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1.
Science ; 267(5206): 1958-65, 1995 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-7701318

RESUMO

The crystal structure of a class I aminoacyl-transfer RNA synthetase, glutamyl-tRNA synthetase (GluRS) from Thermus thermophilus, was solved and refined at 2.5 A resolution. The amino-terminal half of GluRS shows a geometrical similarity with that of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) of the same subclass in class I, comprising the class I-specific Rossmann fold domain and the intervening subclass-specific alpha/beta domain. These domains were found to have two GluRS-specific, secondary-structure insertions, which then participated in the specific recognition of the D and acceptor stems of tRNA(Glu) as indicated by mutagenesis analyses based on the docking properties of GluRS and tRNA. In striking contrast to the beta-barrel structure of the GlnRS carboxyl-terminal half, the GluRS carboxyl-terminal half displayed an all-alpha-helix architecture, an alpha-helix cage, and mutagenesis analyses indicated that it had a role in the anticodon recognition.


Assuntos
Glutamato-tRNA Ligase/química , Thermus thermophilus/enzimologia , Sequência de Aminoácidos , Aminoacil-tRNA Sintetases/química , Anticódon , Evolução Biológica , Gráficos por Computador , Cristalografia por Raios X , Escherichia coli/enzimologia , Glutamato-tRNA Ligase/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Conformação Proteica , Dobramento de Proteína , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , RNA de Transferência de Ácido Glutâmico/química , RNA de Transferência de Ácido Glutâmico/metabolismo , Alinhamento de Sequência
2.
Science ; 256(5056): 523-6, 1992 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-1575827

RESUMO

The x-ray structure of T4 endonuclease V, an enzyme responsible for the first step of a pyrimidine-dimer-specific excision-repair pathway, was determined at a 1.6-angstrom resolution. The enzyme consists of a single compact domain classified into an all-alpha structure. This single domain has two distinct catalytic activities; it functions as a pyrimidine dimer glycosylase and as an apurinic-apyrimidinic endonuclease. The amino-terminal segment penetrates between two major helices and prevents their direct contact. The refined structure suggests the residues involved in the substrate binding and the catalysis of the glycosylation reaction.


Assuntos
Reparo do DNA , Endodesoxirribonucleases/química , Dímeros de Pirimidina/metabolismo , Proteínas Virais , Sequência de Aminoácidos , Desoxirribonuclease (Dímero de Pirimidina) , Eletroquímica , Endodesoxirribonucleases/metabolismo , Glicosilação , Ligação de Hidrogênio , Dados de Sequência Molecular , Estrutura Molecular , Mutagênese Sítio-Dirigida , Conformação Proteica , Relação Estrutura-Atividade , Especificidade por Substrato , Fagos T/enzimologia , Difração de Raios X
3.
J Mol Biol ; 249(2): 360-75, 1995 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-7783199

RESUMO

Crystallographic study of bacteriophage T4 endonuclease V, which is involved in the initial step of the pyrimidine dimer-specific excision repair pathway, has been carried out with respect to the wild-type and three different mutant enzymes. This enzyme catalyzes the cleavage of the N-glycosyl bond at the 5'-side of the pyrimidine dimer, and subsequently incises the phosphodiester bond at the apyrimidinic site through a beta-elimination reaction. The structure of the wild-type enzyme refined at 1.45 A resolution reveals the detailed molecular architecture. The enzyme is composed of a single compact domain classified as an all-alpha structure. The molecule is stabilized mainly by three hydrophobic cores, two of which include many aromatic side-chain interactions. The structure has a unique folding motif, where the amino-terminal segment penetrates between two major alpha-helices and prevents their direct contact, and it is incompatible with the close-packing category of helices for protein folding. The concave surface, covered with many positive charges, implies an interface for DNA binding. The glycosylase catalytic center, which comprises Glu23 and the surrounding basic residues Arg3, Arg22 and Arg26, lie in this basic surface. The crystal structures of the three active-site mutants, in which Glu23 was replaced by Gln(E23Q) and Asp (E23D), respectively, and Arg3 by Gln (R3Q), have been determined at atomic resolution. The backbone structures of the E23Q and R3Q mutants were almost identical with that of the wild-type, while the E23D mutation induces a small, but significant, change in the backbone structure, such as an increase of the central kink of the H1 helix at Pro25. In the catalytic center of the glycosylase, however, these three mutations do not generate notable movements of protein atoms, except for significant shifts of some bound water molecules. Thus, the structural differences between the wild-type and each mutant are confined to the remarkably small region around their replaced chemical groups. Combined with the biochemical studies and the difference circular dichroism measurements, these results allow us to conclude that the negatively charged carboxyl group of Glu23 is essential for the cleavage of the N-glycosyl bond, and that the positively charged guanidino group of Arg3 is crucial to bind the substrate, a DNA duplex containing a pyrimidine dimer. The amino terminal alpha-amino group is located at a position approximately 4.4 A away from the carboxyl group of Glu23. These structural features are generally consistent with the reaction scheme proposed by Dodson and co-workers.


Assuntos
Endodesoxirribonucleases/química , Estrutura Secundária de Proteína , Proteínas Virais , Sequência de Aminoácidos , Sítios de Ligação , Gráficos por Computador , Simulação por Computador , Cristalografia por Raios X/métodos , Reparo do DNA , Desoxirribonuclease (Dímero de Pirimidina) , Endodesoxirribonucleases/metabolismo , Ligação de Hidrogênio , Modelos Moleculares , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Termodinâmica
4.
J Mol Biol ; 230(2): 529-42, 1993 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-8385228

RESUMO

The crystal structure of Thermus thermophilus RNase H was determined at 2.8 A resolution. The structure was solved by the molecular replacement method, based on the accurately refined structure of Escherichia coli RNase HI, which shows 52% amino acid sequence identity. Crystallographic refinement led to an R-factor of 0.205, with a 0.019 A root-mean-square deviation from ideal bond lengths and 0.048 A from ideal bond angle distances. Structural comparison shows a striking similarity in the overall folding of the thermophilic and mesophilic enzymes. The root-mean-square displacement is 0.95 A between equivalent alpha-carbon atoms from all elements of secondary structure (five alpha-helices and five beta-strands). However, some notable differences, which account for the enhanced thermostability of T. thermophilus RNase H, are observed in loop structures and side-chain conformations. The substitution of Gly for the left-handed helical residue (Lys95) in the E. coli enzyme is proposed to substantially enhance the thermostability, due to the release of steric hindrance caused by the beta-carbon atom. Furthermore, it is likely that the expansion of an aromatic cluster, arising from the replacement of Ile78 in the mesophilic enzyme by Phe, and the increased number of salt-bridges additively contribute to the stability.


Assuntos
Estrutura Secundária de Proteína , Ribonuclease H/química , Thermus thermophilus/enzimologia , Sequência de Aminoácidos , Estabilidade Enzimática , Escherichia coli/enzimologia , Ligação de Hidrogênio , Matemática , Modelos Moleculares , Dados de Sequência Molecular , Homologia de Sequência de Aminoácidos , Termodinâmica , Difração de Raios X/métodos
5.
J Mol Biol ; 230(3): 979-96, 1993 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-8386773

RESUMO

RNase F1, a guanine-specific ribonuclease from Fusarium moniliforme, was crystallized in two different forms, in the absence of an inhibitor and in the presence of 2'GMP. The crystal structure of the RNase F1 free form was solved by the molecular replacement method, using the co-ordinates of the RNase T1 complex with 2'GMP, and was refined to a final R-factor of 18.7%, using the data extended to 1.3 A resolution. For the crystal structure of the RNase F1 complex with 2'GMP, the solution of the molecular replacement method was obtained on the basis of the co-ordinates of the RNase F1 free form, and was refined to a final R-factor of 16.8%, using the data up to 2 A resolution. The two crystal structures of the RNase F1 free form and the complex with 2'GMP are very similar to each other as reflected by a small root-mean-square displacement (r.m.s.d.) value of 0.43 A for all C alpha atoms. The main differences between the two structures are associated with binding of 2'GMP in the substrate recognition site in the loop between Tyr42 and Glu46. A structural comparison between RNase F1 and RNase T1 shows a substantial similarity between all the C alpha atoms, as evidenced by a r.m.s.d. value of 1.4 A. The loop from residues 32 to 38 was strikingly different between these two enzymes, in both its conformation and its hydrogen bonding schemes. The side-chain of a catalytically active residue, His92, is shifted away from the catalytic site in RNase F1 by 1.3 A and 0.85 A with respect to the corresponding positions in the RNase T1 free form and in the RNase T1 complex with 2'GMP, respectively. In the RNase F1 complex, the guanine base of 2'GMP has a syn conformation about the glycosyl bond, and the furanose ring assumes a 3'-exo pucker, which is different from that found in the complex with RNase T1. In the catalytic site of the RNase F1 complex with 2'GMP, one water molecule was observed, which bridges the phosphate oxygen atoms of 2'GMP and the side-chains of the catalytically important residues, His92 and Arg77, through hydrogen bonds. A water molecule occupying the same position was found in the RNase F1 free form. The significance of this water molecule in the hydrolytic reaction is discussed.


Assuntos
Fusarium/enzimologia , Guanosina Monofosfato/química , Ribonuclease T1/química , Sequência de Aminoácidos , Guanosina Monofosfato/metabolismo , Ligação de Hidrogênio , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Ribonuclease T1/metabolismo , Homologia de Sequência de Aminoácidos , Água/química , Difração de Raios X
6.
J Mol Biol ; 223(4): 1029-52, 1992 Feb 20.
Artigo em Inglês | MEDLINE | ID: mdl-1311386

RESUMO

The crystal structure of RNase H from Escherichia coli has been determined by the multiple isomorphous replacement method, and refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.196 at 1.48 A resolution. In the final structure, the root-mean-square (r.m.s.) deviation for bond lengths is 0.017 A, and for angle distances 0.036 A. The structure is composed of a five-stranded beta-sheet and five alpha-helices, and reveals the details of hydrogen bonding, electrostatic and hydrophobic interactions between intra- and intermolecular residues. The refined structure allows an explanation of the particular interactions between the basic protrusion, consisting of helix alpha III and the following loop, and the remaining major domain. The beta-sheet, alpha II, alpha III and alpha IV form a central hydrophobic cleft that contains all six tryptophan residues, and presumably serves to fix the orientation of the basic protrusion. Two parallel adjacent helices, alpha I and alpha IV, are associated with a few triads of hydrophobic interactions, including many leucine residues, that are similar to the repeated leucine motif. The well-defined electron density map allows detailed discussion of amino acid residues likely to be involved in binding a DNA/RNA hybrid, and construction of a putative model of the enzyme complexed with a DNA/RNA hybrid oligomer. In this model, a protein region, from the Mg(2+)-binding site to the basic protrusion, covers roughly two turns of a DNA/RNA hybrid double helix. A segment (11-23) containing six glycine residues forms a long loop between the beta A and beta B strands. This loop, which protrudes into the solvent region, lies on the interface between the enzyme and a DNA/RNA hybrid in the model of the complex. The mean temperature factors of main-chain atoms show remarkably high values in helix alpha III that constitutes the basic protrusion, suggesting some correlation between its flexibility and the nucleic acid binding function. The Mg(2+)-binding site, surrounded by four invariant acidic residues, can now be described more precisely in conjunction with the catalytic activity. The arrangement of molecules within the crystal appears to be dominated by the cancelling out of a remarkably biased charge distribution on the molecular surface, which is derived in particular from the separation between the acidic Mg(2+)-binding site and the basic protrusion.


Assuntos
Escherichia coli/enzimologia , Ribonuclease H/ultraestrutura , Sequência de Aminoácidos , Gráficos por Computador , Cristalografia , Cisteína/química , Histidina/química , Ligação de Hidrogênio , Magnésio/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Estrutura Molecular , Conformação Proteica , Ribonuclease H/química , Solubilidade , Triptofano/química , Água/química , Difração de Raios X
7.
J Biochem ; 128(1): 21-7, 2000 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-10876154

RESUMO

To address the effects of single amino acid substitutions on the flexibility of Escherichia coli dihydrofolate reductase (DHFR), the partial specific volume (v(o)) and adiabatic compressibility (beta(s)(o)) were determined for a series of mutants with amino acid replacements at Gly67 (7 mutants), Gly121 (6 mutants), and Ala145 (5 mutants) located in three flexible loops, by means of precise sound velocity and density measurements at 15 degrees C. These mutations induced large changes in v(o) (0.710-0.733 cm(3). g(-1)) and beta(s)(o) (-1.8 x 10(-6)-5.5 x 10(-6) bar(-1)) from the corresponding values for the wild-type enzyme (v(o)=0.723 cm(3). g(-1), beta(s)(o) = 1.7 x 10(-6) bar(-1)), probably due to modifications of internal cavities. The beta(s)(o) value increased with increasing v(o), but showed a decreasing tendency with the volume of the amino acid introduced. There was no significant correlation between beta(s)(o) and the overall stability of the mutants determined from urea denaturation experiments. However, a mutant with a large beta(s)(o) value showed high enzyme activity mainly due to an enhanced catalytic reaction rate (k(cat)) and in part due to increased affinity for the substrate (K(m)), despite the fact that the mutation sites are far from the catalytic site. These results demonstrate that the flexibility of the DHFR molecule is dramatically influenced by a single amino acid substitution in one of these loops and that the flexible loops of this protein play important roles in determining the enzyme function.


Assuntos
Tetra-Hidrofolato Desidrogenase/química , Tetra-Hidrofolato Desidrogenase/genética , Substituição de Aminoácidos , Estabilidade Enzimática , Mutação Puntual
8.
J Biochem ; 115(1): 168-70, 1994 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-8188627

RESUMO

Two proteins that act as alpha-amylase inhibitors, Haim I and Paim I, were crystallized and preliminary X-ray diffraction studies on them were carried out. We also sequenced Haim I prepared from Streptomyces griseosporeus YM-25 and confirmed that it is composed of 78 amino acid residues. Crystals of Haim I were grown from ammonium sulfate solution mixed with ethanol by the vapor diffusion technique. The crystals grew as hexagonal bipyramids and diffracted X-rays beyond 2.0 A resolution. They belong to the space group P6(1)22 (or P6(5)22) with unit cell dimensions of a = b = 36.7 A, c = 192.4 A, and contain one molecule per asymmetric unit. Paim I, a protein of 39 amino acid residues produced by Streptomyces corchorusii, was crystallized under similar conditions to Haim I. The crystals diffracted X-rays beyond 2.5 A. They belong to the space group P4(1)2(1)2 (or P4(3)2(1)2) with unit cell dimensions of a = b = 65.4 A, c = 96.1 A, and contain three molecules per asymmetric unit.


Assuntos
Proteínas de Bactérias/química , Peptídeos/química , alfa-Amilases/antagonistas & inibidores , Sequência de Aminoácidos , Cristalização , Cristalografia por Raios X , Dados de Sequência Molecular , Streptomyces/química
9.
Microsc Res Tech ; 39(1): 71-84, 1997 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-9329020

RESUMO

Several models for preparing and isolating human and animal gallbladder epithelial cells, including low-grade gallbladder carcinoma cells, as well as proposed systems for culturing these isolated epithelial cells are reviewed here. Several reports concerning tissue culture of the gallbladder are also reviewed. The cell culture systems are divided into monolayer cell culture on collagen-coated or uncoated culture dishes or other culture substrate and three-dimensional cell culture in collagen gel. To prepare and isolate gallbladder epithelial cells, digestion of the gallbladder mucosa, abrasion of the mucosal epithelial cells, and excision of epithelial outgrowth of mucosal explants are applied. In monolayer cell culture, most of the specific biological features of isolated and cultured cells characteristic to the gallbladder are gradually lost after several passages, though quantitative and objective analyses of the pathophysiology of cultured cells and their secretory substances can be performed. Tissue culture using explants of the gallbladder has mainly been used for physiological studies of the gallbladder, such as investigating the transport of water and electrolytes. In this tissue culture system, quantitative assessment is difficult, though the original and specific biological and histological characteristics of the gallbladder are retained. Three-dimensional collagen gel culture could be an ideal model combining monolayer cell culture and tissue culture systems, and create controllable conditions or environments when several biologically active substances, such as growth factors, proinflammatory cytokines and adhesion molecules, are added to the culture medium. Advantages and shortcomings of individual cultivation models are discussed, and selecting the culture model most appropriate to the purpose of the study will facilitate investigations of the biology and pathogenetic mechanisms of gallbladder diseases such as cholelithiasis.


Assuntos
Técnicas de Cultura de Células/métodos , Células Epiteliais/citologia , Células Epiteliais/patologia , Vesícula Biliar/citologia , Animais , Biomarcadores , Moléculas de Adesão Celular/farmacologia , Células Cultivadas/citologia , Células Cultivadas/metabolismo , Células Cultivadas/ultraestrutura , Meios de Cultura/metabolismo , Células Epiteliais/ultraestrutura , Substâncias de Crescimento/farmacologia , Humanos , Mediadores da Inflamação/farmacologia , Microscopia Eletrônica , Técnicas de Cultura de Órgãos/métodos , Coelhos , Células Tumorais Cultivadas/citologia , Células Tumorais Cultivadas/metabolismo , Células Tumorais Cultivadas/ultraestrutura
10.
Pathol Res Pract ; 197(2): 65-76, 2001.
Artigo em Inglês | MEDLINE | ID: mdl-11261820

RESUMO

Idiopathic portal hypertension (IPH) is characterized by a long-standing presinusoidal portal hypertension of unknown etiology in adults. Some unidentified agent(s) affect(s) the intrahepatic small portal veins or portal tracts. Immunological disturbance, thromboembolism, infectious etiology and/or increased fibrogenesis in portal tracts are suspected as being candidates for the primary agent(s). During the long clinical course of IPH, several pathological changes may occur, including subcapsular parenchymal atrophy, atrophy of the liver, portal and parenchymal fibrosis, and portal venous phlebosclerosis and thrombosis. The last-named of these lesions is mostly found in patients with a history of splenectomy. Subcapsular parenchymal and hepatic atrophy may result from a hepatocellular dropout via apoptosis or necrosis because of intrahepatic hemodynamic disturbances, particularly chronic portal venous blood insufficiency. Pericellular fibrosis and thin fibrous septa are also frequently found and associated with activated perisinusoidal cells positive for smooth muscle actin. At the same time, vague nodular hyperplasia of hepatocytes not surrounded by fibrous septa is not infrequently seen. It may resemble nodular regenerative hyperplasia, partial nodular transformation, or focal nodular hyperplasia. However, liver cirrhosis does not occur even at the terminal stage. Taking these findings into consideration, a new staging of IPH with a combination of hepatic parenchymal atrophy and portal venous thrombosis was proposed: non-atrophic liver without subcapsular parenchymal atrophy (stage I), non-atrophic liver with subcapsular parenchymal atrophy (stage II), atrophic liver with subcapsular parenchymal atrophy (stage III), and portal venous occlusive thrombosis (stage IV). IPH livers are likely to progress from stage I to stage III. Stage IV, which occurs relatively late, has a poor prognosis. This staging is applicable to clinical and autopsy cases without any histological data.


Assuntos
Hipertensão Portal , Hipertensão Portal/etiologia , Hipertensão Portal/patologia , Fígado/patologia , Adulto , Feminino , Humanos , Hipertensão Portal/fisiopatologia , Masculino , Pessoa de Meia-Idade
11.
Pathol Res Pract ; 192(6): 634-45, 1996 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-8857652

RESUMO

We previously developed a model in which rabbit gall bladder epithelial cells in collagen gels proliferated and formed multicellular spherical cysts after 2 to 4 days. In the present study, we examined in depth the dynamic processes of loss and reestablishment of cell polarity of rabbit gallbladder epithelial cells isolated and cultured in collagen gel. Six hours after being place in culture, the isolated epithelial cells had lost the morphologic features and phenotypic markers inherent in the in vivo gallbladder mucosa, and autophagic vacuoles appeared transiently, reflecting epithelial cell injury, or remodelling, or both. After 12 hours, mucin dots appeared in clumps of epithelial cells and gradually became larger, and the epithelial cell clumps were transformed into multicellular cysts after 1 to 2 days. The luminal surfaces of the mucin dots (intracytoplasmic inclusions or small lumens sealed by several epithelial cells) and multicellular cysts were covered by microvilli and presented profiles of mucus glycoprotein and carbohydrate residues shared with the in vivo gallbladder mucosa. The presence of cellular adhesion structures and the distribution of cellular organelles toward the luminal surface implied the reestablishment of epithelial cell polarity. The addition of cytochalasin B induced many mucin-positive cytoplasmic inclusions covered by microvilli in the epithelial cells of the multicellular cysts, while the addition of transforming growth factor beta 1 promoted maturation of the multicellular cysts. This short term culture is useful for the analysis of the polarity of biliary epithelial cells and for examining disorders in this polarity.


Assuntos
Citocalasina B/farmacologia , Vesícula Biliar/efeitos dos fármacos , Vesícula Biliar/ultraestrutura , Fator de Crescimento Transformador beta/farmacologia , Animais , Sequência de Carboidratos , Técnicas de Cultura de Células/métodos , Colágeno , Meios de Cultura , Células Epiteliais , Epitélio/efeitos dos fármacos , Epitélio/ultraestrutura , Vesícula Biliar/citologia , Géis , Masculino , Coelhos
13.
Liver ; 18(2): 90-8, 1998 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-9588767

RESUMO

We developed methods to isolate biliary epithelial cells (BECs) from the gallbladder (GB), common bile duct (CBD), intrahepatic large bile duct (ILBD) and small bile duct (ISBD) of a mouse, simultaneously. ILBD and ISBD were cut from the biliary tree after collagenase perfusion of the liver. BECs from all of these biliary segments were cultured as explants on collagen gel. BECs spread from the explants and formed cellular sheets. Areas of these sheets composed entirely of BECs were cut and placed on other gels as subculture, and this continued for 10 passages. Primary and passage cultured BECs on gel were composed of a monolayer of epithelial cells. Passaged cultured BECs in gel formed a spherical cyst lined by a single epithelial layer. Ultrastructurally, microvilli were dense on the luminal surface, and junctional complex and interdigitation was identifiable on the lateral surfaces. These features were similar in both primary and passaged cultured BECs, irrespective of their anatomical origin. Major histocompatibility complex antigens and intercellular adhesion molecule-1 were induced on the basolateral cell membranes of primary and passaged cultured BECs, by interferon-gamma. Although several phenotypic, structural and probable biological features of BECs inherent to each anatomical level may be lost after culture on gel, a combination of this method, several immunological modifications in experimental animals, and addition of immunologically active substances to the culture medium will make the immunopathologic analysis of biliary diseases possible.


Assuntos
Ductos Biliares Extra-Hepáticos/citologia , Ductos Biliares Intra-Hepáticos/citologia , Ducto Colédoco/citologia , Células Epiteliais/citologia , Vesícula Biliar/citologia , Animais , Técnicas de Cultura de Células/métodos , Separação Celular/métodos , Células Epiteliais/fisiologia , Antígenos de Histocompatibilidade Classe I/metabolismo , Antígenos de Histocompatibilidade Classe II/metabolismo , Molécula 1 de Adesão Intercelular/metabolismo , Junções Intercelulares/ultraestrutura , Queratinas/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos ICR , Molécula 1 de Adesão de Célula Vascular/metabolismo
14.
Proteins ; 17(4): 337-46, 1993 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-8108376

RESUMO

To obtain more precise insight into the Mg(2+)-binding site essential for RNase HI catalytic activity, we have determined the crystal structure of E. coli RNase HI in complex with Mg2+. The analyzed cocrystal, which is not isomorphous with the Mg(2+)-free crystal previously refined at 1.48 A resolution, was grown at a high MgSO4 concentration more than 100 mM so that even weakly bound Mg2+ sites could be identified. The structure was solved by the molecular replacement method, using the Mg(2+)-free crystal structure as a search model, and was refined to give a final R-value of 0.190 for intensity data from 10 to 2.8 A, using the XPLOR and PROLSQ programs. The backbone structures are in their entirety very similar to each other between the Mg(2+)-bound and the metal-free crystals, except for minor regions in the enzyme interface with the DNA/RNA hybrid. The active center clearly revealed a single Mg2+ atom located at a position almost identical to that previously found by the soaking method. Although the two metal-ion mechanism had been suggested by another group (Yang, W., Hendrickson, W.A., Crouch, R.J., Satow, Y. Science 249:1398-1405, 1990) and partially supported by the crystallographic study of inactive HIV-1 RT RNase H fragment (Davies, J.F., II, Hostomska, Z., Hostomsky, Z., Jordan, S.R., Matthews, D. Science 252:88-95, 1991), the present result excludes the possibility that RNase HI requires two metal-binding sites for activity. In contrast to the features in the metal-free enzyme, the side chains of Asn-44 and Glu-48 are found to form coordinate bonds with Mg2+ in the metal-bound crystal.


Assuntos
Escherichia coli/enzimologia , Magnésio/metabolismo , Ribonuclease H/química , Sítios de Ligação , Cristalografia , Modelos Moleculares , Ribonuclease H/fisiologia
15.
Nucleic Acids Res ; 19(8): 1817-23, 1991 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-1709492

RESUMO

Tertiary models of ribonuclease H (RNase H) domains in reverse transcriptases (RTs) from Moloney murine leukemia virus (MuLV) and human immunodeficiency virus (HIV-1) were built based upon the X-ray structure of RNase H from Escherichia coli (E. coli RNase H). In two models of RT-RNase H domains, not only active site residues but also residues, which construct a hydrophobic core and hydrogen bonds, are located in the same positions as those of E. coli RNase H. The whole backbone structure and the electrostatic molecular surface of MuLV RT-RNase H model are similar to those of E. coli RNase H. On the contrary, HIV-1 RT-RNase H model lacks the third helix and the following loop, resulting no positive charge clusters around the hybrid recognition site. Referring the complex models of RTs with their substrate hybrid, the interaction between DNA-polymerase and RNase H domains in RTs was discussed.


Assuntos
Endorribonucleases/química , HIV-1/enzimologia , Modelos Moleculares , Vírus da Leucemia Murina de Moloney/enzimologia , DNA Polimerase Dirigida por RNA/química , Sequência de Aminoácidos , Endorribonucleases/metabolismo , Escherichia coli/enzimologia , Ligação de Hidrogênio , Dados de Sequência Molecular , DNA Polimerase Dirigida por RNA/metabolismo , Ribonuclease H , Alinhamento de Sequência , Difração de Raios X
16.
J Gastroenterol Hepatol ; 9(1): 75-9, 1994.
Artigo em Inglês | MEDLINE | ID: mdl-8155872

RESUMO

The intrahepatic biliary tree is regarded as an excretory duct of two secretory units: hepatocytes and intrahepatic peribiliary glands. This review describes the anatomy, development and presumed functions of the latter. These glands are preferentially located around the intrahepatic large bile ducts, and are histologically divided into intramural and extramural structures. The former consist of simple tubular glands with much mucin, and are sparsely and irregularly distributed within the ductal wall. The latter are characterized by the presence of excretory units that consist of seromucinous acini and a conducting system in the periductal tissue. Pancreatic exocrine acini are occasionally admixed with extramural glands. These peribiliary glands appear in the late fetal period and complete their development about 15 years after birth. Extramural and intramural glands secrete neutral and acid mucin into the ductal lumen. Extramural glands contain several enzymes for digestion of protein and lipids. Neural and vascular supply of these glands may be related to the regulation of their secretion. Specific and non-specific immune responses within this glandular system may also be essential in the sterility of bile.


Assuntos
Ductos Biliares Intra-Hepáticos/anatomia & histologia , Ductos Biliares Intra-Hepáticos/fisiologia , Ductos Biliares Intra-Hepáticos/crescimento & desenvolvimento , Vasos Sanguíneos/anatomia & histologia , Enzimas/metabolismo , Glicoproteínas/metabolismo , Humanos , Imunidade , Mucinas/metabolismo , Sistema Nervoso/anatomia & histologia
17.
Pathol Int ; 44(9): 704-11, 1994 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-7804433

RESUMO

A case of pseudolymphoma (reactive lymphoid hyperplasia) of the liver in a 66 year old female is presented. A tumor-like lesion was incidentally discovered in the liver during clinical follow up of diabetes mellitus. The hepatic lesion was resected because malignant lymphoma was suspected after a needle biopsy. Grossly, the lesion was well-defined and measured 1.0 x 1.5 x 1.0 cm. Microscopically, the lesion consisted of hyperplastic lymphoid follicles with distinctive germinal centers and interfollicular areas consisting of mature lymphocytes and plasma cells. An immunohistological study revealed that the lymphoid cells of the lesion were polyclonal in immunophenotypes. These histological and immunohistochemical findings strongly suggested a pseudolymphoma and not hepatic inflammatory pseudotumor. This case was diagnosed as pseudolymphoma of liver. Only a few cases of hepatic pseudolymphoma have so far been reported in the English literature.


Assuntos
Hepatopatias/patologia , Tecido Linfoide/patologia , Idoso , Diagnóstico Diferencial , Feminino , Granuloma de Células Plasmáticas/patologia , Humanos , Hiperplasia/patologia , Técnicas Imunoenzimáticas , Leucemia Linfocítica Crônica de Células B/patologia
18.
Histopathology ; 33(2): 145-53, 1998 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-9762547

RESUMO

AIMS: Interleukin-6 (IL-6) has been implicated as a mediator of growth control in several human neoplasms. The significance of IL-6 expression in human cholangiocarcinoma was examined in this study. METHODS AND RESULTS: IL-6 expression was examined in 43 surgically resected cholangiocarcinomas and a cholangiocarcinoma cell line CCKS1, derived from abdominal metastasis of moderately differentiated adenocarcinoma, by immunohistochemical and in-situ hybridization techniques. In non-neoplastic bile ducts, IL-6 was constitutively but weakly expressed. In surgical cases of cholangiocarcinoma, IL-6 was frequently and strongly expressed in the cytoplasm of well-differentiated cholangiocarcinoma, while its expression was decreased, and less intense or absent in moderately and poorly differentiated areas, respectively. IL-6 mRNA was detected in the cytoplasm of carcinoma cells of two cases of cholangiocarcinomas positive for IL-6. IL-6 was detected in hepatic bile from two cholangiocarcinoma cases studied. The proliferation antigen Ki67 was found to be more frequently expressed in IL-6 negative carcinoma cells than in IL-6 positive carcinoma cells (P < 0.01). In cultured carcinoma cells line CCKS1, IL-6, IL-6 mRNA and IL-6 receptor alpha chain were detected in the cytoplasm of carcinoma cells, suggesting an autocrine effect of IL-6 on carcinoma cells. CONCLUSION: IL-6 expression is inversely related to cell proliferation and positively related to differentiation in cholangiocarcinoma.


Assuntos
Neoplasias dos Ductos Biliares/imunologia , Ductos Biliares Intra-Hepáticos , Colangiocarcinoma/imunologia , Colangiocarcinoma/patologia , Interleucina-6/metabolismo , Idoso , Animais , Bile/imunologia , Neoplasias dos Ductos Biliares/patologia , Western Blotting , Diferenciação Celular , Divisão Celular , Feminino , Humanos , Imuno-Histoquímica , Hibridização In Situ , Antígeno Ki-67/metabolismo , Masculino , Camundongos , Camundongos Nus , Pessoa de Meia-Idade , Transplante de Neoplasias , RNA Mensageiro/análise , Células Tumorais Cultivadas
19.
Eur J Biochem ; 198(2): 437-40, 1991 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-1645658

RESUMO

To examine the role of histidine residues in ribonuclease H from Escherichia coli, kinetic parameters for the enzymatic activity and conformational stabilities against guanidine hydrochloride denaturation of mutant enzymes, in which each of the five histidine residues was replaced with alanine, were determined and compared with the wild-type enzyme. The mutation of His83 resulted in a marked increase in Km along with an increase in kcat. The mutation of His114 caused a large reduction in both the free energy of unfolding in water, delta GH2O, and the mid-point of the unfolding curve, [D]1/2. These results indicate that His83, which is one of the four well-exposed histidine residues in the crystal structure, is located close to a substrate-binding site, and His114, which is buried inside the protein molecule, contributes to the conformational stability, probably through the formation of a hydrogen bond with a main-chain carbonyl group. None of the histidine residues is required for activity.


Assuntos
Endorribonucleases/genética , Escherichia coli/enzimologia , Histidina , Mutagênese Sítio-Dirigida , Sequência de Bases , Endorribonucleases/química , Endorribonucleases/metabolismo , Estabilidade Enzimática , Escherichia coli/genética , Guanidina , Guanidinas/farmacologia , Cinética , Modelos Moleculares , Dados de Sequência Molecular , Sondas de Oligonucleotídeos , Conformação Proteica , Desnaturação Proteica/efeitos dos fármacos , Mapeamento por Restrição , Ribonuclease H , Termodinâmica
20.
Mod Pathol ; 14(12): 1304-9, 2001 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-11743055

RESUMO

Biliary cystadenocarcinoma with oncocytic differentiation was first reported in 1992. This is a report of a second case. The patient (a 71-year-old man) was admitted to our hospital complaining of abdominal fullness. Multicystic lesions were identified in the left hepatic lobe radiologically. The patient died of peritoneal dissemination of carcinoma 20 months later. At autopsy, the tumor of the left hepatic lobe was found to be composed of adjoining multiple cystic lesions and a solid lesion with infiltration of the hepatic hilus and peritoneal dissemination. Histologically, the multicystic lesions were covered by papillary neoplastic epithelial cells with an eosinophilic granular cytoplasm resembling that of oncocytes and a fine fibrovascular core. The cyst wall was fibrous, but there was no mesenchymal stroma. In the solid lesion and infiltrated areas, acidophilic and granular carcinoma cells formed small glandular or solid cord patterns with much mucin secretion (mucinous carcinoma). Immunohistochemically, carcinoma cells of both components were found to contain many mitochondria and showed the phenotypes of hepatocytes and cholangiocytes. Interestingly, the intrahepatic biliary tree also was invaded by carcinoma cells. This may be a case of intraductal oncocytic papillary neoplasm of the left hepatic lobe followed by secondary cystic dilatation of the affected bile duct.


Assuntos
Adenoma Oxífilo/secundário , Neoplasias dos Ductos Biliares/patologia , Ductos Biliares Intra-Hepáticos/patologia , Cistadenocarcinoma Papilar/secundário , Neoplasias Hepáticas/patologia , Células Oxífilas/patologia , Adenoma Oxífilo/química , Adenoma Oxífilo/diagnóstico por imagem , Idoso , Neoplasias dos Ductos Biliares/química , Neoplasias dos Ductos Biliares/diagnóstico por imagem , Biomarcadores Tumorais/análise , Cistadenocarcinoma Papilar/química , Cistadenocarcinoma Papilar/diagnóstico por imagem , Evolução Fatal , Humanos , Neoplasias Hepáticas/química , Neoplasias Hepáticas/diagnóstico por imagem , Masculino , Proteínas de Neoplasias/análise , Tomografia Computadorizada por Raios X
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