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1.
Cell Commun Signal ; 19(1): 38, 2021 03 24.
Artículo en Inglés | MEDLINE | ID: mdl-33761918

RESUMEN

BACKGROUND: CP12 is a small chloroplast protein that is widespread in various photosynthetic organisms and is an actor of the redox signaling pathway involved in the regulation of the Calvin Benson Bassham (CBB) cycle. The gene encoding this protein is conserved in many diatoms, but the protein has been overlooked in these organisms, despite their ecological importance and their complex and still enigmatic evolutionary background. METHODS: A combination of biochemical, bioinformatics and biophysical methods including electrospray ionization-mass spectrometry, circular dichroism, nuclear magnetic resonance spectroscopy and small X ray scattering, was used to characterize a diatom CP12. RESULTS: Here, we demonstrate that CP12 is expressed in the marine diatom Thalassiosira pseudonana constitutively in dark-treated and in continuous light-treated cells as well as in all growth phases. This CP12 similarly to its homologues in other species has some features of intrinsically disorder protein family: it behaves abnormally under gel electrophoresis and size exclusion chromatography, has a high net charge and a bias amino acid composition. By contrast, unlike other known CP12 proteins that are monomers, this protein is a dimer as suggested by native electrospray ionization-mass spectrometry and small angle X-ray scattering. In addition, small angle X-ray scattering revealed that this CP12 is an elongated cylinder with kinks. Circular dichroism spectra indicated that CP12 has a high content of α-helices, and nuclear magnetic resonance spectroscopy suggested that these helices are unstable and dynamic within a millisecond timescale. Together with in silico predictions, these results suggest that T. pseudonana CP12 has both coiled coil and disordered regions. CONCLUSIONS: These findings bring new insights into the large family of dynamic proteins containing disordered regions, thus increasing the diversity of known CP12 proteins. As it is a protein that is more abundant in many stresses, it is not devoted to one metabolism and in particular, it is not specific to carbon metabolism. This raises questions about the role of this protein in addition to the well-established regulation of the CBB cycle. Choregraphy of metabolism by CP12 proteins in Viridiplantae and Heterokonta. While the monomeric CP12 in Viridiplantae is involved in carbon assimilation, regulating phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) through the formation of a ternary complex, in Heterokonta studied so far, the dimeric CP12 is associated with Ferredoxin-NADP reductase (FNR) and GAPDH. The Viridiplantae CP12 can bind metal ions and can be a chaperone, the Heterokonta CP12 is more abundant in all stresses (C, N, Si, P limited conditions) and is not specific to a metabolism. Video Abstract.


Asunto(s)
Organismos Acuáticos/metabolismo , Proteínas de Cloroplastos/metabolismo , Diatomeas/metabolismo , Secuencia de Aminoácidos , Proteínas de Cloroplastos/química , Simulación por Computador , Espectroscopía de Resonancia Magnética , Multimerización de Proteína , Estructura Secundaria de Proteína , Dispersión del Ángulo Pequeño , Difracción de Rayos X
2.
Int J Mol Sci ; 22(16)2021 Aug 13.
Artículo en Inglés | MEDLINE | ID: mdl-34445427

RESUMEN

Carbonic anhydrases (CAs) are a family of ubiquitous enzymes that catalyze the interconversion of CO2 and HCO3-. The "iota" class (ι-CA) was first found in the marine diatom Thalassiosira pseudonana (tpι-CA) and is widespread among photosynthetic microalgae and prokaryotes. The ι-CA has a domain COG4875 (or COG4337) that can be repeated from one to several times and resembles a calcium-calmodulin protein kinase II association domain (CaMKII-AD). The crystal structure of this domain in the ι-CA from a cyanobacterium and a chlorarachniophyte has been recently determined. However, the three-dimensional organization of the four domain-containing tpι-CA is unknown. Using biophysical techniques and 3-D modeling, we show that the homotetrameric tpι-CA in solution has a flat "drone-like" shape with a core formed by the association of the first two domains of each monomer, and four protruding arms formed by domains 3 and 4. We also observe that the short linker between domains 3 and 4 in each monomer confers high flexibility, allowing for different conformations to be adopted. We propose the possible 3-D structure of a truncated tpι-CA containing fewer domain repeats using experimental data and discuss the implications of this atypical shape on the activity and metal coordination of the ι-CA.


Asunto(s)
Anhidrasas Carbónicas/química , Diatomeas/enzimología , Cristalografía por Rayos X , Diatomeas/química , Espectroscopía de Resonancia Magnética , Modelos Moleculares , Fotosíntesis , Dominios Proteicos , Espectrometría de Masa por Ionización de Electrospray , Ultracentrifugación
3.
Arch Biochem Biophys ; 672: 108070, 2019 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-31408624

RESUMEN

Intrinsically disordered proteins (IDPs) are proteins that provide many functional advantages in a large number of metabolic and signalling pathways. Because of their high flexibility that endows them with pressure-, heat- and acid-resistance, IDPs are valuable metabolic regulators that help algae to cope with extreme conditions of pH, temperature, pressure and light. They have, however, been overlooked in these organisms. In this review, we present some well-known algal IDPs, including the conditionally disordered CP12, a protein involved in the regulation of CO2 assimilation, as probably the best known example, whose disorder content is strongly dependent on the redox conditions, and the essential pyrenoid component 1 that serves as a scaffold for ribulose-1, 5-bisphosphate carboxylase/oxygenase. We also describe how some enzymes are regulated by protein regions, called intrinsically disordered regions (IDRs), such as ribulose-1, 5-bisphosphate carboxylase/oxygenase activase, the A2B2 form of glyceraldehyde-3-phosphate dehydrogenase and the adenylate kinase. Several molecular chaperones, which are crucial for cell proteostasis, also display significant disorder propensities such as the algal heat shock proteins HSP33, HSP70 and HSP90. This review confirms the wide distribution of IDPs in algae but highlights that further studies are needed to uncover their full role in orchestrating algal metabolism.


Asunto(s)
Proteínas Algáceas/metabolismo , Chlorophyta/metabolismo , Proteínas Intrínsecamente Desordenadas/metabolismo , Proteínas Algáceas/química , Chlorophyta/química , Proteínas Intrínsecamente Desordenadas/química , Microalgas/química , Microalgas/metabolismo , Chaperonas Moleculares/química , Chaperonas Moleculares/metabolismo , Fotosíntesis/fisiología
4.
Biochemistry ; 56(24): 3029-3048, 2017 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-28535337

RESUMEN

Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a RNA-binding phosphoprotein composed of a N-terminal membrane anchor (AH), a structured domain 1 (D1), and two intrinsically disordered domains (D2 and D3). The knowledge of the functional architecture of this multifunctional protein remains limited. We report here that NS5A-D1D2D3 produced in a wheat germ cell-free system is obtained under a highly phosphorylated state. Its NMR analysis revealed that these phosphorylations do not change the disordered nature of D2 and D3 domains but increase the number of conformers due to partial phosphorylations. By combining NMR and small angle X-ray scattering, we performed a comparative structural characterization of unphosphorylated recombinant D2 domains of JFH1 (genotype 2a) and the Con1 (genotype 1b) strains produced in Escherichia coli. These analyses highlighted a higher intrinsic folding of the latter, revealing the variability of intrinsic conformations in HCV genotypes. We also investigated the effect of D2 mutations conferring resistance of HCV replication to cyclophilin A (CypA) inhibitors on the structure of the recombinant D2 Con1 mutants and their binding to CypA. Although resistance mutations D320E and R318W could induce some local and/or global folding perturbation, which could thus affect the kinetics of conformer interconversions, they do not significantly affect the kinetics of CypA/D2 interaction measured by surface plasmon resonance (SPR). The combination of all our data led us to build a model of the overall structure of NS5A, which provides a useful template for further investigations of the structural and functional features of this enigmatic protein.


Asunto(s)
Antivirales/farmacología , Ciclosporina/farmacología , Farmacorresistencia Viral/efectos de los fármacos , Hepacivirus/efectos de los fármacos , Mutación , Proteínas no Estructurales Virales/química , Proteínas no Estructurales Virales/genética , Replicación Viral/efectos de los fármacos , Hepacivirus/genética , Hepacivirus/crecimiento & desarrollo , Espectrometría de Masas , Pruebas de Sensibilidad Microbiana , Modelos Moleculares , Conformación Proteica
5.
Biochem Biophys Res Commun ; 477(1): 20-26, 2016 08 12.
Artículo en Inglés | MEDLINE | ID: mdl-27268235

RESUMEN

The redox switch protein CP12 is a key player of the regulation of the Benson-Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold.


Asunto(s)
Proteínas Intrínsecamente Desordenadas/química , Resonancia Magnética Nuclear Biomolecular , Oxidación-Reducción , Conformación Proteica , Dispersión del Ángulo Pequeño , Difracción de Rayos X
6.
Biochim Biophys Acta ; 1834(12): 2564-72, 2013 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-24075929

RESUMEN

The TTSS is used by Salmonella and many bacterial pathogens to inject virulence factors directly into the cytoplasm of target eukaryotic cells. Once translocated these so-called effector proteins hijack a vast array of crucial cellular functions to the benefit of the bacteria. In the bacterial cytoplasm, some effectors are stabilized and maintained in a secretion competent state by interaction with specific type III chaperones. In this work we studied the conformation of the Chaperone Binding Domain of the effector named Salmonella Outer protein B (SopB) alone and in complex with its cognate chaperone SigE by a combination of biochemical, biophysical and structural approaches. Our results show that the N-terminus part of SopB is mainly composed by α-helices and unfolded regions whose organization/stabilization depends on their interaction with the different partners. This suggests that the partially unfolded state of this N-terminal region, which confers the adaptability of the effector to bind very different partners during the infection cycle, allows the bacteria to modulate numerous host cells functions limiting the number of translocated effectors.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Chaperonas Moleculares/química , Salmonella typhimurium/química , Factor sigma/metabolismo , Proteínas Bacterianas/genética , Chaperonas Moleculares/genética , Chaperonas Moleculares/metabolismo , Estructura Cuaternaria de Proteína , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Salmonella typhimurium/genética , Salmonella typhimurium/metabolismo , Factor sigma/genética
7.
J Appl Crystallogr ; 56(Pt 5): 1313-1314, 2023 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-37791368

RESUMEN

A recent article by Brookes, Rocco, Vachette & Trewhella [J. Appl. Cryst. (2023), 56, 910-926] on improving the accuracy of AlphaFold structural predictions for disordered proteins is discussed.

8.
FEBS Lett ; 597(23): 2853-2878, 2023 12.
Artículo en Inglés | MEDLINE | ID: mdl-37827572

RESUMEN

Carbon acquisition, assimilation and storage in eukaryotic microalgae and cyanobacteria occur in multiple compartments that have been characterised by the location of the enzymes involved in these functions. These compartments can be delimited by bilayer membranes, such as the chloroplast, the lumen, the peroxisome, the mitochondria or monolayer membranes, such as lipid droplets or plastoglobules. They can also originate from liquid-liquid phase separation such as the pyrenoid. Multiple exchanges exist between the intracellular microcompartments, and these are reviewed for the CO2 concentration mechanism, the Calvin-Benson-Bassham cycle, the lipid metabolism and the cellular energetic balance. Progress in microscopy and spectroscopic methods opens new perspectives to characterise the molecular consequences of the location of the proteins involved, including intrinsically disordered proteins.


Asunto(s)
Chlamydomonas reinhardtii , Microalgas , Microalgas/metabolismo , Carbono/metabolismo , Fotosíntesis , Cloroplastos/metabolismo , Dióxido de Carbono/metabolismo
9.
Biomolecules ; 12(8)2022 07 28.
Artículo en Inglés | MEDLINE | ID: mdl-36008940

RESUMEN

The chloroplast protein CP12, which is widespread in photosynthetic organisms, belongs to the intrinsically disordered proteins family. This small protein (80 amino acid residues long) presents a bias in its composition; it is enriched in charged amino acids, has a small number of hydrophobic residues, and has a high proportion of disorder-promoting residues. More precisely, CP12 is a conditionally disordered proteins (CDP) dependent upon the redox state of its four cysteine residues. During the day, reducing conditions prevail in the chloroplast, and CP12 is fully disordered. Under oxidizing conditions (night), its cysteine residues form two disulfide bridges that confer some stability to some structural elements. Like many CDPs, CP12 plays key roles, and its redox-dependent conditional disorder is important for the main function of CP12: the dark/light regulation of the Calvin-Benson-Bassham (CBB) cycle responsible for CO2 assimilation. Oxidized CP12 binds to glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase and thereby inhibits their activity. However, recent studies reveal that CP12 may have other functions beyond the CBB cycle regulation. In this review, we report the discovery of this protein, its features as a disordered protein, and the many functions this small protein can have.


Asunto(s)
Cloroplastos , Cisteína , Proteínas de Cloroplastos/química , Cloroplastos/metabolismo , Cisteína/metabolismo , Gliceraldehído-3-Fosfato Deshidrogenasas/química , Gliceraldehído-3-Fosfato Deshidrogenasas/metabolismo , Fotosíntesis/fisiología
10.
BMC Struct Biol ; 11: 4, 2011 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-21266026

RESUMEN

BACKGROUND: Type IV secretion (T4S) systems are involved in secretion of virulence factors such as toxins or transforming molecules, or bacterial conjugation. T4S systems are composed of 12 proteins named VirB1-B11 and VirD4. Among them, three ATPases are involved in the assembly of the T4S system and/or provide energy for substrate transfer, VirB4, VirB11 and VirD4. The X-ray crystal structures of VirB11 and VirD4 have already been solved but VirB4 has proven to be reluctant to any structural investigation so far. RESULTS: Here, we have used small-angle X-ray scattering to obtain the first structural models for the membrane-extracted, dimeric form of the TraB protein, the VirB4 homolog encoded by the E. coli pKM101 plasmid, and for the monomeric soluble form of the LvhB4 protein, the VirB4 homolog of the T4S system encoded by the Legionella pneumophila lvh operon. We have obtained the low resolution structures of the full-length TraB and of its N- and C-terminal halves. From these SAXS models, we derive the internal organisation of TraB. We also show that the two TraB N- and C-terminal domains are independently involved in the dimerisation of the full-length protein. CONCLUSIONS: These models provide the first structural insights into the architecture of VirB4 proteins. In particular, our results highlight the modular arrangement and functional relevance of the dimeric-membrane-bound form of TraB.


Asunto(s)
Proteínas de la Membrana Bacteriana Externa/química , Proteínas Bacterianas/química , Membrana Celular/ultraestructura , Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Proteínas de la Membrana Bacteriana Externa/ultraestructura , Proteínas Bacterianas/ultraestructura , Conjugación Genética , Cristalografía por Rayos X , Escherichia coli/genética , Escherichia coli/metabolismo , Plásmidos/genética , Conformación Proteica , Multimerización de Proteína , Dispersión del Ángulo Pequeño , Factores de Virulencia/genética , Difracción de Rayos X/métodos
11.
Biomolecules ; 11(5)2021 05 08.
Artículo en Inglés | MEDLINE | ID: mdl-34066751

RESUMEN

In the chloroplast, Calvin-Benson-Bassham enzymes are active in the reducing environment created in the light by electrons from the photosystems. In the dark, these enzymes are inhibited, mainly caused by oxidation of key regulatory cysteine residues. CP12 is a small protein that plays a role in this regulation with four cysteine residues that undergo a redox transition. Using amide-proton exchange with solvent, measured by nuclear magnetic resonance (NMR) and mass-spectrometry, we confirmed that reduced CP12 is intrinsically disordered. Using real-time NMR, we showed that the oxidation of the two disulfide bridges is simultaneous. In oxidized CP12, the C23-C31 pair is in a region that undergoes a conformational exchange in the NMR-intermediate timescale. The C66-C75 pair is in the C-terminus that folds into a stable helical turn. We confirmed that these structural states exist in a physiologically relevant environment: a cell extract from Chlamydomonas reinhardtii. Consistent with these structural equilibria, the reduction is slower for the C66-C75 pair than for the C23-C31 pair. The redox mid-potentials for the two cysteine pairs differ and are similar to those found for glyceraldehyde 3-phosphate dehydrogenase and phosphoribulokinase, consistent with the regulatory role of CP12.


Asunto(s)
Chlamydomonas reinhardtii/metabolismo , Proteínas de Cloroplastos/química , Proteínas de Cloroplastos/metabolismo , Cisteína/química , Proteínas Algáceas/química , Proteínas Algáceas/metabolismo , Chlamydomonas reinhardtii/química , Concentración de Iones de Hidrógeno , Espectroscopía de Resonancia Magnética , Espectrometría de Masas , Modelos Moleculares , Oxidación-Reducción , Fotosíntesis , Conformación Proteica
12.
Proteins ; 78(6): 1441-56, 2010 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-20034112

RESUMEN

The 101-residue long Tat protein of primary isolate 133 of the human immunodeficiency virus type 1 (HIV-1), wt-Tat(133) displays a high transactivation activity in vitro, whereas the mutant thereof, STLA-Tat(133), a vaccine candidate for HIV-1, has none. These two proteins were chemically synthesized and their biological activity was validated. Their structural properties were characterized using circular dichroism (CD), fluorescence emission, gel filtration, dynamic light scattering, and small angle X-ray scattering (SAXS) techniques. SAXS studies revealed that both proteins were extended and belong to the family of intrinsically unstructured proteins. CD measurements showed that wt-Tat(133) or STLA-Tat(133) underwent limited structural rearrangements when complexed with specific fragments of antibodies. Crystallization trials have been performed on the two forms, assuming that the Tat(133) proteins might have a better propensity to fold in supersaturated conditions, and small crystals have been obtained. These results suggest that biologically active Tat protein is natively unfolded and requires only a limited gain of structure for its function.


Asunto(s)
VIH-1/química , Proteínas Mutantes/química , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/química , Vacunas contra el SIDA/química , Vacunas contra el SIDA/genética , Vacunas contra el SIDA/inmunología , Secuencia de Aminoácidos , Cromatografía en Gel , Dicroismo Circular , Cristalografía por Rayos X , VIH-1/genética , VIH-1/aislamiento & purificación , Interacciones Hidrofóbicas e Hidrofílicas , Fragmentos de Inmunoglobulinas , Luz , Metilaminas , Datos de Secuencia Molecular , Pliegue de Proteína , Dispersión de Radiación , Dispersión del Ángulo Pequeño , Espectrofotometría Ultravioleta , Trifluoroetanol , Agua , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/genética , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/inmunología , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/metabolismo
13.
Biochem J ; 407(2): 293-302, 2007 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-17635108

RESUMEN

The psychrophilic cellulase, Cel5G, from the Antarctic bacterium Pseudoalteromonas haloplanktis is composed of a catalytic module (CM) joined to a carbohydrate-binding module (CBM) by an unusually long, extended and flexible linker region (LR) containing three loops closed by three disulfide bridges. To evaluate the possible role of this region in cold adaptation, the LR was sequentially shortened by protein engineering, successively deleting one and two loops of this module, whereas the last disulfide bridge was also suppressed by replacing the last two cysteine residue by two alanine residues. The kinetic and thermodynamic properties of the mutants were compared with those of the full-length enzyme, and also with those of the cold-adapted CM alone and with those of the homologous mesophilic enzyme, Cel5A, from Erwinia chrysanthemi. The thermostability of the mutated enzymes as well as their relative flexibility were evaluated by differential scanning calorimetry and fluorescence quenching respectively. The topology of the structure of the shortest mutant was determined by SAXS (small-angle X-ray scattering). The data indicate that the sequential shortening of the LR induces a regular decrease of the specific activity towards macromolecular substrates, reduces the relative flexibility and concomitantly increases the thermostability of the shortened enzymes. This demonstrates that the long LR of the full-length enzyme favours the catalytic efficiency at low and moderate temperatures by rendering the structure not only less compact, but also less stable, and plays a crucial role in the adaptation to cold of this cellulolytic enzyme.


Asunto(s)
Celulasa/química , Celulasa/fisiología , Frío , Pseudoalteromonas/enzimología , Aclimatación , Catálisis , Celulasa/genética , Estabilidad de Enzimas , Mutación , Conformación Proteica
14.
J Mol Biol ; 430(8): 1218-1234, 2018 04 13.
Artículo en Inglés | MEDLINE | ID: mdl-29501381

RESUMEN

Among intrinsically disordered proteins, conditionally disordered proteins undergo dramatic structural disorder rearrangements upon environmental changes and/or post-translational modifications that directly modulate their function. Quantifying the dynamics of these fluctuating proteins is extremely challenging but paramount to understanding the regulation of their function. The chloroplast protein CP12 is a model of such proteins and acts as a redox switch by formation/disruption of its two disulfide bridges. It regulates the Calvin cycle by forming, in oxidized conditions, a supramolecular complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and then phosphoribulokinase. In this complex, both enzymes are inactive. The highly dynamic nature of CP12 has so far hindered structural characterization explaining its mode of action. Thanks to a synergistic combination of small-angle X-ray scattering, nuclear magnetic resonance and circular dichroism that drove the molecular modeling of structural ensembles, we deciphered the structural behavior of Chlamydomonas reinhardtii oxidized CP12 alone and in the presence of GAPDH. Contrary to sequence-based structural predictions, the N-terminal region is unstable, oscillates at the ms timescale between helical and random conformations, and is connected through a disordered linker to its C-terminus, which forms a stable helical turn. Upon binding to GAPDH, oxidized CP12 undergoes an induced unfolding of its N-terminus. This phenomenon called cryptic disorder contributes to decrease the entropy cost and explains CP12 unusual high affinity for its partners.


Asunto(s)
Chlamydomonas reinhardtii/metabolismo , Proteínas de Cloroplastos/química , Proteínas de Cloroplastos/metabolismo , Gliceraldehído-3-Fosfato Deshidrogenasas/metabolismo , Proteínas Algáceas/química , Proteínas Algáceas/metabolismo , Chlamydomonas reinhardtii/química , Cloroplastos/metabolismo , Dicroismo Circular , Proteínas Intrínsecamente Desordenadas/química , Proteínas Intrínsecamente Desordenadas/metabolismo , Modelos Moleculares , Oxidación-Reducción , Fosfotransferasas (Aceptor de Grupo Alcohol)/metabolismo , Unión Proteica , Estructura Secundaria de Proteína , Desplegamiento Proteico
15.
Proteins ; 62(1): 24-45, 2006 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-16287116

RESUMEN

Intrinsically disordered proteins (IDPs) defy the structure-function paradigm as they fulfill essential biological functions while lacking well-defined secondary and tertiary structures. Conformational and spectroscopic analyses showed that IDPs do not constitute a uniform family, and can be divided into subfamilies as a function of their residual structure content. Residual intramolecular interactions are thought to facilitate binding to a partner and then induced folding. Comprehensive information about experimental approaches to investigate structural disorder and induced folding is still scarce. We herein provide hints to readily recognize features typical of intrinsic disorder and review the principal techniques to assess structural disorder and induced folding. We describe their theoretical principles and discuss their respective advantages and limitations. Finally, we point out the necessity of using different approaches and show how information can be broadened by the use of multiples techniques.


Asunto(s)
Proteínas/química , Proteínas/metabolismo , Secuencia de Aminoácidos , Dicroismo Circular , Conformación Proteica , Pliegue de Proteína , Estructura Secundaria de Proteína , Difracción de Rayos X
16.
Proteins ; 63(1): 235-42, 2006 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-16421930

RESUMEN

Resolution of the crystal structure of the banana fruit endo-beta-1,3-glucanase by synchrotron X-ray diffraction at 1.45-A resolution revealed that the enzyme possesses the eightfold beta/alpha architecture typical for family 17 glycoside hydrolases. The electronegatively charged catalytic central cleft harbors the two glutamate residues (Glu94 and Glu236) acting as hydrogen donor and nucleophile residue, respectively. Modeling using a beta-1,3 linked glucan trisaccharide as a substrate confirmed that the enzyme readily accommodates a beta-1,3-glycosidic linkage in the slightly curved catalytic groove between the glucose units in positions -2 and -1 because of the particular orientation of residue Tyr33 delimiting subsite -2. The location of Phe177 in the proximity of subsite +1 suggested that the banana glucanase might also cleave beta-1,6-branched glucans. Enzymatic assays using pustulan as a substrate demonstrated that the banana glucanase can also cleave beta-1,6-glucans as was predicted from docking experiments. Similar to many other plant endo-beta-1,3-glucanases, the banana glucanase exhibits allergenic properties because of the occurrence of well-conserved IgE-binding epitopes on the surface of the enzyme. These epitopes might trigger some cross-reactions toward IgE antibodies and thus account for the IgE-binding cross-reactivity frequently reported in patients with the latex-fruit syndrome.


Asunto(s)
Alérgenos/química , Cristalografía por Rayos X/métodos , Hipersensibilidad a los Alimentos , Glucano Endo-1,3-beta-D-Glucosidasa/química , Proteínas/química , Proteómica/métodos , Secuencia de Aminoácidos , Sitios de Unión , Catálisis , Dominio Catalítico , Reacciones Cruzadas , Epítopos/química , Epítopos de Linfocito B/química , Frutas , Glucosa/química , Ácido Glutámico/química , Inmunoglobulina E/química , Látex , Modelos Moleculares , Conformación Molecular , Datos de Secuencia Molecular , Musa , Fenilalanina/química , Polisacáridos/química , Unión Proteica , Conformación Proteica , Estructura Secundaria de Proteína , Especificidad por Sustrato , Síndrome , Factores de Tiempo , Triosa-Fosfato Isomerasa/química , Tirosina/química
17.
J Mol Biol ; 348(5): 1211-24, 2005 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-15854656

RESUMEN

Pseudoalteromonas haloplanktis is a psychrophilic Gram-negative bacterium isolated in Antarctica, that lives on organic remains of algae. This bacterium converts the cellulose, highly constitutive of algae, into an immediate nutritive form by biodegrading this biopolymer. To understand the mechanisms of cold adaptation of its enzymatic components, we studied the structural properties of an endoglucanase, Cel5G, by complementary methods, X-ray crystallography and small angle X-ray scattering. Using X-ray crystallography, we determined the structure of the catalytic core module of this family 5 endoglucanase, at 1.4A resolution in its native form and at 1.6A in the cellobiose-bound form. The catalytic module of Cel5G presents the (beta/alpha)(8)-barrel structure typical of clan GH-A of glycoside hydrolase families. The structural comparison of the catalytic core of Cel5G with the mesophilic catalytic core of Cel5A from Erwinia chrysanthemi revealed modifications at the atomic level leading to higher flexibility and thermolability, which might account for the higher activity of Cel5G at low temperatures. Using small angle X-ray scattering we further explored the structure at the entire enzyme level. We analyzed the dimensions, shape, and conformation of Cel5G full length in solution and especially of the linker between the catalytic module and the cellulose-binding module. The results showed that the linker is unstructured, and unusually long and flexible, a peculiarity that distinguishes it from its mesophilic counterpart. Loops formed at the base by disulfide bridges presumably add constraints to stabilize the most extended conformations. These results suggest that the linker plays a major role in cold adaptation of this psychrophilic enzyme, allowing steric optimization of substrate accessibility.


Asunto(s)
Proteínas Bacterianas/química , Celulasa/química , Pseudoalteromonas/enzimología , Secuencia de Aminoácidos , Sitios de Unión , Catálisis , Celobiosa/metabolismo , Biología Computacional , Cristalografía por Rayos X , Datos de Secuencia Molecular , Estructura Molecular , Conformación Proteica , Dispersión de Radiación , Electricidad Estática , Rayos X
18.
Sci Rep ; 6: 37743, 2016 11 25.
Artículo en Inglés | MEDLINE | ID: mdl-27886223

RESUMEN

A major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. This holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. This large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (Mo/W-bisPGD) and Fe/S clusters. Here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational changes accompanying Mo/W-bisPGD and Fe/S cofactors insertion. Identified conformational changes are shown to be essential for recognition of the dedicated chaperone involved in cofactors insertion. A solvent-exposed salt bridge is shown to play a key role in enzyme folding after cofactors insertion. Furthermore, this salt bridge is shown to be strictly conserved within this prokaryotic molybdoenzyme family as deduced from a phylogenetic analysis issued from 3D structure-guided multiple sequence alignment. A biochemical analysis with a distantly-related member of the family, respiratory complex I, confirmed the critical importance of the salt bridge for folding. Overall, our results point to a conserved cofactors insertion mechanism within the Mo/W-bisPGD family.


Asunto(s)
Metaloproteínas/metabolismo , Molibdeno/metabolismo , Nitrato-Reductasa/metabolismo , Secuencia de Aminoácidos , Metaloproteínas/química , Nitrato-Reductasa/química , Oxidación-Reducción , Pliegue de Proteína , Dispersión del Ángulo Pequeño , Homología de Secuencia de Aminoácido , Difracción de Rayos X
19.
Protein Sci ; 14(8): 1975-92, 2005 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-16046624

RESUMEN

Measles virus is a negative-sense, single-stranded RNA virus within the Mononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. The measles virus nucleoprotein consists of a structured N-terminal domain, and of an intrinsically disordered C-terminal domain, N(TAIL) (aa 401-525), which undergoes induced folding in the presence of the C-terminal domain (XD, aa 459-507) of the viral phosphoprotein. With in N(TAIL), an alpha-helical molecular recognition element (alpha-MoRE, aa 488-499) involved in binding to P and in induced folding was identified and then observed in the crystal structure of XD. Using small-angle X-ray scattering, we have derived a low-resolution structural model of the complex between XD and N(TAIL), which shows that most of N(TAIL) remains disordered in the complex despite P-induced folding within the alpha-MoRE. The model consists of an extended shape accommodating the multiple conformations adopted by the disordered N-terminal region of N(TAIL), and of a bulky globular region, corresponding to XD and to the C terminus of N(TAIL) (aa 486-525). Using surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and heteronuclear magnetic resonance, we show that N(TAIL) has an additional site (aa 517-525) involved in binding to XD but not in the unstructured-to-structured transition. This work provides evidence that intrinsically disordered domains can establish complex interactions with their partners, and can contact them through multiple sites that do not all necessarily gain regular secondary structure.


Asunto(s)
Nucleoproteínas/química , Fosfoproteínas/química , Proteínas Virales/química , Sitios de Unión , Clonación Molecular , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Proteínas de la Nucleocápside , Nucleoproteínas/genética , Nucleoproteínas/metabolismo , Fosfoproteínas/metabolismo , Pliegue de Proteína , Estructura Terciaria de Proteína , Dispersión de Radiación , Eliminación de Secuencia , Espectrometría de Fluorescencia , Resonancia por Plasmón de Superficie , Proteínas Virales/genética , Proteínas Virales/metabolismo , Rayos X
20.
Artículo en Inglés | MEDLINE | ID: mdl-16511005

RESUMEN

The deblocking aminopeptidase (DAP) of Pyrococcus horikoshii is a hyperthermophilic exoprotease that cleaves the N-terminal amino acid of peptide substrates with a putative deblocking activity for acylated peptides. DAP has been found to be homologous to a tetrahedral aminopeptidase from the halophilic Haloarcula marismortui. The latter enzyme is a dodecameric complex and has been revealed to be a self-compartmentalized protease whose central cavity harbouring the catalytic site is accessible through several channels of different size, unlike all other known proteolytic complexes. Three paralogues of DAP have been identified in P. horikoshii, with about 40% identity between them. Each of them has been overexpressed in Escherichia coli, purified and crystallized in the native and selenomethionine-substituted states. The results indicate that they form two kinds of assemblies, of 12 and of 24 subunits, with a molecular weight of approximately 400 and approximately 800 kDa, respectively. Crystals of the different variants of DAP and in their different oligomeric states diffract up to a resolution of 3 A.


Asunto(s)
Aminopeptidasas/genética , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Pyrococcus horikoshii/enzimología , Aminopeptidasas/química , Aminopeptidasas/aislamiento & purificación , Proteínas Bacterianas/aislamiento & purificación , Escherichia coli/enzimología , Peso Molecular , Subunidades de Proteína/química , Subunidades de Proteína/aislamiento & purificación , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Difracción de Rayos X
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