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1.
J Nanosci Nanotechnol ; 12(11): 8613-8, 2012 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-23421252

RESUMEN

Magnetic properties of compacted Sm0.8Ca0.2MnO3 (SCMO) particles with average particle size of 23-100 nm, prepared by the glycine-nitrate method, have been investigated. It was found that the relative volume of the ferromagnetic phase decreases with decreasing particle size. Curves of field cooled and zero filed cooled magnetization (M(ZFC)) exhibit a bifurcation just below the Curie temperature (T(c) approximately 55-64 K) for all particles studied. The field dependence of M(ZFC) peak follows de Almeida-Thouless line. Both features are characteristic of spin-glasses (SG). Measurements of ac-susceptibility in the temperature range 5-300 K and the frequency range f = 10 Hz-10 kHz show a sharp peak for both real and imaginary components in the vicinity of T(c), apparently attributed to the Hopkinson effect. A second small peak is seemingly associated with antiferromagnetic or ferrimagnetic ordering. Though, for smaller particles both peaks depend on frequency, no shift to higher temperatures with increasing f, characteristic for SG systems, was observed. The dissimilarity in magnetic properties and dynamic characteristics observed for SCMO and for La0.8Ca0.2MnO3 nanoparticles is discussed, taking into account a difference in the width of the band and the strength of double exchange and interparticle interactions.


Asunto(s)
Compuestos de Calcio/química , Campos Magnéticos , Compuestos de Manganeso/química , Nanoestructuras/química , Nanoestructuras/ultraestructura , Óxidos/química , Samario/química , Ensayo de Materiales , Tamaño de la Partícula
2.
J Nanosci Nanotechnol ; 12(11): 8607-12, 2012 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-23421251

RESUMEN

Structural and magnetic properties of La0.2Ca0.8MnO3 nanoparticles with average size of 15-37 nm, prepared by the glycine-nitrate method, have been studied. Synchrotron experiments performed in the temperature range of 80-300 K have shown that a structural transition from room temperature orthorhombic Pnma to monoclinic P2(1)/m space group, associated with orbital ordering, occurs below 200 K in the studied particles. This transition observed for the largest particles of 37 nm is very close to that of bulk, as seen by similar temperature variation of lattice parameters and orthorhombic strain. The transition is highly suppressed for smaller 15 nm particles. Horizontal and vertical shifts of magnetic hysteresis loops (M(Shift) and H(EB)), displayed in a field cooled process, indicate size dependent exchange bias effect. It is also shown that M(shift) and H(EB), as well as the remanent magnetization M(r) and coercive field H(c) at low temperatures, exhibit a non-monotonic size dependence for particles around 23 nm. These effects may be attributed to the changes in uncompensated spins at the surface, anisotropy or alternatively to a transition from a multi-domain to the single domain state.


Asunto(s)
Calcio/química , Cerámica/química , Lantano/química , Compuestos de Manganeso/química , Nanoestructuras/química , Nanoestructuras/ultraestructura , Óxidos/química , Campos Magnéticos , Ensayo de Materiales , Tamaño de la Partícula
3.
Science ; 229(4714): 625-9, 1985 Aug 16.
Artículo en Inglés | MEDLINE | ID: mdl-4023701

RESUMEN

The structure of a T = 1 icosahedral particle (where T is the triangulation number), assembled from southern bean mosaic virus coat protein fragments that lacked the amino-terminal arm, was solved by means of model building procedures with the use of 6-angstrom resolution x-ray diffraction data. The icosahedral five-, three-, and twofold contacts were found to be similar, at this resolution, to the analogous contacts (icosahedral five-, quasi-three-, and quasi-twofolds) found in the parent T = 3 southern bean mosaic virus. However, the icosahedral fivefold contacts of the T = 3 structure are the most conserved in the T = 1 capsid. These results are consistent with a mechanism in which pentameric caps of dimers are the building blocks for the assembly of T = 1 and T = 3 icosahedral viruses.


Asunto(s)
Virus del Mosaico/ultraestructura , Proteínas Virales , Cápside/ultraestructura , Sustancias Macromoleculares , Modelos Moleculares , Unión Proteica , Conformación Proteica , Difracción de Rayos X
4.
J Photochem Photobiol B ; 189: 274-282, 2018 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-30428450

RESUMEN

Spectral Solar Photosynthetically Photon Flux Density (PPFD) (380 to 780 nm) reaching the surface of a plant in different lighting conditions has been analyzed in order to better understand the different photosynthetic performance of plants depending on their spatial situation and the vegetation surrounding. A comparison between the shadow of several trees in a sunny day and the case of a cloudy day in an open space has been studied. Three isolated trees (a palm tree, an olive tree and a shrub oleander) and a tipuana grove have been studied. The study has been developed in Valencia (Spain) during January and February 2017. A portable Asensetek Standard ALP-01 spectrometer with a measurement wavelength range of 380 to 780 nm, has been used. Conditions with higher PPFD received are found to be, apart from those of a sunny day, those for cloudy day (with a spectral maximum in the Green region of the spectrum), and those for individual trees and shrub shadows in a sunny day (with a spectral maximum in the Blue region). The case in which less amount of PPFD is received is that under the shadow of tipuana grove (with a spectral maximum in the Infrared region of the spectrum). In fact the order of magnitude in which the PPFD in a cloudy day exceeds the PPFD under the tipuana grove shade is up to 20.


Asunto(s)
Fotosíntesis , Hojas de la Planta/efectos de la radiación , Luz Solar , Tiempo (Meteorología) , Nerium , Olea , Phoeniceae , España , Árboles
5.
Structure ; 3(5): 491-502, 1995 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-7663946

RESUMEN

BACKGROUND: Catalase is a ubiquitous enzyme present in both the prokaryotic and eukaryotic cells of aerobic organisms. It serves, in part, to protect the cell from the toxic effects of small peroxides. Escherichia coli produces two catalases, HPI and HPII, that are quite distinct from other catalases in physical structure and catalytic properties. HPII, studied in this work, is encoded by the katE gene, and has been characterized as an oligomeric, monofunctional catalase containing one cis-heme d prosthetic group per subunit of 753 residues. RESULTS: The crystal structure of catalase HPII from E. coli has been determined to 2.8 A resolution. The asymmetric unit of the crystal contains a whole molecule, which is a tetramer with accurate 222 point group symmetry. In the model built, that includes residues 27-753 and one heme group per monomer, strict non-crystallographic symmetry has been maintained. The crystallographic agreement R-factor is 20.1% for 58,477 reflections in the resolution shell 8.0-2.8 A. CONCLUSIONS: Despite differences in size and chemical properties, which were suggestive of a unique catalase, the deduced structure of HPII is related to the structure of catalase from Penicillium vitale, whose sequence is not yet known. In particular, both molecules have an additional C-terminal domain that is absent in the bovine catalase. This extra domain contains a Rossmann fold but no bound nucleotides have been detected, and its physiological role is unknown. In HPII, the heme group is modified to a heme d and inverted with respect to the orientation determined in all previously reported heme catalases. HPII is the largest catalase for which the structure has been determined to almost atomic resolution.


Asunto(s)
Proteínas Bacterianas/química , Catalasa/química , Modelos Moleculares , Conformación Proteica , Secuencia de Aminoácidos , Animales , Proteínas Bacterianas/genética , Sitios de Unión , Catalasa/genética , Bovinos , Cristalografía por Rayos X , Escherichia coli/enzimología , Escherichia coli/genética , Proteínas Fúngicas/química , Hemo/química , Enlace de Hidrógeno , Hígado/enzimología , Micrococcus/enzimología , Datos de Secuencia Molecular , Penicillium/enzimología , Proteus mirabilis/enzimología , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Relación Estructura-Actividad
6.
J Mol Biol ; 185(1): 21-37, 1985 Sep 05.
Artículo en Inglés | MEDLINE | ID: mdl-4046038

RESUMEN

The refined structure of beef liver catalase (I. Fita, A. M. Silva, M. R. N. Murthy & M. G. Rossmann, unpublished results) is here examined with regard to possible catalytic mechanisms. The distal side of the deeply buried heme pocket is connected with the surface of the molecule by one (or possibly two) channel. The electron density representing the heme group, in each of the two crystallographically independent subunits, is consistent with degradation of the porphyrin rings. The heme group appears to be buckled, reflecting the high content of bile pigment in liver catalase. The spatial organization on the proximal side (where the fifth ligand of the iron is located) shows an elaborate network of interactions. The distal side contains the substrate pocket. The limited space in this region severely constrains possible substrate positions and orientations. The N delta atom of the essential His74 residue hydrogen bonds with O gamma of Ser113, which in turn hydrogen bonds to a water molecule associated with the propionic carbonylic group of pyrrole III. These interactions are also visible in the refined structure of Penicillium vitale catalase (B. K. Vainshtein, W. R. Melik-Adamyan, V. V. Barynin, A. A. Vagin, A. I. Grebenko, V. V. Borisov, K. S. Bartels, I. Fita, & M. G. Rossmann, unpublished results). Model building suggests a pathway for a catalase mechanism (compound I formation, as well as catalatic and peroxidatic reactions). There are some similarities in compound I formation of catalase and cytochrome c peroxidase.


Asunto(s)
Catalasa , Secuencia de Aminoácidos , Animales , Sitios de Unión , Bovinos , Cristalografía , Hemo , Enlace de Hidrógeno , Hígado/enzimología , Sustancias Macromoleculares , Modelos Moleculares , Conformación Molecular , Temperatura
7.
J Mol Biol ; 300(5): 1179-94, 2000 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-10903863

RESUMEN

Human rhinoviruses are classified into a major and a minor group based on their binding to ICAM-1 or to members of the LDL-receptor family, respectively. They can also be divided into groups A and B, according to their sensitivity towards a panel of antiviral compounds. The structure of human rhinovirus 2 (HRV2), which uses the LDL receptor for cell attachment and is included in antiviral group B, has been solved and refined at 2.6 A resolution by X-ray crystallography to gain information on the peculiarities of rhinoviruses, in particular from the minor receptor group. The main structural differences between HRV2 and other rhinoviruses, including the minor receptor group serotype HRV1A, are located at the internal protein shell surface and at the external antigenic sites. In the interior, the N termini of VP1 and VP4 form a three-stranded beta-sheet in an arrangement similar to that present in poliovirus, although myristate was not visible at the amino terminus of VP4 in the HRV2 structure. The betaE-betaF loop of VP2, a linear epitope within antigenic site B recognized by monoclonal antibody 8F5, adopts a conformation considerably different from that found in the complex of 8F5 with a synthetic peptide of the same sequence. This either points to considerable structural changes impinged on this loop upon antibody binding, or to the existence of more than one single conformation of the loop when the virus is in solution. The hydrophobic pocket of VP1 was found to be occupied by a pocket factor apparently identical with that present in the major receptor group virus HRV16. Electron density, consistent with the presence of a viral RNA fragment, is seen stacked against a conserved tryptophan residue.


Asunto(s)
Antígenos Virales/química , Rhinovirus/química , Rhinovirus/clasificación , Anticuerpos Antivirales/inmunología , Antígenos Virales/inmunología , Antígenos Virales/metabolismo , Sitios de Unión , Cápside/química , Cápside/inmunología , Cápside/metabolismo , Cristalografía por Rayos X , Humanos , Modelos Moleculares , Conformación Proteica , ARN Viral/metabolismo , Receptores de LDL/metabolismo , Receptores Virales/metabolismo , Rhinovirus/inmunología , Proteínas Virales/química , Proteínas Virales/inmunología , Proteínas Virales/metabolismo , Agua/metabolismo
8.
J Mol Biol ; 235(4): 1345-7, 1994 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-8308897

RESUMEN

Crystals of carbamate kinase (E.C.2.7.2.2) suitable for high resolution studies have been obtained, using the hanging drop vapour diffusion technique, with polyethylene glycol 8000 and NaCl as precipitants at pH 6.5 and a temperature of 4 degrees C. Crystals of about 0.3 mm x 0.2 mm x 0.2 mm in size diffract to at least 3.2 A resolution and are stable to X-radiation for more than ten hours. The space group is P2(1)2(1)2(1), with unit cell dimensions a = 84.5 A, b = 99.6 A, c = 173.3 A. Density packing considerations are consistent with the presence of four to five monomers (M(r) of the monomer = 33,000) in the asymmetric unit, two dimers or even a tetramer being favoured by the results of cross-linking experiments of the enzyme in solution.


Asunto(s)
Enterococcus faecium/enzimología , Fosfotransferasas (aceptor de Grupo Carboxilo)/química , Secuencia de Aminoácidos , Cristalización , Datos de Secuencia Molecular , Fosfotransferasas (aceptor de Grupo Carboxilo)/metabolismo , Homología de Secuencia de Aminoácido , Difracción de Rayos X
9.
J Mol Biol ; 167(1): 157-77, 1983 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-6864799

RESUMEN

It is shown that the formation of complexes with several arginine peptides stabilizes the B-form of DNA with 10 (+/- 0.15) base-pairs per turn at all relative humidities, even upon complete dehydration. From an analysis of the packing arrangement and from the calculated diffraction patterns, it is concluded that arginine is associated with DNA in its major groove. It is also shown that the diffraction pattern of nucleoprotamine can be interpreted by placing the protamine on the major groove of DNA. The strong intensity on the first layer-line is due to the influence of neutral residues on the diffraction pattern. Thus, we conclude that protamine is bound to the major groove of DNA.


Asunto(s)
Arginina , ADN , Péptidos , Composición de Base , Humedad , Sustancias Macromoleculares , Modelos Moleculares , Conformación de Ácido Nucleico , Protaminas , Difracción de Rayos X
10.
J Mol Biol ; 256(2): 364-76, 1996 Feb 23.
Artículo en Inglés | MEDLINE | ID: mdl-8594203

RESUMEN

The three-dimensional structure of the Fab fragment of a neutralizing monoclonal antibody (SD6) elicited against foot-and-mouth disease virus (FMDV) has been determined at 2.5 A resolution and refined to a crystallography agreement R-factor of 0.186. The structure has been compared with that of the same Fab molecule complexes with a 15 amino acid peptide (A15) representing a major antigenic site of FMDV, and determined at 2.8 A resolution. The Fab quaternary structure, defined both by the elbow angle between modules and by the relative disposition of the light and heavy domains inside the modules, remains essentially unchanged. However, the comparison shows important conformational variations in the paratope, especially in the hypervariable loops of the heavy chain. The CDR-H3 loop has a peculiar amino acid sequence (RREDGGDEGF) with a high content of charged residues. Some of these Fab residues were fully reoriented upon complex formation. The reorientation resulted not only in an alteration of shape but also in an important redistribution of charges, providing multiple points of interaction with the A15 antigen and in particular with the cell attachment Arg-Gly-Asp motif in the peptide. Thus the recognition of A15 by SD6 represents an extreme example of the induced fit mechanism in antibody interactions. The electron density maps provide evidence that in the uncomplexed Fab structure some CDR residues show, with lower occupancy, the conformations found in the complex, suggesting that the rearrangements observed can have only minor energetic requirements.


Asunto(s)
Anticuerpos Antivirales/química , Aphthovirus/inmunología , Fragmentos Fab de Inmunoglobulinas/química , Oligopéptidos/inmunología , Secuencia de Aminoácidos , Animales , Anticuerpos Monoclonales/química , Anticuerpos Monoclonales/inmunología , Anticuerpos Antivirales/inmunología , Reacciones Antígeno-Anticuerpo , Antígenos Virales/química , Antígenos Virales/inmunología , Secuencia de Bases , Sitios de Unión de Anticuerpos/inmunología , Cristalografía por Rayos X , ADN , Fragmentos Fab de Inmunoglobulinas/inmunología , Datos de Secuencia Molecular , Pruebas de Neutralización , Conformación Proteica
11.
J Mol Biol ; 213(2): 219-20, 1990 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-2187997

RESUMEN

Green crystals of the hexameric catalase HPII from Escherichia coli have been obtained by the hanging-drop method. The crystals belong to the monoclinic space group P2 with a = 123 A, b = 132 A, c = 93 A, beta = 112.5 degrees. There are three subunits in the asymmetric unit. The crystals diffract at least to 3.2 A resolution and are suitable for further X-ray diffraction studies.


Asunto(s)
Catalasa , Escherichia coli/enzimología , Cristalización , Difracción de Rayos X
12.
J Mol Biol ; 299(2): 463-76, 2000 Jun 02.
Artículo en Inglés | MEDLINE | ID: mdl-10860751

RESUMEN

Carbamoyl phosphate (CP), an essential precursor of arginine and the pyrimidine bases, is synthesized by CP synthetase (CPS) in three steps. The last step, the phosphorylation of carbamate, is also catalyzed by carbamate kinase (CK), an enzyme used by microorganisms to produce ATP from ADP and CP. Although the recently determined structures of CPS and CK show no obvious mutual similarities, a CK-like CPS reported in hyperthermophilic archaea was postulated to be a missing link in the evolution of CP biosynthesis. The 1.5 A resolution structure of this enzyme from Pyrococcus furiosus shows both a subunit topology and a homodimeric molecular organization, with a 16-stranded open beta-sheet core surrounded by alpha-helices, similar to those in CK. However, the pyrococcal enzyme exhibits many solvent-accessible ion-pairs, an extensive, strongly hydrophobic, intersubunit surface, and presents a bound ADP molecule, which does not dissociate at 22 degrees C from the enzyme. The ADP nucleotide is sequestered in a ridge formed over the C-edge of the core sheet, at the bottom of a large cavity, with the purine ring enclosed in a pocket specific for adenine. Overall, the enzyme structure is ill-suited for catalyzing the characteristic three-step reaction of CPS and supports the view that the CK-like CPS is in fact a highly thermostable and very slow (at 37 degrees C) CK that, in the extreme environment of P. furiosus, may have the new function of making, rather than using, CP. The thermostability of the enzyme may result from the extension of the hydrophobic intersubunit contacts and from the large number of exposed ion-pairs, some of which form ion-pair networks across several secondary structure elements in each enzyme subunit. The structure provides the first information on substrate binding and catalysis in CKs, and suggests that the slow rate at 37 degrees C is possibly a consequence of slow product dissociation.


Asunto(s)
Adenosina Difosfato/metabolismo , Fosfotransferasas (aceptor de Grupo Carboxilo)/química , Fosfotransferasas (aceptor de Grupo Carboxilo)/metabolismo , Pyrococcus furiosus/enzimología , Secuencia de Aminoácidos , Sitios de Unión , Carbamoil Fosfato/metabolismo , Catálisis , Cristalografía por Rayos X , Dimerización , Enterococcus faecalis/enzimología , Estabilidad de Enzimas , Cinética , Modelos Moleculares , Datos de Secuencia Molecular , Unión Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Solventes , Electricidad Estática , Relación Estructura-Actividad , Temperatura
13.
J Mol Biol ; 236(4): 1186-95, 1994 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-8120895

RESUMEN

Molecular dynamics simulations have been used to investigate the flexibility and variations in the shape of the binding site of an antibody against human Rhinovirus serotype 2 (HRV2) and its complex with a 15 amino acid oligopeptide, the structure of which has been recently determined by X-ray crystallography. During the simulation of the unbound antibody the binding site, defined in terms of the hypervariable regions or complementarity determining regions (CDRs), shows significant fluctuations in shape. For the complex such variations in the shape of the binding site were reduced. The largest fluctuations in the unbound antibody occurred within the CDR-H3. The largest differences between the bound and unbound crystal structures are also associated with CDR-H3. The relative displacements of the loops have been analysed in terms of internal distortions, rigid body motions of the loops and changes with respect to the framework regions. The degree to which the motions of the loops are correlated and the variation in the volume of the binding pocket during the simulation have also been examined.


Asunto(s)
Sitios de Unión de Anticuerpos , Secuencia de Aminoácidos , Anticuerpos Antivirales/química , Reacciones Antígeno-Anticuerpo , Cápside/genética , Cápside/inmunología , Proteínas de la Cápside , Simulación por Computador , Cristalografía por Rayos X , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Rhinovirus/genética , Rhinovirus/inmunología , Termodinámica , Proteínas Virales/genética , Proteínas Virales/inmunología
14.
J Mol Biol ; 302(5): 1227-40, 2000 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-11183785

RESUMEN

The structures of the two leader protease (Lpro) variants of foot-and-mouth disease virus known to date were solved using crystals in which molecules were organized as molecular fibers. Such crystals diffract to a resolution of only approximately 3 A. This singular, pseudo-polymeric organization is present in a new Lpro crystal form showing a cubic packing. As molecular fiber formation appeared unrelated to crystallization conditions, we mutated the reactive cysteine 133 residue, which makes a disulfide bridge between adjacent monomers in the fibers, to serine. None of the intermolecular contacts found in the molecular fibers was present in crystals of this variant. Analysis of this Lpro structure, refined at 1.9 A resolution, enables a detailed definition of the active center of the enzyme, including the solvent organization. Assay of Lpro activity on a fluorescent hexapeptide substrate showed that Lpro, in contrast to papain, was highly sensitive to increases in the cation concentration and was active only across a narrow pH range. Examination of the Lpro structure revealed that three aspartate residues near the active site, not present in papain-like enzymes, are probably responsible for these properties.


Asunto(s)
Aphthovirus/enzimología , Endopeptidasas/química , Endopeptidasas/metabolismo , Papaína/química , Papaína/metabolismo , Sustitución de Aminoácidos/genética , Aphthovirus/genética , Sitios de Unión , Catálisis/efectos de los fármacos , Cationes/farmacología , Cristalización , Cristalografía por Rayos X , Disulfuros/química , Endopeptidasas/genética , Enlace de Hidrógeno , Concentración de Iones de Hidrógeno , Modelos Moleculares , Mutación/genética , Estructura Secundaria de Proteína , Sales (Química)/farmacología , Solventes , Especificidad por Sustrato
15.
J Mol Biol ; 311(4): 837-49, 2001 Aug 24.
Artículo en Inglés | MEDLINE | ID: mdl-11518534

RESUMEN

Protein kinase Cepsilon (PKCepsilon) is a member of the novel PKCs which are activated by acidic phospholipids, diacylglycerol and phorbol esters, but lack the calcium dependence of classical PKC isotypes. The crystal structures of the C2 domain of PKCepsilon, crystallized both in the absence and in the presence of the two acidic phospholipids, 1,2-dicaproyl-sn-phosphatidyl-l-serine (DCPS) and 1,2-dicaproyl-sn-phosphatidic acid (DCPA), have now been determined at 2.1, 1.7 and 2.8 A resolution, respectively. The central feature of the PKCepsilon-C2 domain structure is an eight-stranded, antiparallel, beta-sandwich with a type II topology similar to that of the C2 domains from phospholipase C and from novel PKCdelta. Despite the similar topology, important differences are found between the structures of C2 domains from PKCs delta and epsilon, suggesting they be considered as different PKC subclasses. Site-directed mutagenesis experiments and structural changes in the PKCepsilon-C2 domain from crystals with DCPS or DCPA indicate, though phospholipids were not visible in these structures, that loops joining strands beta1-beta2 and beta5-beta6 participate in the binding to anionic membranes. The different behavior in membrane-binding and activation between PKCepsilon and classical PKCs appears to originate in localized structural changes, which include a major reorganization of the region corresponding to the calcium binding pocket in classical PKCs. A mechanism is proposed for the interaction of the PKCepsilon-C2 domain with model membranes that retains basic features of the docking of C2 domains from classical, calcium-dependent, PKCs.


Asunto(s)
Isoenzimas/química , Isoenzimas/metabolismo , Proteína Quinasa C/química , Proteína Quinasa C/metabolismo , Secuencia de Aminoácidos , Animales , Sitios de Unión , Calcio/metabolismo , Membrana Celular/metabolismo , Cristalografía por Rayos X , Isoenzimas/genética , Liposomas/metabolismo , Proteínas de la Membrana/química , Proteínas de la Membrana/genética , Proteínas de la Membrana/metabolismo , Modelos Biológicos , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Mutación , Ácidos Fosfatidicos/metabolismo , Fosfatidilserinas/metabolismo , Fosfolípidos/metabolismo , Unión Proteica , Proteína Quinasa C/genética , Proteína Quinasa C-epsilon , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Ratas , Alineación de Secuencia
16.
J Mol Biol ; 188(1): 63-72, 1986 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-3712444

RESUMEN

The structures of Penicillium vitale and beef liver catalase have been determined to atomic resolution. Both catalases are tetrameric proteins with deeply buried heme groups. The amino acid sequence of beef liver catalase is known and contains (at least) 506 amino acid residues. Although the sequence of P. vitale catalase has not yet been determined chemically, 670 residues have been built into the 2 A resolution electron density map and have been given tentative assignments. A large portion of each catalase molecule (91% of residues in beef liver catalase and 68% of residues in P. vitale catalase) shows structural homology. The root-mean-square deviation between 458 equivalenced C alpha atoms is 1.17 A. The dissimilar parts include a small fragment of the N-terminal arm and an additional "flavodoxin-like" domain at the carboxy end of the polypeptide chain of P. vitale catalase. In contrast, beef liver catalase contains one bound NADP molecule per subunit in a position equivalent to the chain region, leading to the flavodoxin-like domain, of P. vitale catalase. The position and orientation of the buried heme group in the two catalases, relative to the mutually perpendicular molecular dyad axes, are identical within experimental error. A mostly hydrophobic channel leads to the buried heme group. The surface opening to the channel differs due to the different disposition of the amino-terminal arm and the presence of the additional flavodoxin-like domain in P. vitale catalase. Possible functional implications of these comparisons are discussed.


Asunto(s)
Catalasa , Hígado/enzimología , Penicillium/enzimología , Secuencia de Aminoácidos , Animales , Evolución Biológica , Bovinos , Clostridium/análisis , Cristalografía , Flavodoxina , Hemo , Sustancias Macromoleculares , Modelos Moleculares , NADP , Conformación Proteica
17.
J Mol Biol ; 221(2): 623-35, 1991 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-1920437

RESUMEN

We have determined the crystal structure of the dodecamer d(CCCCCGCGGGGG), showing for the first time a complete turn of A-DNA. It has average structural parameters similar to those determined in fibres. Nevertheless it shows a considerable local variation in structure which is in part associated with the presence of a bound spermine molecule. We conclude that the local DNA conformation does not only depend on the base sequence, but may be strongly modified upon interaction with other molecules. In particular, the CpG sequence, which is found in hypersensitive regions of the genome, appears to be able to easily change its conformation under external influences.


Asunto(s)
ADN/química , Conformación de Ácido Nucleico , Secuencia de Bases , Sitios de Unión , ADN/metabolismo , Fosfatos de Dinucleósidos/química , Datos de Secuencia Molecular , Espermina/química , Agua/química , Difracción de Rayos X
18.
J Mol Biol ; 286(1): 135-49, 1999 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-9931255

RESUMEN

The structure of the peroxisomal catalase A from the budding yeast Saccharomyces cerevisiae, with 515 residues per subunit, has been determined and refined to 2.4 A resolution. The crystallographic agreement factors R and Rfree are 15.4% and 19.8%, respectively. A tetramer with accurate 222-molecular symmetry is located in the asymmetric unit of the crystal. The conformation of the central core of catalase A, about 300 residues, remains similar to the structure of catalases from distantly related organisms. In contrast, catalase A lacks a carboxy-terminal domain equivalent to that found in catalase from Penicillium vitalae, the only other fungal catalase structure available. Structural peculiarities related with the heme and NADP(H) binding pockets can be correlated with biochemical characteristics of the catalase A enzyme. The network of molecular cavities and channels, filled with solvent molecules, supports the existence of one major substrate entry and at least two possible alternative pathways to the heme active site. The structure of the variant protein Val111Ala, also determined by X-ray crystallography at 2.8 A resolution, shows a few, well-localized, differences with respect to the wild-type enzyme. These differences, that include the widening of the entry channel in its narrowest point, provide an explanation for both the increased peroxidatic activity and the reduced catalatic activity of this mutant.


Asunto(s)
Catalasa/química , Saccharomyces cerevisiae/enzimología , Alanina/genética , Sitios de Unión , Catalasa/genética , Cristalografía por Rayos X , Hemo/química , Modelos Moleculares , Mutagénesis Sitio-Dirigida , NADP/metabolismo , Conformación Proteica , Valina/genética
19.
J Mol Biol ; 188(1): 49-61, 1986 Mar 05.
Artículo en Inglés | MEDLINE | ID: mdl-3712443

RESUMEN

The three-dimensional structure analysis of crystalline fungal catalase from Penicillium vitale has been extended to 2.0 A resolution. The crystals belong to space group P3(1)21, with the unit cell parameters of a = b = 144.4 A and c = 133.8 A. The asymmetric unit contains half a tetrameric molecule of 222 symmetry. Each subunit is a single polypeptide chain of approximately 670 amino acid residues and binds one heme group. The amino acid sequence has been tentatively determined by computer graphics model building (using the FRODO system) and comparison with the known sequence of beef liver catalase. The atomic model has been refined by the Hendrickson & Konnert (1981) restrained least-squares program against 68,000 reflections between 5 A and 2 A resolution. The final R-factor is 0.31 after 24 refinement cycles. The secondary and tertiary structure of the catalase has been analyzed.


Asunto(s)
Catalasa , Penicillium/enzimología , Secuencia de Aminoácidos , Aminoácidos/análisis , Cristalografía , Hemo , Enlace de Hidrógeno , Sustancias Macromoleculares , Modelos Moleculares , Conformación Proteica
20.
Protein Sci ; 1(9): 1154-61, 1992 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-1338980

RESUMEN

The crystal structure of the antigen-binding fragment of a monoclonal antibody (8F5) that neutralizes human rhinovirus serotype 2 has been determined by X-ray diffraction studies. Antibody 8F5, obtained by immunization with native HRV2 virions, cross-reacts with peptides of the viral capsid protein VP2, which contribute to the neutralizing immunogenic site B in this serotype. The structure was solved by the molecular replacement method and has been refined to an R-factor of 18.9% at 2.8 A resolution. The elbow angle, relating the variable and constant modules of the molecule is 127 degrees, representing the smallest elbow angle observed so far in an Fab fragment. Furthermore, the charged residues of the epitope can be well accommodated in the antigen-binding site. This is the first crystal structure reported for an antibody directed against an icosahedral virus.


Asunto(s)
Anticuerpos Monoclonales/química , Anticuerpos Antivirales/química , Fragmentos Fab de Inmunoglobulinas/química , Conformación Proteica , Estructura Secundaria de Proteína , Rhinovirus/inmunología , Secuencia de Aminoácidos , Anticuerpos Monoclonales/genética , Anticuerpos Antivirales/genética , Antígenos Virales/inmunología , Secuencia de Bases , Cápside/inmunología , Reacciones Cruzadas , Humanos , Fragmentos Fab de Inmunoglobulinas/genética , Cadenas Pesadas de Inmunoglobulina/química , Cadenas Pesadas de Inmunoglobulina/genética , Cadenas Ligeras de Inmunoglobulina/química , Cadenas Ligeras de Inmunoglobulina/genética , Región Variable de Inmunoglobulina/química , Región Variable de Inmunoglobulina/genética , Modelos Moleculares , Datos de Secuencia Molecular , Pruebas de Neutralización , Rhinovirus/clasificación , Serotipificación , Virión/inmunología , Difracción de Rayos X
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