growth factor-2 (FGF2) plays a major role in angiogenesis. The pattern recognition receptor long-pentraxin 3 (PTX3) inhibits the angiogenic activity of FGF2. To identify novel FGF2-antagonistic peptide(s), four acetylated (Ac) synthetic peptides overlapping the FGF2-binding region PTX3-(97-110) were assessed for their FGF2-binding capacity. Among them, the shortest pentapeptide Ac-ARPCA-NH(2) (PTX3-[100-104]) inhibits the interaction of FGF2 with PTX3 immobilized to a BIAcore sensorchip and suppresses FGF2-dependent proliferation in endothelial cells, without affecting the activity of unrelated mitogens. Also, Ac-ARPCA-NH(2) inhibits angiogenesis triggered by FGF2 or by tumorigenic FGF2-overexpressing murine endothelial cells in chick and zebrafish embryos, respectively. Accordingly, the peptide hampers the binding of FGF2 to Chinese Hamster ovary cells overexpressing the tyrosine-kinase FGF receptor-1 (FGFR1) and to recombinant FGFR1 immobilized to a BIAcore sensorchip without affecting heparin interaction. In all the assays the mutated Ac-ARPSA-NH(2) peptide was ineffective. In keeping with the observation that hydrophobic interactions dominate the interface between FGF2 and the FGF-binding domain of the Ig-like loop D2 of FGFR1, amino acid substitutions in Ac-ARPCA-NH(2) and saturation transfer difference-nuclear magnetic resonance analysis of its mode of interaction with FGF2 implicate the hydrophobic methyl groups of the pentapeptide in FGF2 binding. These results will provide the basis for the design of novel PTX3-derived anti-angiogenic FGF2 antagonists.
Assuntos
Proteína C-Reativa/química , Fator 2 de Crescimento de Fibroblastos/antagonistas & inibidores , Oligopeptídeos/farmacologia , Componente Amiloide P Sérico/química , Sequência de Aminoácidos , Inibidores da Angiogênese/farmacologia , Animais , Sítios de Ligação/genética , Proteína C-Reativa/metabolismo , Células CHO , Proliferação de Células/efeitos dos fármacos , Transplante de Células/métodos , Embrião de Galinha , Cricetinae , Cricetulus , Células Endoteliais/metabolismo , Células Endoteliais/transplante , Feminino , Fator 2 de Crescimento de Fibroblastos/genética , Fator 2 de Crescimento de Fibroblastos/metabolismo , Humanos , Espectroscopia de Ressonância Magnética , Masculino , Neovascularização Fisiológica/efeitos dos fármacos , Oligopeptídeos/metabolismo , Ligação Proteica/efeitos dos fármacos , Receptor Tipo 1 de Fator de Crescimento de Fibroblastos/metabolismo , Componente Amiloide P Sérico/metabolismo , Transplante Heterólogo , Peixe-ZebraRESUMO
A nuclear magnetic resonance (NMR) method was implemented to assess in vivo oxygenation levels by a quantitative determination of the 1H NMR myoglobin (Mb) resonances. The proximal His-F8 NdeltaH at 70-90 ppm and Val-E11 gammaCH3 resonance at -2.8 ppm, reflecting deoxygenated (deoxy-Mb) and oxygenated (met-Mb) states, were alternately recorded. The method was developed in vitro choosing a couple of NMR sequences that could each maximize the signal-to-noise ratio (SNR) while avoiding baseline rolling and suppressing the water signal. Two quantitative calibration methods were implemented for deoxy- and met-Mb samples (0.1-1 mM), respectively. The respective limit of detection (LOD) and limit of quantification (LOQ) were 0.015 and 0.05 mM for met-Mb and 0.013 and 0.042 mM for deoxy-Mb. Sequences and calibration curves were employed in vivo in Arenicola marina to obtain, for the first time, an accurate measurement of oxy- and deoxy-Mb actual concentrations. In Arenicola, the peaks at approximately 87 and -2.7 ppm, reflecting the deoxy- and oxy-Mb states, respectively, were alternately recorded during increasing hypoxia. The deoxy-Mb concentrations were obtained from the calibration curve. The oxy-Mb concentrations were calculated from the calibration of met-Mb because it was proved that oxy- and met-Mb gave the same NMR molar response. From oxy- and deoxy-Mb concentrations, the intracellular oxygen partial pressure (PiO2) trend was determined.
Assuntos
Músculo Esquelético/metabolismo , Mioglobina/química , Ressonância Magnética Nuclear Biomolecular/métodos , Consumo de Oxigênio/fisiologia , Animais , Respiração Celular , Hipóxia , Mioglobina/metabolismo , Poliquetos/metabolismoRESUMO
Full-length CXCL4 chemokine and a peptide derived from its carboxyl-terminal domain exhibits significant antiangiogenic and anti-tumor activity in vivo and in vitro by interacting with fibroblast growth factor (FGF). In this study we used NMR spectroscopy to characterize at a molecular level the interactions between CXCL4 (47-70) and FGF-2 identifying the peptide residues mainly involved in the contact area with the growth factor. Altogether NMR data point to a major role of the hydrophobic contributions of the C-terminal region of CXCL4 (47-70) peptide in addition to specific contacts established by the N-terminal region through cysteine side chain. The proposed recognition mode constitutes a rationale for the observed effects of CXCL4 (47-70) on FGF-2 biological activity and lays the basis for developing novel inhibitors of angiogenesis.
Assuntos
Fator 2 de Crescimento de Fibroblastos/metabolismo , Fator Plaquetário 4/metabolismo , Sequência de Aminoácidos , Cisteína/química , Cisteína/genética , Cisteína/metabolismo , Fator 2 de Crescimento de Fibroblastos/química , Fator 2 de Crescimento de Fibroblastos/genética , Humanos , Ressonância Magnética Nuclear Biomolecular , Peptídeos/química , Peptídeos/genética , Peptídeos/metabolismo , Fator Plaquetário 4/química , Fator Plaquetário 4/genética , Mapeamento de Interação de Proteínas , Estrutura Terciária de ProteínaRESUMO
Understanding how proteins are approached by surrounding molecules is fundamental to increase our knowledge of life at atomic resolution. Here, the surface accessibility of a multifunctional small protein, the archaeal protein Sso7d from Sulfolobus solfataricus, has been investigated by using TEMPOL and Gd(III)(DTPA-BMA) as paramagnetic probes. The DNA binding domain of Sso7d appears very accessible both to TEMPOL and Gd(III)(DTPA-BMA). Differences in paramagnetic attenuation profiles of (1)H-(15)N HSQC protein backbone amide correlations, observed in the presence of the latter paramagnetic probes, are consistent with the hydrogen bond acceptor capability of the N-oxyl moiety of TEMPOL to surface exposed Sso7d amide groups. By using the gadolinium complex as a paramagnetic probe a better agreement between Sso7d structural features and attenuation profile is achieved. It is interesting to note that the protein P-loop region, in spite of the high surface exposure predicted by the available protein structures, is not approached by TEMPOL and only partially by Gd(III)(DTPA-BMA).
Assuntos
Proteínas Arqueais/química , Óxidos N-Cíclicos/química , Proteínas de Ligação a DNA/química , Gadolínio DTPA/química , Ressonância Magnética Nuclear Biomolecular/métodos , Amidas/química , Sequência de Aminoácidos , Ligação de Hidrogênio , Modelos Moleculares , Isótopos de Nitrogênio/química , Prótons , Marcadores de Spin , Propriedades de SuperfícieRESUMO
Chicken liver bile acid binding protein (cL-BABP) is involved in bile acid transport in the liver cytosol. A detailed study of the mechanism of binding and selectivity of bile acids binding proteins towards the physiological pool of bile salts is a key issue for the complete understanding of the role of these proteins and their involvement in cholesterol homeostasis. In the present study, we modeled the ternary complex of cL-BABP with two molecules of bile salts using the data driven docking program HADDOCK on the basis of NMR and mass spectrometry data. Docking resulted in good 3D models, satisfying the majority of experimental restraints. The docking procedure represents a necessary step to help in the structure determination and in functional analysis of such systems, in view of the high complexity of the 3D structure determination of a ternary complex with two identical ligands. HADDOCK models show that residues involved in binding are mainly located in the C-terminal end of the protein, with two loops, CD and EF, playing a major role in ligand binding. A spine, comprising polarresidues pointing toward the protein interior and involved in motion communication, has a prominent role in ligand interaction. The modeling approach has been complemented with NMR interaction and competition studies of cL-BABP with chenodeoxycholic and cholic acids. A higher affinity for chenodeoxycholic acid was observed and a Kd upper limit estimate was obtained. The binding is highly cooperative and no site selectivity was detected for the different bile salts, thus indicating that site selectivity and cooperativity are not correlated. Differences in physiological pathways and bile salt pools in different species is discussed in light of the binding results thus enlarging the body of knowledge of BABPs biological functions.
Assuntos
Ácidos e Sais Biliares/metabolismo , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Glicoproteínas de Membrana/química , Glicoproteínas de Membrana/metabolismo , Sequência de Aminoácidos , Animais , Ácidos e Sais Biliares/química , Galinhas , Íleo/metabolismo , Processamento de Imagem Assistida por Computador/métodos , Fígado , Espectrometria de Massas/métodos , Modelos Moleculares , Dados de Sequência Molecular , Ressonância Magnética Nuclear Biomolecular/métodos , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismoRESUMO
By combining NMR relaxation spectroscopy and magnetic resonance imaging techniques, unsalted (us) and salted (s) caviar (Acipenser transmontanus) oocytes were characterized over a storage period of up to 90 days. The aging and the salting effects on the two major cell constituents, water and lipids, were separately assessed. T1 and T2 decays were interpreted by assuming a two-site exchange model. At Day 0, two water compartments that were not in fast exchange were identified by the T1 relaxation measurements on the us oocytes. In the s samples, T1 decay was monoexponential. During the time of storage, an increment of the free water amount was found for the us oocytes, ascribed to an increased metabolism. T1 and T2 of the s oocytes shortened as a consequence of the osmotic stress produced by salting. Selective images showed the presence of water endowed with different regional mobility that severely changed during the storage. Lipid T1 relaxation decays collected on us and s samples were found to be biexponential, and the T1 values lengthened during storage. In us and s oocytes, the increased lipid mobility with the storage was ascribed to lipolysis. Selective images of us samples showed lipids that were confined to the cytoplasm for up to 60 days of storage.
Assuntos
Peixes/anatomia & histologia , Peixes/metabolismo , Oócitos/citologia , Oócitos/metabolismo , Animais , Senescência Celular , Feminino , Técnicas In Vitro , Metabolismo dos Lipídeos , Imageamento por Ressonância Magnética , Espectroscopia de Ressonância Magnética , Microscopia Eletrônica de Varredura , Pressão Osmótica , Cloreto de Sódio , Água/metabolismoRESUMO
The effects of storage at 4 degrees C on the quantity and quality of chemical components in the caviar from farmed Acipenser transmontanus have been analyzed by SEM, chemical methods, and NMR and MRI techniques. Particular attention has been focused on the lipid components, the distribution and mobility of which were strongly affected by the storage time. MRI and relaxation data indicated that lipids are endowed with two different mobility regimes, one slow (short T1) and one fast (long T1), both lengthening with the storage time. Chemical analysis assessed a total fat content that remained practically unchanged and a constant fatty acid composition during the total storage time. The combination of the two methods allowed one (a) to suppose that a mechanism of lipid hydrolysis (faster in unsalted than in salted eggs) is still occurring during storage of caviar at 4 degrees C for up to approximately 4 months and (b) to exclude that an intensive oxidative process is active in the same storage period.
Assuntos
Peixes , Conservação de Alimentos , Óvulo/química , Óvulo/ultraestrutura , Animais , Ácidos Graxos/análise , Feminino , Imageamento por Ressonância Magnética , Espectroscopia de Ressonância Magnética , Microscopia Eletrônica de VarreduraRESUMO
The temperature (T)-dependence of energy consumption of resting anaerobic frog gastrocnemii exposed to different, changing electrochemical gradients was assessed. To this aim, the rate of ATP resynthesis (delta approximately P/deltat) was determined by (31)P- and (1)H-MRS as the sum of the rates of PCr hydrolysis (delta[PCr]/deltat) and of anaerobic glycolysis (delta[La]/ deltat, based on a approximately P/La ratio of 1.5). The investigated T levels were 15, 20 and 25 degrees C, whereas initial extracellular pH (pHe) values were 7.9, 7.3 and 7.0, i.e. higher, equal or lower, respectively, than intracellular pH (pHi). The latter was changing with T according to the neutrality point (dpH/dT=-0.0165 pH units/ degrees C). Both rates of PCr hydrolysis and of lactate accumulation and that of their sum, expressed as delta approximately P/deltat, were highly T-dependent. By contrast, the pHe-dependence of the muscle energy balance was nil or extremely limited at 15 and 20 degrees C, respectively, but remarkable at 25 degrees C (with a depression of the ATP resynthesis rate up to 25% with a decrease of pHe from 7.9 to 7.0). The pHe-dependent reduction of metabolic rate was associated with a down-regulation of anaerobic glycolysis due to reduced activity of ion-transporters controlling acid-base balance and/or to a shift from Na(+)/H(+) to a more efficient Na(+)-dependent Cl(-)/HCO(3)(-) exchanger. Uncoupling of glycogenolysis from P-metabolite concentrations, both as function of T (>or=20 degrees C) and of pHe (Assuntos
Espectroscopia de Ressonância Magnética/métodos
, Músculo Esquelético/metabolismo
, Trifosfato de Adenosina/biossíntese
, Anaerobiose
, Animais
, Anuros
, Metabolismo Energético
, Concentração de Íons de Hidrogênio
, Técnicas In Vitro
, Ácido Láctico/metabolismo
, Fibras Musculares Esqueléticas/química
, Fibras Musculares Esqueléticas/metabolismo
, Músculo Esquelético/química
, Fosfatos/química
, Fosfatos/metabolismo
, Fosfocreatina/metabolismo
, Força Próton-Motriz
, Temperatura
Assuntos
Proteínas Arqueais/química , Proteínas de Ligação a DNA/química , Mutação Puntual , Termodinâmica , Substituição de Aminoácidos , Aminoácidos/química , Aminoácidos/genética , Aminoácidos/metabolismo , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Dicroísmo Circular , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Espectroscopia de Ressonância Magnética , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Dobramento de Proteína , Estrutura Secundária de Proteína , Eletricidade Estática , Homologia Estrutural de Proteína , Relação Estrutura-Atividade , Temperatura de TransiçãoRESUMO
Fibroblast growth factors (FGFs) are recognized targets for the development of therapies against angiogenesis-driven diseases, including cancer. The formation of a ternary complex with the transmembrane tyrosine kinase receptors (FGFRs), and heparan sulphate proteoglycans (HSPGs) is required for FGF2 pro-angiogenic activity. Here by using a combination of techniques including Nuclear Magnetic Resonance, Molecular Dynamics, Surface Plasmon Resonance and cell-based binding assays we clarify the molecular mechanism of inhibition of an angiostatic small molecule, sm27, mimicking the endogenous inhibitor of angiogenesis, thrombospondin-1. NMR and MD data demonstrate that sm27 engages the heparin-binding site of FGF2 and induces long-range dynamics perturbations along FGF2/FGFR1 interface regions. The functional consequence of the inhibitor binding is an impaired FGF2 interaction with both its receptors, as demonstrated by SPR and cell-based binding assays. We propose that sm27 antiangiogenic activity is based on a twofold-direct and allosteric-mechanism, inhibiting FGF2 binding to both its receptors.
Assuntos
Inibidores da Angiogênese/farmacologia , Fator 2 de Crescimento de Fibroblastos/antagonistas & inibidores , Fator 2 de Crescimento de Fibroblastos/química , Proteoglicanas de Heparan Sulfato/antagonistas & inibidores , Proteoglicanas de Heparan Sulfato/química , Receptor Tipo 1 de Fator de Crescimento de Fibroblastos/antagonistas & inibidores , Receptor Tipo 1 de Fator de Crescimento de Fibroblastos/química , Regulação Alostérica/efeitos dos fármacos , Inibidores da Angiogênese/química , Humanos , Técnicas In Vitro , Modelos Moleculares , Simulação de Dinâmica Molecular , Mimetismo Molecular , Complexos Multiproteicos/antagonistas & inibidores , Complexos Multiproteicos/química , Naftalenossulfonatos/química , Naftalenossulfonatos/farmacologia , Ressonância Magnética Nuclear Biomolecular , Mapeamento de Interação de Proteínas , Ressonância de Plasmônio de Superfície , Trombospondina 1/química , Trombospondina 1/farmacologiaRESUMO
Heat shock protein 90 (Hsp90) is a prime target for antitumor therapies. The information obtained by molecular dynamics (MD) simulations is combined with NMR data to provide a cross-validated atomic resolution model of the complementary interactions of heat shock protein 90 with a peptidic (shepherdin) and a non-peptidic (5-aminoimidazole-4-carboxamide-1-ß-d-ribofuranoside, AICAR) inhibitor, showing antiproliferative and proapoptotic activity in multiple tumor cell lines. This approach highlights the relevant role of imidazolic moiety in the interaction of both antagonist molecules. In 5-aminoimidazole-4-carboxamide-1-ß-d-ribofuranoside bound state, one conformation of those present in solution is selected, where imidazolic, H4 and H5 protons have a key role in defining a non-polar region contacting heat shock protein 90 surface. The dynamic equilibrium between N-type and S-type puckered forms of 5-aminoimidazole-4-carboxamide-1-ß-d-ribofuranoside moiety is shown to be functional to inhibitor binding. The first experimental structural data on these inhibitors are presented and discussed as hints for future design of improved molecules.
Assuntos
Aminoimidazol Carboxamida/análogos & derivados , Proteínas de Choque Térmico HSP90/antagonistas & inibidores , Peptídeos/química , Ribonucleotídeos/química , Aminoimidazol Carboxamida/química , Aminoimidazol Carboxamida/farmacologia , Sítios de Ligação , Linhagem Celular Tumoral , Desenho de Fármacos , Proteínas de Choque Térmico HSP90/metabolismo , Humanos , Espectroscopia de Ressonância Magnética , Simulação de Dinâmica Molecular , Peptídeos/farmacologia , Ligação Proteica , Estrutura Terciária de Proteína , Ribonucleotídeos/farmacologiaRESUMO
Bile acid-binding proteins (BABPs) are cytosolic lipid chaperones that play central roles in driving bile flow, as well as in the adaptation to various pathological conditions, contributing to the maintenance of bile acid homeostasis and functional distribution within the cell. Understanding the mode of binding of bile acids with their cytoplasmic transporters is a key issue in providing a model for the mechanism of their transfer from the cytoplasm to the nucleus, for delivery to nuclear receptors. A number of factors have been shown to modulate bile salt selectivity, stoichiometry, and affinity of binding to BABPs, e.g. chemistry of the ligand, protein plasticity and, possibly, the formation of disulfide bridges. Here, the effects of the presence of a naturally occurring disulfide bridge on liver BABP ligand-binding properties and backbone dynamics have been investigated by NMR. Interestingly, the disulfide bridge does not modify the protein-binding stoichiometry, but has a key role in modulating recognition at both sites, inducing site selectivity for glycocholic and glycochenodeoxycholic acid. Protein conformational changes following the introduction of a disulfide bridge are small and located around the inner binding site, whereas significant changes in backbone motions are observed for several residues distributed over the entire protein, both in the apo form and in the holo form. Site selectivity appears, therefore, to be dependent on protein mobility rather than being governed by steric factors. The detected properties further establish a parallelism with the behaviour of human ileal BABP, substantiating the proposal that BABPs have parallel functions in hepatocytes and enterocytes.
Assuntos
Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Dissulfetos/química , Fígado/metabolismo , Glicoproteínas de Membrana/química , Glicoproteínas de Membrana/metabolismo , Sítios de Ligação , Proteínas de Transporte/genética , Humanos , Espectroscopia de Ressonância Magnética , Glicoproteínas de Membrana/genética , Estrutura Secundária de ProteínaRESUMO
Bile acids are physiological detergents facilitating absorption, transport, and distribution of lipid-soluble vitamins and dietary fats;they also play a role as signaling molecules that activate nuclear receptors and regulate cholesterol metabolism. Bile acid circulation is mediated by bile acid binding proteins (BABPs), and a detailed structural study of the complex of BABPs with bile salts has become a key issue for the complete understanding of the role of these proteins and their involvement in cholesterol homeostasis. The solution structure here reported describes, at variance with previously determined singly ligated structures, a BABP in a ternary complex with two bile acid molecules, obtained by employing a variety of NMR experiments. Exchange processes between the two bound chenodeoxycholate molecules as well as the more superficial ligand and the free pool have been detected through ROESY and diffusion experiments. Significant backbone flexibility has been observed in regions located at the protein open end, facilitating bile salts exchange. A detailed description of the protonation states and tautomeric forms of histidines strongly supports the view that histidine protonation modulates backbone flexibility and regulates ligand binding. This structure opens the way to targeted site-directed mutagenesis and interaction studies to investigate both binding and nuclear localization mechanisms.
Assuntos
Ácidos e Sais Biliares/metabolismo , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Ligantes , Glicoproteínas de Membrana/química , Glicoproteínas de Membrana/metabolismo , Ressonância Magnética Nuclear Biomolecular , Animais , Ácidos e Sais Biliares/química , Ácido Quenodesoxicólico/química , Ácido Quenodesoxicólico/metabolismo , Galinhas , Fígado/metabolismo , Modelos Moleculares , Complexos Multiproteicos/química , Ligação Proteica , Estrutura Terciária de ProteínaRESUMO
Apo chicken liver bile acid-binding protein has been structurally characterized by NMR. The dynamic behavior of the protein in its apo- and holo-forms, complexed with chenodeoxycholate, has been determined via (15)N relaxation and steady state heteronuclear (15)N((1)H) nuclear Overhauser effect measurements. The dynamic parameters were obtained at two pH values (5.6 and 7.0) for the apoprotein and at pH 7.0 for the holoprotein, using the model free approach. Relaxation studies, performed at three different magnetic fields, revealed a substantial conformational flexibility on the microsecond to millisecond time scales, mainly localized in the C-terminal face of the beta-barrel. The observed dynamics are primarily caused by the protonation/deprotonation of a buried histidine residue, His(98), located on this flexible face. A network of polar buried side chains, defining a spine going from the E to J strand, is likely to provide the long range connectivity needed to communicate motion from His(98) to the EF loop region. NMR data are accompanied by molecular dynamics simulations, suggesting that His(98) protonation equilibrium is the triggering event for the modulation of a functionally important motion, i.e. the opening/closing at the protein open end, whereas ligand binding stabilizes one of the preexisting conformations (the open form). The results presented here, complemented with an analysis of proteins belonging to the intracellular lipid-binding protein family, are consistent with a model of allosteric activation governing the binding mechanism. The functional role of this mechanism is thoroughly discussed within the framework of the mechanism for the enterohepatic circulation of bile acids.
Assuntos
Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Glicoproteínas de Membrana/química , Glicoproteínas de Membrana/metabolismo , Ligação Proteica , Regulação Alostérica , Sequência de Aminoácidos , Animais , Apolipoproteínas/química , Apolipoproteínas/metabolismo , Ácidos e Sais Biliares/metabolismo , Sítios de Ligação , Galinhas , Ligantes , Fígado/enzimologia , Dados de Sequência Molecular , Ressonância Magnética Nuclear Biomolecular , Conformação ProteicaRESUMO
Environmental stress, such as low temperature, extracellular acidosis and anoxia, is known to play a key role in metabolic regulation. The aim of the present study was to gain insight into the combined temperature-pH regulation of metabolic rate in frog muscle, i.e. an anoxia-tolerant tissue. The rate of exergonic metabolic processes occurring in resting isolated muscles was determined at 15 degrees C and 25 degrees C as well as at extracellular pH values higher (7.9), similar (7.3) and lower (7.0) than the physiological intracellular pH. (31)P and (1)H nuclear magnetic resonance spectroscopy high-resolution measurements were carried out at 4.7 T in isolated frog (Rana esculenta) gastrocnemius muscle during anoxia to assess, by means of reference compounds, the concentration of all phosphate metabolites and lactate. Intra- and extracellular pH was also determined. In the range of examined temperatures (15-25 degrees C), the temperature dependence of anaerobic glycolysis was found to be higher than that of PCr depletion (Q(10)=2.3). High-energy phosphate metabolism was confirmed to be the initial and preferential energy source. The rate of phosphocreatine hydrolysis did not appear to be affected by extracellular pH changes. By contrast, independent of the intracellular pH value, at the higher temperature (25 degrees C) a lowering of the extracellular pH from 7.9 to 7.0 caused a depression in lactate accumulation. This mechanism was ascribed to the transmembrane proton concentration gradient. This parameter was demonstrated to regulate glycolysis, probably through a reduced lactate efflux, depending on the activity of the lactate-H(+) co-transporter. The calculated intracellular buffer capacity was related to intra- and extracellular pH and temperature. At the experimental extracellular pH of 7.9 and at a temperature of 15 degrees C and 25 degrees C, calculated intracellular buffering capacity was 29.50 micromol g(-1) pH unit(-1) and 69.98 micromol g(-1) pH unit(-1), respectively.
Assuntos
Metabolismo Energético/fisiologia , Hipóxia/fisiopatologia , Músculo Esquelético/fisiologia , Rana esculenta/fisiologia , Temperatura , Animais , Glicólise/fisiologia , Hidrogênio , Concentração de Íons de Hidrogênio , Ácido Láctico , Espectroscopia de Ressonância Magnética , Fosfatos/metabolismo , Isótopos de FósforoRESUMO
Chicken liver basic fatty acid binding protein (Lb-FABP) belongs to the basic-type fatty acid binding proteins, a novel group of proteins isolated from liver of different non mammalian species whose structure is not known. The structure of Lb-FABP has been solved by (1)H NMR. The overall fold of Lb-FABP, common to the other proteins of the family, consists of ten antiparallel beta-strands organised in two nearly ortogonal beta-sheets with two alpha helices closing the protein cavity where small hydrophobic ligands can be bound. The binding specificity of the protein is not known, however, based on the high sequence and structural similarity with an orthologous protein, ileal lipid binding protein, it is suggested that bile acids may be the putative ligands.
Assuntos
Proteínas de Transporte/química , Fígado/metabolismo , Proteínas de Neoplasias , Sequência de Aminoácidos , Animais , Proteínas de Transporte/metabolismo , Galinhas , Proteínas de Ligação a Ácido Graxo , Ácidos Graxos/metabolismo , Espectroscopia de Ressonância Magnética/métodos , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Secundária de Proteína , SoluçõesRESUMO
Beta-lactoglobulins, belonging to the lipocalin family, are a widely studied group of proteins, characterized by the ability to solubilize and transport hydrophobic ligands, especially fatty acids. Despite many reports, the mechanism of ligand binding and the functional role of these proteins is still unclear, and many contradicting concepts are often encountered in the literature. In the present paper the comparative analysis of the binding properties of beta-lactoglobulins has been performed using sequence-derived information, structure-based electrostatic calculations, docking simulations, and NMR experiments. Our results reveal for the first time the mechanism of beta-lactoglobulin ligand binding, which is completely determined by the opening-closing of EF loop, triggered by Glu89 protonation. The alkaline shift observed for Glu89 pKa in porcine beta-lactoglobulin (pKa 9.7) with respect to the bovine species (pKa 5.5) depends upon the interplay of electrostatic effects of few nearby key residues. Porcine protein is therefore able to bind fatty acids provided that the appropriate pH solution conditions are met (pH > 8.6), where the EF loop conformational change can take place. The unusually high pH of binding detected for porcine beta-lactoglobulin seems to be functional to lipases activity. Theoretical pKa calculations extended to representative beta-lactoglobulins allowed the identification of key residues involved in structurally and functionally important electrostatic interactions. The results presented here provide a strong indication that the described conformational change is a common feature of all beta-lactoglobulins.
Assuntos
Lactoglobulinas/química , Sequência de Aminoácidos , Animais , Bovinos , Ácidos Graxos/química , Concentração de Íons de Hidrogênio , Cinética , Lactoglobulinas/metabolismo , Ligantes , Lisina/química , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Dados de Sequência Molecular , Filogenia , Ligação Proteica , Conformação Proteica , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , SuínosRESUMO
In an attempt to characterize the early folding events in bovine beta-lactoglobulin (BLG), a set of peptides, covering the flexible N-terminal region and the stable C-terminus beta-core, was synthesized and analyzed by circular dichroism and by nuclear magnetic resonance in water, trifluoroethanol (TFE), and sodium dodecyl sulfate (SDS) below and above the critical micellar concentration. The role of local and long-range hydrophobic interactions in guiding the folding has been investigated. For the peptide fragment covering the more flexible N-terminal region of BLG (beta-strands A, B), where both theoretical predictions and kinetic refolding experiments suggested the formation of non-native alpha-helix, no native long-range contacts were identified, and a helical secondary structure was stabilized only in the presence of 25 mM SDS. At variance, in 50% (v/v) TFE, native, long-range hydrophobic interactions were observed in the peptide covering the core region comprising G and H beta-strands. The side chains involved in these interactions form a nativelike hydrophobic cluster, thus suggesting that the GH region may act as the folding initiation site for BLG. This result is reinforced by the identification, in the urea denaturated BLG, of residual structure located at the level of the GH interface, as evidenced by NMR analysis. These results, in excellent agreement with kinetic, thermodynamic, and cold denaturation folding data, once more underline the utmost importance of the GH region for the stability and folding of BLG. Severe aggregation effects prevented the structural analysis of the peptide covering the EFGH region, indicating that this larger segment does not represent an independent folding domain and that the terminal alpha-helix is necessary for stabilizing the BLG folding core.
Assuntos
Lactoglobulinas/química , Modelos Químicos , Peptídeos/química , Dobramento de Proteína , Sequência de Aminoácidos , Animais , Bovinos , Dicroísmo Circular , Dados de Sequência Molecular , Ressonância Magnética Nuclear Biomolecular , Espectrofotometria Ultravioleta , Ureia/químicaRESUMO
Sso7d is a small basic protein consisting of 62 amino acids isolated from the thermoacidophilic archeobacterium Sulfolobus solfataricus. The protein is endowed with DNA binding properties, RNase activity, and the capability of rescuing aggregated proteins in the presence of ATP. In this study, the electrostatic properties of Sso7d are investigated by using the Poisson-Boltzmann calculation of the surface potential distribution and following by NMR spectroscopy the proton chemical shift pH titration of acidic residues. Although the details of the catalytic mechanism still have to be defined, the results from NMR experiments confirm the possible involvement of Glu35 as the proton acceptor in the catalytic reaction, as seen by its abnormally high pK(a) value. Poisson-Boltzmann calculations and NMR titration shifts suggest the presence of a possible hydrogen bond between Glu35 and Tyr33, with a consequent rather rigid arrangement at these positions. Comparison with RNase T1 suggests that Tyr7 may be a good candidate for acting as a proton donor in the active site of Sso7d as shown by its low phenolic pK(a) of approximately 9.3. Titration experiments performed with the UpA, a RNA dinucleotide model, showed that the protein residues affected by the interaction are mainly located in a different region with respect to the surface affected by DNA recognition, in good agreement with the surface potential distribution found with electrostatic calculations.