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1.
Methods Mol Biol ; 2247: 125-143, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33301115

RESUMO

Interactions between protein complexes and DNA are central regulators of the cell life. They control the activation and inactivation of a large set of nuclear processes including transcription, replication, recombination, repair, and chromosome structures. In the literature, protein-DNA interactions are characterized by highly complementary approaches including large-scale studies and analyses in cells. Biophysical approaches with purified materials help to evaluate if these interactions are direct or not. They provide quantitative information on the strength and specificity of the interactions between proteins or protein complexes and their DNA substrates. Isothermal titration calorimetry (ITC) and microscale thermophoresis (MST) are widely used and are complementary methods to characterize nucleo-protein complexes and quantitatively measure protein-DNA interactions. We present here protocols to analyze the interactions between a DNA repair complex, Ku70-Ku80 (Ku) (154 kDa), and DNA substrates. ITC is a label-free method performed with both partners in solution. It serves to determine the dissociation constant (Kd), the enthalpy (ΔH), and the stoichiometry N of an interaction. MST is used to measure the Kd between the protein or the DNA labeled with a fluorescent probe. We report the data obtained on Ku-DNA interactions with ITC and MST and discuss advantages and drawbacks of both the methods.


Assuntos
Proteínas de Ligação a DNA/química , DNA/química , Substâncias Macromoleculares/química , Fenômenos Bioquímicos , Calorimetria , DNA/genética , DNA/metabolismo , Proteínas de Ligação a DNA/metabolismo , Modelos Moleculares , Conformação Molecular , Ligação Proteica , Relação Estrutura-Atividade , Termodinâmica
2.
J Med Chem ; 63(18): 10330-10338, 2020 09 24.
Artigo em Inglês | MEDLINE | ID: mdl-32866001

RESUMO

The protein FKBP52 is a steroid hormone receptor coactivator likely involved in neurodegenerative disease. A series of small, water-soluble, bioinspired, pseudopeptidic fluorescent ligands for the FK1 domain of this protein are described. The design is such that engulfing of the ligand in the pocket of this domain is accompanied by hydrogen-bonding of the dansyl chromophore which functions as both an integral part of the ligand and a fluorescent reporter. Binding is concomitant with a significant wavelength shift and an enhancement of the ligand fluorescence signal. Excitation of FK1 domain native tryptophan residues in the presence of bound ligand results in Förster resonance energy transfer. Variation of key ligand residues within the short sequence was undertaken, and the interaction of the resulting library with the protein was measured by techniques including isothermal calorimetry analysis, fluorescence, and FRET quenching, and a range of Kd values were determined. Cocrystallization of a protein ligand complex at 2.30 Å resolution provided detailed information at the atomic scale, while also providing insight into native substrate binding.


Assuntos
Corantes Fluorescentes/metabolismo , Oligopeptídeos/metabolismo , Proteínas de Ligação a Tacrolimo/metabolismo , Transferência Ressonante de Energia de Fluorescência , Corantes Fluorescentes/síntese química , Humanos , Ligantes , Oligopeptídeos/síntese química , Ligação Proteica , Domínios Proteicos , Proteínas de Ligação a Tacrolimo/química
3.
Sci Rep ; 9(1): 1178, 2019 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-30718544

RESUMO

Artificial proteins binding any predefined "target" protein can now be efficiently generated using combinatorial libraries based on robust protein scaffolds. αRep is such a family of artificial proteins, based on an α-solenoid protein repeat scaffold. The low aggregation propensity of the specific "binders" generated from this library opens new protein engineering opportunities such as the creation of biosensors within multidomain constructions. Here, we have explored the properties of two new types of artificial bidomain proteins based on αRep structures. Their structural and functional properties are characterized in detail using biophysical methods. The results clearly show that both bidomain proteins adopt a closed bivalve shell-like conformation, in the ligand free form. However, the presence of ligands induces a conformational transition, and the proteins adopt an open form in which each domain can bind its cognate protein partner. The open/closed equilibria alter the affinities of each domain and induce new cooperative effects. The binding-induced relative domain motion was monitored by FRET. Crystal structures of the chimeric proteins indicate that the conformation of each constituting domain is conserved but that their mutual interactions explain the emergent properties of these artificial bidomain proteins. The ligand-induced structural transition observed in these bidomain proteins should be transferable to other αRep proteins with different specificity and could provide the basis of a new generic biosensor design.


Assuntos
Conformação Proteica/efeitos dos fármacos , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Técnicas de Transferência de Energia por Ressonância de Bioluminescência , Fenômenos Biofísicos , Cristalografia por Raios X , Ligantes , Ligação Proteica , Proteínas Recombinantes/genética
4.
Biochim Biophys Acta Proteins Proteom ; 1866(2): 348-355, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29101077

RESUMO

Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 PDF specific activity to values similar to those of bacterial PDFs. We next show that Vp16 PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness.


Assuntos
Amidoidrolases/química , Bacteriófagos/enzimologia , Vibrio parahaemolyticus/virologia , Proteínas Virais/química , Amidoidrolases/genética , Bacteriófagos/genética , Domínio Catalítico , Estabilidade Enzimática , Vibrio parahaemolyticus/genética , Proteínas Virais/genética
5.
Biochem Soc Trans ; 43(5): 819-24, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26517888

RESUMO

We have designed a new family of artificial proteins, named αRep, based on HEAT (acronym for Huntingtin, elongation factor 3 (EF3), protein pphosphatase 2A (PP2A), yeast kinase Tor1) repeat proteins containing an α-helical repeated motif. The sequence of the repeated motifs, first identified in a thermostable archae protein was optimized using a consensus design strategy and used for the construction of a library of artificial proteins. All proteins from this library share the same general fold but differ both in the number of repeats and in five highly randomized amino acid positions within each repeat. The randomized side chains altogether provide a hypervariable surface on αRep variants. Sequences from this library are efficiently expressed as soluble, folded and very stable proteins. αRep binders with high affinity for various protein targets were selected by phage display. Low micromolar to nanomolar dissociation constants between partners were measured and the structures of several complexes (specific αRep/protein target) were solved by X-ray crystallography. Using GFP as a model target, it was demonstrated that αReps can be used as bait in pull-down experiments. αReps can be expressed in eukaryotic cells and specifically interact with their target addressed to different cell compartments.


Assuntos
Cristalização/métodos , Técnicas de Silenciamento de Genes , Modelos Moleculares , Engenharia de Proteínas , Proteínas Recombinantes de Fusão/química , Sequências Repetitivas de Aminoácidos , Animais , Sítios de Ligação , Linhagem Celular , Sequência Consenso , Biblioteca Gênica , Humanos , Biblioteca de Peptídeos , Conformação Proteica , Dobramento de Proteína , Estabilidade Proteica , Estrutura Secundária de Proteína , Proteínas Recombinantes de Fusão/metabolismo
6.
Biosci Rep ; 35(4)2015 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-26182430

RESUMO

A family of artificial proteins, named αRep, based on a natural family of helical repeat was previously designed. αRep members are efficiently expressed, folded and extremely stable proteins. A large αRep library was constructed creating proteins with a randomized interaction surface. In the present study, we show that the αRep library is an efficient source of tailor-made specific proteins with direct applications in biochemistry and cell biology. From this library, we selected by phage display αRep binders with nanomolar dissociation constants against the GFP. The structures of two independent αRep binders in complex with the GFP target were solved by X-ray crystallography revealing two totally different binding modes. The affinity of the selected αReps for GFP proved sufficient for practically useful applications such as pull-down experiments. αReps are disulfide free proteins and are efficiently and functionally expressed in eukaryotic cells: GFP-specific αReps are clearly sequestrated by their cognate target protein addressed to various cell compartments. These results suggest that αRep proteins with tailor-made specificity can be selected and used in living cells to track, modulate or interfere with intracellular processes.


Assuntos
Engenharia de Proteínas/métodos , Cristalografia por Raios X , Proteínas de Fluorescência Verde/química , Ligação Proteica , Estrutura Secundária de Proteína
7.
J Am Chem Soc ; 137(3): 1141-6, 2015 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-25563067

RESUMO

The idea of a possible control of metal ion properties by constraining the coordination sphere geometry was introduced by Vallee and Williams with the concept of entasis, which is frequently postulated to be at stake in metallobiomolecules. However, the interactions controlling the geometry at metal centers remain often elusive. In this study, the coordination properties toward copper ions­Cu(II) or Cu(I)­of a geometrically constrained glycoligand centered on a sugar scaffold were compared with those of an analogous ligand built on an unconstrained alkyl chain. The sugar-centered ligand was shown to be more preorganized for Cu(II) coordination than its open-chain analogue, with an unusual additional stabilization of the Cu(I) redox state. This preference for Cu(I) was suggested to arise from geometric constraints favoring an optimized folding of the glycoligand minimizing steric repulsions. In other words, the Cu(I) d(10) species is stabilized by valence shell electron pair repulsion (VSEPR). This idea was rationalized by a theoretical noncovalent interactions (NCI) analysis. The cumulative effects of weak forces were shown to create an efficient buckle as in a hook-and-loop fastener, and fine structural features within the glycoligand reduce repulsive interactions for the Cu(I) state. This study emphasizes that monosaccharide platforms are appropriate ligand backbones for a delicate geometric control at the metal center, with a network of weak interactions within the ligand. This structuration availing in glycoligands makes them attractive for metallic entasis.


Assuntos
Carboidratos/química , Cobre/química , Compostos Organometálicos/química , Ligantes , Modelos Moleculares , Estrutura Molecular
8.
J Inorg Biochem ; 135: 40-4, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24657806

RESUMO

In the field of pharmaceuticals there is an increasing need for new delivery systems to overcome the issues of solubility, penetration, toxicity and drug resistance. One of the possible strategies is to use biocarriers such as proteins to encourage the cell-penetration of drugs. In this paper, the use of the apo-protein neocarzinostatin (apo-NCS) as a carrier-protein for two Cu(II) glycocomplexes, previously characterized, and Cu(II) ions was investigated. Its interaction with the metallic compounds was analyzed using microcalorimetry. The dissociation constants were shown to be in the micromolar range. The Cu(II) glycocomplexes, in absence of apo-NCS, were found to be cytotoxic in the U937 and HT29 cell lines whereas the corresponding glycoligands showed no toxicity. The leukemic cell line (U937) seems to be more sensitive to glycocomplexes than the colon cancer cell line (HT29). Interestingly, apo-NCS was shown to increase systematically the antiproliferative activity by a factor of 2 and 3 for Cu(II) glycocomplexes and Cu(II) respectively. The antiproliferative activity detected was not related to proteasome inhibition. This result stresses the importance of new molecular tools for the delivery of Cu(II) to tumor cells using non-covalent association with carriers proteins.


Assuntos
Antineoplásicos/química , Proteínas de Bactérias/química , Complexos de Coordenação/química , Cobre/química , Portadores de Fármacos/química , Zinostatina/química , Antineoplásicos/metabolismo , Antineoplásicos/farmacologia , Apoproteínas/química , Complexos de Coordenação/metabolismo , Complexos de Coordenação/farmacologia , Portadores de Fármacos/metabolismo , Portadores de Fármacos/farmacologia , Ensaios de Seleção de Medicamentos Antitumorais , Glicolipídeos/química , Células HT29 , Humanos , Concentração Inibidora 50
9.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 2): 242-52, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24531459

RESUMO

Peptide deformylases (PDFs), which are essential and ubiquitous enzymes involved in the removal of the N-formyl group from nascent chains, are classified into four subtypes based on the structural and sequence similarity of specific conserved domains. All PDFs share a similar three-dimensional structure, are functionally interchangeable in vivo and display similar properties in vitro, indicating that their molecular mechanism has been conserved during evolution. The human mitochondrial PDF is the only exception as despite its conserved fold it reveals a unique substrate-binding pocket together with an unusual kinetic behaviour. Unlike human PDF, the closely related mitochondrial PDF1As from plants have catalytic efficiencies and enzymatic parameters that are similar to those of other classes of PDFs. Here, the aim was to identify the structural basis underlying the properties of human PDF compared with all other PDFs by focusing on plant mitochondrial PDF1A. The construction of a chimaera composed of plant PDF1A with the nonrandom substitutions found in a conserved motif of its human homologue converted it into an enzyme with properties similar to the human enzyme, indicating the crucial role of these positions. The crystal structure of this human-like plant PDF revealed that substitution of two residues leads to a reduction in the volume of the ligand-binding site together with the introduction of negative charges, unravelling the origin of the weak affinity of human PDF for its substrate. In addition, the substitution of the two residues of human PDF modifies the transition state of the reaction through alteration of the network of interactions between the catalytic residues and the substrate, leading to an overall reduced reaction rate.


Assuntos
Amidoidrolases/química , Proteínas de Arabidopsis/química , Arabidopsis/química , Proteínas de Bactérias/química , Escherichia coli/química , Leptospira interrogans/química , Amidoidrolases/genética , Sequência de Aminoácidos , Arabidopsis/enzimologia , Proteínas de Arabidopsis/genética , Proteínas de Bactérias/genética , Biocatálise , Domínio Catalítico , Cristalografia por Raios X , Escherichia coli/enzimologia , Escherichia coli/genética , Expressão Gênica , Humanos , Cinética , Leptospira interrogans/enzimologia , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/genética , Alinhamento de Sequência , Eletricidade Estática , Relação Estrutura-Atividade , Especificidade por Substrato
10.
PLoS One ; 8(8): e71512, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24014183

RESUMO

We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a "filtration" procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×10(9) independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties.


Assuntos
Biblioteca de Peptídeos , Peptídeos/química , Sequência de Aminoácidos , Cristalografia por Raios X , Ensaio de Imunoadsorção Enzimática , Proteínas de Fluorescência Verde/química , Proteínas Imobilizadas/química , Ligação Proteica , Estabilidade Proteica , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Termodinâmica
11.
Biochem Biophys Res Commun ; 419(2): 356-61, 2012 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-22342729

RESUMO

The transcriptional activity of human estrogen receptor ERα is modulated by a number of coregulatory proteins among which calmodulin (CaM). Segment 295-311 in the hinge region of ERα has previously been proposed to be the CaM binding site. In this work, we investigate the molecular mechanism of the interaction of CaM with peptides derived from the hinge region of ERα, using a biophysical approach combining isothermal titration calorimetry, fluorescence, CD and NMR. The ERα17p peptide, corresponding to the previously identified 295-311 region of ERα, recruits mainly the C-terminal domain of Ca(4)CaM, as shown by NMR spectroscopy. In contrast, a longer peptide, ERα25p, extended on the N-terminal side (residues 287-311) interacts with both N- and C-terminal domains of Ca(4)CaM. These results lead to a new delineation of the CaM binding site, encompassing residues 287-294. In particular, fluorescence spectroscopy reveals that the conserved W(292) residue is engaged within hydrophobic pockets on Ca(4)CaM. ITC results show that ERα25p binds Ca(4)CaM with an atypical 2:1 stoichiometry and a dissociation constant in the micromolar range. Based on the NMR titration of Ca(4)CaM by ERα25p showing a biphasic behavior for several residues, we suggest that concerted conformational changes of CaM domains may be required to accommodate the binding of a second peptide. CD spectra indicate that ERα25p partially folds into an α-helix upon binding to Ca(4)CaM. Hence, ERα25p is a new CaM-binding ligand that could be appropriate for the synthesis of derivatives able to control ER-dependent transcription, particularly in the context of hormone-dependent breast tumors.


Assuntos
Calmodulina/química , Receptor alfa de Estrogênio/química , Fenômenos Biofísicos , Humanos , Ressonância Magnética Nuclear Biomolecular , Fragmentos de Peptídeos/química , Ligação Proteica , Mapeamento de Interação de Proteínas
12.
PLoS Biol ; 9(5): e1001066, 2011 May.
Artigo em Inglês | MEDLINE | ID: mdl-21629676

RESUMO

For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.


Assuntos
Amidoidrolases/química , Proteínas de Arabidopsis/química , Arabidopsis/enzimologia , Inibidores Enzimáticos/química , Amidoidrolases/antagonistas & inibidores , Amidoidrolases/genética , Motivos de Aminoácidos , Arabidopsis/genética , Proteínas de Arabidopsis/antagonistas & inibidores , Proteínas de Arabidopsis/genética , Domínio Catalítico , Cristalografia por Raios X , Ligação de Hidrogênio , Ácidos Hidroxâmicos/química , Cinética , Modelos Moleculares , Mutagênese Sítio-Dirigida , Mutação de Sentido Incorreto , Ligação Proteica/genética , Termodinâmica
13.
J Mol Biol ; 404(2): 307-27, 2010 Nov 26.
Artigo em Inglês | MEDLINE | ID: mdl-20887736

RESUMO

Repeat proteins have a modular organization and a regular architecture that make them attractive models for design and directed evolution experiments. HEAT repeat proteins, although very common, have not been used as a scaffold for artificial proteins, probably because they are made of long and irregular repeats. Here, we present and validate a consensus sequence for artificial HEAT repeat proteins. The sequence was defined from the structure-based sequence analysis of a thermostable HEAT-like repeat protein. Appropriate sequences were identified for the N- and C-caps. A library of genes coding for artificial proteins based on this sequence design, named αRep, was assembled using new and versatile methodology based on circular amplification. Proteins picked randomly from this library are expressed as soluble proteins. The biophysical properties of proteins with different numbers of repeats and different combinations of side chains in hypervariable positions were characterized. Circular dichroism and differential scanning calorimetry experiments showed that all these proteins are folded cooperatively and are very stable (T(m) >70 °C). Stability of these proteins increases with the number of repeats. Detailed gel filtration and small-angle X-ray scattering studies showed that the purified proteins form either monomers or dimers. The X-ray structure of a stable dimeric variant structure was solved. The protein is folded with a highly regular topology and the repeat structure is organized, as expected, as pairs of alpha helices. In this protein variant, the dimerization interface results directly from the variable surface enriched in aromatic residues located in the randomized positions of the repeats. The dimer was crystallized both in an apo and in a PEG-bound form, revealing a very well defined binding crevice and some structure flexibility at the interface. This fortuitous binding site could later prove to be a useful binding site for other low molecular mass partners.


Assuntos
Engenharia de Proteínas/métodos , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Sequência de Aminoácidos , Fenômenos Biofísicos , Dicroísmo Circular , Cristalografia por Raios X , Dimerização , Desenho de Fármacos , Modelos Moleculares , Dados de Sequência Molecular , Biblioteca de Peptídeos , Estabilidade Proteica , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Proteínas Recombinantes/genética , Sequências Repetitivas de Aminoácidos , Espalhamento a Baixo Ângulo , Temperatura , Difração de Raios X
14.
Inorg Chem ; 49(16): 7282-8, 2010 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-20690737

RESUMO

In coordination chemistry, ligand shape can be used to tune properties, such as metal selectivity, coordination number, electronic structure, redox potential, and metal center stereochemistry including coordination helicates formation, and also to generate cavities for encapsulation. The results presented in this article indicate that two epimeric glycoligands (3 and 4) based on the conformationally restrained xylo- and ribo-1,2-O-isopropylidenefurano scaffolds are preorganized in water through pi-pi stacking due to hydrophobic interactions, as evidenced from excimer observation. The structure obtained in the solid state for one of the Cu(II) complexes (5) is chiral, with an original helical chirality arising from the coiling of the two ligands around the Cu-Cu axis. It shows an unusual double-deck type structure, with pi-pi interaction between two triazoyl-pyridyl rings and with a small cavity between the two Cu(II) ions able to host a bridging water molecule, as suggested by electron paramagnetic resonance. The Cu(II) complex from the epimeric ligand (6) shows similar properties with a mirror-image CD spectrum in the d-d region of the Cu(II). There is a predetermination of chirality at the metal center by the glycoligand induced by the C3 configuration, 6 and 5 being pseudoenantiomers. Interestingly, the stereochemistry at the metal center is here controlled by the combination of pi-stacking and chiral backbone.


Assuntos
Carboidratos/química , Conformação Molecular , Compostos Organometálicos/química , Cobre/química , Cristalografia por Raios X , Ligantes , Modelos Moleculares , Análise Espectral , Estereoisomerismo
15.
Arch Biochem Biophys ; 498(2): 95-104, 2010 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-20416269

RESUMO

Glucosamine-6-phosphate synthase (GlmS) is responsible for the first and rate-limiting step in the hexosamine biosynthetic pathway. It catalyzes the conversion of D-fructose-6P (F6P) into D-glucosamine-6P (GlcN6P) using L-glutamine (Gln) as nitrogen donor (synthase activity) according to an ordered bi-bi process where F6P binds first. In the absence of F6P, the enzyme exhibits a weak hydrolyzing activity of Gln into Glu and ammonia (glutaminase activity), whereas the presence of F6P strongly stimulates it (hemi-synthase activity). Until now, these different activities were indirectly measured using either coupled enzyme or colorimetric methods. In this work, we have developed a direct assay monitoring the heat released by the reaction. Isothermal titration calorimetry and differential scanning calorimetry were used to determine kinetic and thermodynamic parameters of GlmS. The direct determination at 37 degrees C of kinetic parameters and affinity constants for both F6P and Gln demonstrated that part of the ammonia produced by Gln hydrolysis in the presence of both substrates is not used for the formation of the GlcN6P. The full characterization of this phenomenon allowed to identify experimental conditions where this leak of ammonia is negligible. Enthalpy measurements at 25 degrees C in buffers of various heats of protonation demonstrated that no proton exchange with the medium occurred during the enzyme-catalyzed glutaminase or synthase reaction suggesting for the first time that both products are released as a globally neutral pair composed by the Glu carboxylic side chain and the GlcN6P amine function. Finally we showed that the oligomerization state of GlmS is concentration-dependent.


Assuntos
Escherichia coli/enzimologia , Glutamina-Frutose-6-Fosfato Transaminase (Isomerizante)/química , Varredura Diferencial de Calorimetria , Calorimetria Indireta , Catálise , Proteínas de Escherichia coli , Glucosamina/análogos & derivados , Glucosamina/química , Glucose-6-Fosfato/análogos & derivados , Glucose-6-Fosfato/química , Temperatura Alta , Cinética
16.
J Mol Recognit ; 23(3): 301-15, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-19718689

RESUMO

The major inducible 70 kDa heat shock protein (hsp70) binds the measles virus (MeV) nucleocapsid with high affinity in an ATP-dependent manner, stimulating viral transcription and genome replication, and profoundly influencing virulence in mouse models of brain infection. Binding is mediated by two hydrophobic motifs (Box-2 and Box-3) located within the C-terminal domain (N(TAIL)) of the nucleocapsid protein, with N(TAIL) being an intrinsically disordered domain. The current work showed that high affinity hsp70 binding to N(TAIL) requires an hsp40 co-chaperone that interacts primarily with the hsp70 nucleotide binding domain (NBD) and displays no significant affinity for N(TAIL). Hsp40 directly enhanced hsp70 ATPase activity in an N(TAIL)-dependent manner, and formation of hsp40-hsp70-N(TAIL) intracellular complexes required the presence of N(TAIL) Box-2 and 3. Results are consistent with the functional interplay between hsp70 nucleotide and substrate binding domains (SBD), where ATP hydrolysis is rate limiting to high affinity binding to client proteins and is enhanced by hsp40. As such, hsp40 is an essential variable in understanding the outcome of MeV-hsp70 interactions.


Assuntos
Proteínas de Choque Térmico HSP40/química , Proteínas de Choque Térmico HSP40/metabolismo , Proteínas de Choque Térmico HSP70/química , Proteínas de Choque Térmico HSP70/metabolismo , Nucleoproteínas/química , Nucleoproteínas/metabolismo , Proteínas Virais/química , Proteínas Virais/metabolismo , Sequência de Aminoácidos , Animais , Sítios de Ligação , Linhagem Celular , Proteínas de Choque Térmico HSP40/genética , Proteínas de Choque Térmico HSP70/genética , Camundongos , Modelos Moleculares , Proteínas do Nucleocapsídeo , Nucleoproteínas/genética , Ligação Proteica , Estrutura Terciária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Virais/genética
17.
Biophys J ; 97(5): 1390-7, 2009 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-19720027

RESUMO

We investigated the specificity of interaction of a new type A lantibiotic, clausin, isolated from Bacillus clausii, with lipid intermediates of bacterial envelope biosynthesis pathways. Isothermal calorimetry and steady-state fluorescence anisotropy (with dansylated derivatives) identified peptidoglycan lipids I and II, embedded in dodecylphosphocholine micelles, as potential targets. Complex formation with dissociation constants of approximately 0.3 muM and stoichiometry of approximately 2:1 peptides/lipid intermediate was observed. The interaction is enthalpy-driven. For the first time, to our knowledge, we evidenced the interaction between a lantibiotic and C(55)-PP-GlcNAc, a lipid intermediate in the biosynthesis of other bacterial cell wall polymers, including teichoic acids. The pyrophosphate moiety of these lipid intermediates was crucial for the interaction because a strong binding with undecaprenyl pyrophosphate, accounting for 80% of the free energy of binding, was observed. No binding occurred with the undecaprenyl phosphate derivative. The pentapeptide and the N-acetylated sugar moieties strengthened the interaction, but their contributions were weaker than that of the pyrophosphate group. The lantibiotic decreased the mobility of the pentapeptide. Clausin did not interact with the water-soluble UDP-MurNAc- and pyrophosphoryl-MurNAc-pentapeptides, pointing out the importance of the hydrocarbon chain of the lipid target.


Assuntos
Bactérias/metabolismo , Bacteriocinas/metabolismo , Parede Celular/metabolismo , Bacillus/isolamento & purificação , Bacillus/metabolismo , Bacteriocinas/isolamento & purificação , Calorimetria , Compostos de Dansil/metabolismo , Fluorescência , Polarização de Fluorescência , Cinética , Monossacarídeos/metabolismo , Movimento (Física) , Oligopeptídeos/metabolismo , Fosfatos de Poli-Isoprenil/metabolismo , Ligação Proteica , Rotação , Termodinâmica , Fatores de Tempo , Uridina Difosfato Ácido N-Acetilmurâmico/análogos & derivados , Uridina Difosfato Ácido N-Acetilmurâmico/metabolismo
18.
J Pept Sci ; 15(7): 455-64, 2009 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-19424961

RESUMO

Polyproline II (PPII) helix is an extended secondary structure present in a number of proteins. PPII-containing sequences mediate specific protein-protein interactions with partners containing appropriate cognate domains called PPII-recognizing domains (PRDs) and are involved in the activation of intracellular signaling pathways. Thus, the identification of PPII structures in proteins is of great interest, not only to explore molecular and physiological mechanisms, but also to elaborate new potential drugs. By revisiting X-ray crystal structures of liganded alpha-type human estrogen receptor (ERalpha), we have identified an 11-residue PPII-helical sequence (D(321)AEPPILYSEY(331)) in the ligand-binding domain of the receptor. The data recorded by far-ultraviolet circular dichroism (far-UV CD), vibrational Raman optical activity (ROA) and differential scanning calorimetry (DSC) show that the corresponding peptide (Ac-DAEPPILYSEY-NH(2)) is particularly well structured in PPII, with the same proportion of PPII as observed from X-ray structures (approximately 85%). In addition, studies carried out on ERalpha-negative Evsa-T breast cancer cells transiently co-transfected with a pcDNA3-ERalpha plasmid and a Vit-tk-Luc reporter gene revealed that the peptide antagonizes the estradiol-induced transcription providing perspectives for researching new molecules with antagonistic properties.


Assuntos
Moduladores de Receptor Estrogênico/química , Receptor alfa de Estrogênio/química , Peptídeos/química , Sequência de Aminoácidos , Linhagem Celular Tumoral , Dicroísmo Circular , Humanos , Dados de Sequência Molecular , Conformação Proteica
19.
Chembiochem ; 10(8): 1349-59, 2009 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-19415706

RESUMO

Breaking ties: The antitumour protein, neocarzinostatin (NCS), is one of the few drug-carrying proteins used in human therapeutics. However, the presence of disulfide bonds limits this protein's potential development for many applications. This study describes a generic directed-evolution approach starting from NCS-3.24 (shown in the figure complexed with two testosterone molecules) to engineer stable disulfide-free NCS variants suitable for a variety of purposes, including intracellular applications.The chromoprotein neocarzinostatin (NCS) has been intensively studied for its antitumour properties. It has recently been redesigned as a potential drug-carrying scaffold. A potential limit of this protein scaffold, especially for intracellular applications, is the presence of disulfide bonds. The objective of this work was to create a disulfide-free NCS-derived scaffold. A generic targeted approach was developed by using directed evolution methods. As a starting point we used a previously engineered NCS variant in which a hapten binding site had been created. A library was then generated in which cysteine Cys88 and Cys93 and neighbouring residues were randomly substituted. Variants that preserved the hapten binding function were selected by phage display and further screened by colony filtration methods. Several sequences with common features emerged from this process. The corresponding proteins were expressed, purified and their biophysical properties characterised. How these selected sequences rescued folding ability and stability of the disulfide-free protein was carefully examined by using calorimetry and the results were interpreted with molecular simulation techniques.


Assuntos
Antineoplásicos/química , Dissulfetos/química , Zinostatina/química , Sequência de Aminoácidos , Antineoplásicos/metabolismo , Sequência de Bases , Simulação por Computador , Cristalografia por Raios X , Evolução Molecular Direcionada , Mutagênese Sítio-Dirigida , Proteínas Mutantes/química , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Biblioteca de Peptídeos , Ligação Proteica , Engenharia de Proteínas , Testosterona/química , Termodinâmica , Zinostatina/metabolismo
20.
Inorg Chem ; 47(7): 2243-5, 2008 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-18321040

RESUMO

A pair of novel C3-epimeric sugar-derived ligands (glycoligands) with a neutral N4O donor set was synthesized. Copper(II) complexes of both ligands were obtained and characterized by X-ray crystallography. Cyclic voltammetry, electron paramagnetic resonance, and UV-vis spectroscopies showed similar electronic properties. Mirror-image CD spectra were obtained for the Cu(II) d-d band, indicating an enantiomeric character of the coordination sphere, which has been rationalized structurally. This example shows the possible predetermination of stereochemistry for complexes by ligands based on a glycoscaffold.


Assuntos
Carboidratos/química , Cobre/química , Dicroísmo Circular , Cristalografia por Raios X , Espectroscopia de Ressonância de Spin Eletrônica , Ligantes , Modelos Moleculares , Estrutura Molecular , Estereoisomerismo
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