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1.
IUCrJ ; 10(Pt 5): 579-583, 2023 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-37493524

RESUMO

The great success of single-particle electron cryo-microscopy (cryoEM) during the last decade has involved the development of powerful new computer programs and packages that guide the user along a recommended processing workflow, in which the wisdom and choices made by the developers help everyone, especially new users, to obtain excellent results. The ability to carry out novel, non-standard or unusual combinations of image-processing steps is sometimes compromised by the convenience of a standard procedure. Some of the older programs were written with great flexibility and are still very valuable. Among these, the original MRC image-processing programs for structure determination by 2D crystal and helical processing alongside general-purpose utility programs such as Ximdisp, label, imedit and twofile are still available. This work describes an updated version of the MRC software package (MRC2020) that is freely available from CCP-EM. It includes new features and improvements such as extensions to the MRC format that retain the versatility of the package and make it particularly useful for testing novel computational procedures in cryoEM.

2.
Oncogene ; 40(18): 3260-3272, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33846571

RESUMO

The molecular mechanisms of luminal cell differentiation are not understood well enough to determine how differentiation goes awry during oncogenesis. Using RNA-Seq analysis, we discovered that CREB1 plays a central role in maintaining new luminal cell survival and that oncogenesis dramatically changes the CREB1-induced transcriptome. CREB1 is active in luminal cells, but not basal cells. We identified ING4 and its E3 ligase, JFK, as CREB1 transcriptional targets in luminal cells. During luminal cell differentiation, transient induction of ING4 expression is followed by a peak in CREB1 activity, while JFK increases concomitantly with CREB1 activation. Transient expression of ING4 is required for luminal cell induction; however, failure to properly down-regulate ING4 leads to luminal cell death. Consequently, blocking CREB1 increased ING4 expression, suppressed JFK, and led to luminal cell death. Thus, CREB1 is responsible for the suppression of ING4 required for luminal cell survival and maintenance. Oncogenic transformation by suppressing PTEN resulted in constitutive activation of CREB1. However, the tumor cells could no longer fully differentiate into luminal cells, failed to express ING4, and displayed a unique CREB1 transcriptome. Blocking CREB1 in tumorigenic cells suppressed tumor growth in vivo, rescued ING4 expression, and restored luminal cell formation, but ultimately induced luminal cell death. IHC of primary prostate tumors demonstrated a strong correlation between loss of ING4 and loss of PTEN. This is the first study to define a molecular mechanism whereby oncogenic loss of PTEN, leading to aberrant CREB1 activation, suppresses ING4 expression causing disruption of luminal cell differentiation.


Assuntos
Próstata , Neoplasias da Próstata , Proteínas de Ciclo Celular , Diferenciação Celular , Humanos , Masculino , PTEN Fosfo-Hidrolase
3.
Nat Prod Rep ; 33(2): 317-47, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26699732

RESUMO

Nonribosomal peptides are amongst the most widespread and structurally diverse secondary metabolites in nature with many possessing bioactivity that can be exploited for therapeutic applications. Due to the major challenges associated with total- and semi-synthesis, bioengineering approaches have been developed to increase yields and generate modified peptides with improved physicochemical properties or altered bioactivity. Here we review the major advances that have been made over the last decade in engineering the biosynthesis of nonribosomal peptides. Structural diversity has been introduced by the modification of enzymes required for the supply of precursors or by heterologous expression of tailoring enzymes. The modularity of nonribosomal peptide synthetase (NRPS) assembly lines further supports module or domain swapping methodologies to achieve changes in the amino acid sequence of nonribosomal peptides. We also review the new synthetic biology technologies promising to speed up the process, enabling the creation and optimisation of many more assembly lines for heterologous expression, offering new opportunities for engineering the biosynthesis of novel nonribosomal peptides.


Assuntos
Peptídeo Sintases/metabolismo , Peptídeos/química , Sequência de Aminoácidos , Modelos Moleculares , Estrutura Molecular
4.
Pediatr Crit Care Med ; 12(6): e395-7, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21116210

RESUMO

OBJECTIVE: In patients who require extracorporeal membrane oxygenation for prolonged periods, it is uncertain whether nosocomial bacteremia that persists throughout an entire extracorporeal membrane oxygenation run can be associated with good outcomes. DESIGN: Case report. SETTING: Tertiary pediatric intensive care unit. PATIENT: A 6-yr-old boy with acute myeloid leukemia and prolonged mechanical ventilatory support. INTERVENTIONS: Venovenous extracorporeal membrane oxygenation. MEASUREMENTS AND MAIN RESULTS: The patient required extracorporeal membrane oxygenation for refractory hypoxia secondary to nosocomial pneumonia. On day 2 of the extracorporeal membrane oxygenation run and every day thereafter, blood cultures were consistently positive for Stenotrophomonas maltophilia despite combination therapy with intravenous polymyxin B and cotrimoxazole. Excluding the cannulae, the extracorporeal membrane oxygenation circuit was electively changed once during the run but without any effect on bacteremia. After 38 days of extracorporeal membrane oxygenation, the patient was successfully decannulated and the bacteremia ceased. He remains completely well and disease-free at 6-month follow-up. CONCLUSIONS: Sustained bacteremia during an extracorporeal membrane oxygenation run should not be regarded as a reason to withdraw extracorporeal support, although efforts are clearly warranted to identify possible sources of sepsis and wean off extracorporeal membrane oxygenation at the earliest opportunity.


Assuntos
Oxigenação por Membrana Extracorpórea/métodos , Infecções por Bactérias Gram-Negativas/complicações , Hemofiltração , Leucemia Mieloide Aguda/complicações , Criança , Infecção Hospitalar , Infecções por Bactérias Gram-Negativas/tratamento farmacológico , Humanos , Unidades de Terapia Intensiva Pediátrica , Masculino , Avaliação de Resultados em Cuidados de Saúde , Stenotrophomonas maltophilia , Fatores de Tempo , Vitória
5.
Acta Crystallogr D Biol Crystallogr ; 62(Pt 10): 1170-83, 2006 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17001094

RESUMO

The Structural Proteomics In Europe (SPINE) consortium contained a workpackage to address the automated X-ray analysis of macromolecules. The aim of this workpackage was to increase the throughput of three-dimensional structures while maintaining the high quality of conventional analyses. SPINE was able to bring together developers of software with users from the partner laboratories. Here, the results of a workshop organized by the consortium to evaluate software developed in the member laboratories against a set of bacterial targets are described. The major emphasis was on molecular-replacement suites, where automation was most advanced. Data processing and analysis, use of experimental phases and model construction were also addressed, albeit at a lower level.


Assuntos
Cristalografia por Raios X/métodos , Proteômica/métodos , Algoritmos , Automação , Interpretação Estatística de Dados , Bases de Dados Factuais , Modelos Químicos , Modelos Moleculares , Conformação Proteica , Controle de Qualidade , Software
6.
Cell Mol Life Sci ; 63(21): 2506-11, 2006 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-16952054

RESUMO

An increasing cause of end-stage renal disease is the pathological lesion focal and segmental glomerulosclerosis (FSGS). FSGS is characterized by proteinuria and frequently nephrotic syndrome with ensuing renal failure. The etiology remains unknown in the majority of individuals. The idiopathic form of FSGS is most common; however, secondary forms of FSGS do exist. There is a form of FSGS that is fulminant that frequently recurs after renal transplantation with an estimated frequency of approximately 30%, suggesting that the pathogenesis is not solely a result of intrinsic kidney disease. Recently, hereditary forms of the disease were recognized as well as those associated with other congenital syndromes. Known genetic causes of the hereditary form of this disease have been suggested to account for upwards of 18% of cases. This review will address recent discoveries of the genetic mechanisms of hereditary FSGS and the current interpretations of their interactions at the slit diaphragm.


Assuntos
Glomerulosclerose Segmentar e Focal/patologia , Genoma Humano/genética , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/genética , Proteínas de Membrana/genética , Mutação/genética , Canais de Cátion TRPV/genética
7.
Aliment Pharmacol Ther ; 21(9): 1127-33, 2005 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-15854175

RESUMO

BACKGROUND: Studies suggest obstructive sleep apnea syndrome (OSAS) frequently manifests in patients with gastroesophageal reflux disease (GERD) and that there may be a causal relationship. AIM: To determine the relationship between OSAS and symptoms of GERD. METHODS: Consecutive patients referred to the Sleep Disorders Center (SDC) 18 years and older with polysomnographically defined OSAS were evaluated prospectively for GERD using a validated symptoms questionnaire. The GERD and OSAS relationship was assessed by 1) determining frequency of GERD in patients with and without OSAS; 2) ascertaining the relationship between OSAS severity categories and presence of GERD; 3) examining GERD score in relation to those factors that might affect both GERD and OSAS, e.g. obesity. RESULTS: One thousand and twenty-three SDC patients met entry criteria. Amongst participants, GERD was common (29% of women and 17% of males) and OSAS extremely common (58% of women and 80% of males). GERD score did not correlate with OSAS variables. The severity of OSAS did not influence the prevalence of GERD. CONCLUSION: In a large group of patients referred to a sleep disorders center, there was no relationship between OSAS and GERD symptoms. Also, there was no relationship between the severity of OSAS and the likelihood of GERD symptoms.


Assuntos
Refluxo Gastroesofágico/complicações , Apneia Obstrutiva do Sono/complicações , Adulto , Idoso , Índice de Massa Corporal , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Polissonografia , Encaminhamento e Consulta
8.
Acta Crystallogr D Biol Crystallogr ; 60(Pt 12 Pt 1): 2250-5, 2004 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-15572778

RESUMO

The new CCP4 Coordinate Library is a development aiming to provide a common layer of coordinate-related functionality to the existing applications in the CCP4 suite, as well as a variety of tools that can simplify the design of new applications where they relate to atomic coordinates. The Library comprises a wide spectrum of useful functions, ranging from parsing coordinate formats and elementary editing operations on the coordinate hierarchy of biomolecules, to high-level functionality such as calculation of secondary structure, interatomic bonds, atomic contacts, symmetry transformations, structure superposition and many others. Most of the functions are available in a C++ object interface; however, a Fortran interface is provided for compatibility with older CCP4 applications. The paper describes the general principles of the Library design and the most important functionality. The Library, together with documentation, is available under the LGPL license from the CCP4 suite version 5.0 and higher.


Assuntos
Cristalografia por Raios X/estatística & dados numéricos , Proteínas/química , Software , Gráficos por Computador , Bases de Dados de Proteínas , Modelos Moleculares , Conformação Proteica , Interface Usuário-Computador
9.
Endocrinology ; 145(6): 2784-94, 2004 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-15001551

RESUMO

alpha(2)-Macroglobulin (alpha(2)-M) inhibits proteinases and modulates the actions of growth factors and cytokines. Despite the key roles proteinases, growth factors, and cytokines have in folliculogenesis, the role of alpha(2)-M in follicular development is unknown. Our objectives were to: 1) determine whether granulosa cells produce alpha(2)-M and have alpha(2)-M receptors, 2) examine the effect of alpha(2)-M on estradiol production by granulosa cells, 3) establish whether amounts of alpha(2)-M and alpha(2)-M receptors were altered during dominant nonovulatory follicle development, and 4) examine alpha(2)-M's mechanism of action. The results demonstrated that bovine granulosa cells contain 5.2- and 15-kb mRNAs and 720- and 500-kDa proteins that correspond, respectively, to sizes of mRNAs and proteins for alpha(2)-M and the alpha(2)-M receptor. Treatment of granulosa cells with alpha(2)-M resulted in a specific dose-responsive increase in estradiol production. Cell viability, cell number, and the amount of aromatase in granulosa cells were not altered by alpha(2)-M. Treatment of granulosa cells with factors that bind alpha(2)-M or its receptor did not mimic alpha(2)-M action. Although intrafollicular amounts of alpha(2)-M remained unchanged, amounts of alpha(2)-M receptor in granulosa cells were strongly inversely associated with concentrations of estradiol in dominant and subordinate follicles. Based on these results, we concluded that alpha(2)-M may have autocrine or paracrine roles in granulosa cells potentially important for regulation of estradiol production and development of dominant follicles.


Assuntos
Comunicação Autócrina/fisiologia , Estradiol/biossíntese , Células da Granulosa/metabolismo , Folículo Ovariano/fisiologia , Comunicação Parácrina/fisiologia , alfa-Macroglobulinas/fisiologia , Animais , Bovinos , Células Cultivadas , Estradiol/metabolismo , Feminino , Células da Granulosa/efeitos dos fármacos , Proteína-1 Relacionada a Receptor de Lipoproteína de Baixa Densidade/isolamento & purificação , Folículo Ovariano/metabolismo , Ovulação , alfa-Macroglobulinas/metabolismo , alfa-Macroglobulinas/farmacologia
10.
Biol Reprod ; 70(5): 1475-84, 2004 May.
Artigo em Inglês | MEDLINE | ID: mdl-14736815

RESUMO

We hypothesize that granulosa and theca cells from growing dominant follicles, with relatively high intrafollicular concentrations of estradiol, have a greater expression of genes involved in inhibiting apoptosis pathways and lower expression of genes involved in apoptosis pathways than growing subordinate follicles with lower estradiol concentrations. Using the well-characterized bovine dominant follicle model, we collected granulosa and theca cells from individual dominant and the largest subordinate follicle 3 days after initiation of a follicular wave in four animals. Based on ultrasound analysis, both follicle types were in the growth phase at the time of ovariectomy. However, dominant follicles were larger (9.8 +/- 1.0 versus 7.6 +/- 0.6 mm in diameter, P < 0.05) and had greater intrafollicular concentrations of estradiol (132.2 +/-3 8.5 versus 24.1 +/- 12.1 ng/ml, P < 0.05), compared with the largest subordinate follicles. We used bovine cDNA microarrays, which contained a total of 1400 genes, including a subset of 53 genes known to be involved in apoptosis pathways, to determine which apoptosis and marker genes from each of the four dominant versus subordinate follicles were potentially differentially expressed. Using a low stringency-screening criterion, 22 genes were identified. Quantitative real-time polymerase chain reaction confirmed that 16 of these genes were differentially expressed. Our novel results demonstrate that the high intrafollicular concentrations of estradiol in growing dominant follicles were positively associated with enhanced expression of mRNAs in granulosa cells for aromatase, LH receptor, estradiol receptor beta, DICE-1, and MCL-1, compared with granulosa cells from subordinate follicles (all survival-associated genes). In contrast, the relatively low intrafollicular concentrations of estradiol in growing subordinate follicles were positively associated with enhanced expression of mRNAs in granulosa cells for beta glycan, cyclo-oxygenase-1, tumor necrosis factor alpha, caspase-activated DNase, and DRAK-2, and in theca cells for beta glycan, caspase 13, P58(IPK), Apaf-1, BTG-3, and TS-BCLL, compared with granulosa or theca cells from dominant follicles (genes that are all associated with cell death and/or apoptosis). We suggest that that these genes may be candidate estradiol target genes and that they may be early markers for the final stages of follicle differentiation or initiation of apoptosis and thus selection of dominant follicles during follicular waves.


Assuntos
Apoptose/genética , Bovinos/fisiologia , Perfilação da Expressão Gênica , Folículo Ovariano/fisiologia , Animais , Bovinos/genética , Sistemas Computacionais , Feminino , Marcadores Genéticos , Análise de Sequência com Séries de Oligonucleotídeos , Reação em Cadeia da Polimerase
11.
Endocrinology ; 144(5): 1876-86, 2003 May.
Artigo em Inglês | MEDLINE | ID: mdl-12697695

RESUMO

Intrafollicular concentrations of inhibin A and estradiol vary inversely during development of dominant follicles in cattle. Thus, we hypothesized that inhibin has a negative autocrine or paracrine effect on estradiol production by granulosa cells. To examine this hypothesis, a homologous model system was used to test the effects of bovine antibovine inhibin antibodies, bovine inhibin, and a peptide fragment of bovine inhibin (bINH) on capacity of granulosa cells isolated from individual estrogen-active or -inactive dominant or subordinate follicles to produce estradiol during short-term (18 h) serum-free culture. Immunoblot analysis of media demonstrated that granulosa cells basally produce different molecular weight forms of inhibin, similar to those in bovine follicular fluid. Immunoneutralization of endogenous inhibin in culture with different doses (12.5-1000 microg) of highly purified bovine antibovine inhibin antibodies increased estradiol production 2- to 15-fold, compared with controls. Preadsorption of the anti-inhibin antibodies with bINH precursors or bovine pro-alpha(C) suppressed the capacity of anti-inhibin antibodies to enhance estradiol production by granulosa cells, compared with controls. Treatment of granulosa cells with an immunoaffinity-purified preparation of bINH suppressed basal estradiol production 60%, compared with controls. In contrast, treatment of granulosa cells with the bINH peptide increased estradiol production 14-fold, compared with controls. Based on these results, we concluded that both anti-inhibin antibodies and bINH blocked the suppressive local effects of basally produced inhibin on estradiol production during culture of granulosa cells and that inhibin has a negative autocrine or paracrine effect on the in vitro capacity of granulosa cells isolated from dominant or subordinate follicles to produce estradiol.


Assuntos
Estradiol/biossíntese , Células da Granulosa/metabolismo , Inibinas/fisiologia , Animais , Anticorpos/administração & dosagem , Anticorpos/farmacologia , Bovinos , Sobrevivência Celular/efeitos dos fármacos , Sobrevivência Celular/fisiologia , Células Cultivadas , Relação Dose-Resposta a Droga , Feminino , Células da Granulosa/efeitos dos fármacos , Células da Granulosa/fisiologia , Inibinas/imunologia , Inibinas/farmacologia , Fragmentos de Peptídeos/farmacologia
12.
J Synchrotron Radiat ; 10(Pt 1): 23-5, 2003 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-12511787

RESUMO

The Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. CCP4 now distributes a large software suite and is active in developing new software. Equally importantly, CCP4 provides a focus for the whole protein crystallography community via meetings, workshops, email lists and various publications. In this Article, an overview is given of CCP4 activities and their administration. The emphasis is on generic features of the collaboration rather than details specific to protein crystallography. The CCP4 model has inspired similar developments in NMR, and it is hoped that the biological XAS community may pursue similar collaboration.


Assuntos
Proteínas/química , Software , Cristalografia por Raios X/métodos , Educação Continuada , Relações Interinstitucionais , Software/tendências , Reino Unido
13.
Acta Crystallogr D Biol Crystallogr ; 58(Pt 11): 1929-36, 2002 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-12393924

RESUMO

Collaborative Computational Project Number 4 (CCP4) was established in 1979 to promote collaboration between UK groups writing software for protein crystallography. From these beginnings, CCP4 now distributes a large software suite and is active in developing new software. In this article, an overview is given of recent and ongoing developments in the CCP4 software suite, in particular as they pertain to high-throughput studies. Developments in individual programs are discussed first, although these are covered in more detail elsewhere. The bulk of the article focuses on the infrastructure of the software suite which allows the user to move effortlessly between different programs or to create automated schemas. Major changes to the software library at the heart of the CCP4 suite, developments in the CCP4 graphical user interface, and data management within CCP4 are discussed. The latter is crucial to high-throughput studies, where a large number of data are imported, created and finally archived.


Assuntos
Cristalografia por Raios X/métodos , Proteínas/química , Software
14.
Acta Crystallogr D Biol Crystallogr ; 58(Pt 1): 70-80, 2002 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-11752780

RESUMO

The serum transferrins are monomeric proteins with a molecular mass of around 80 kDa and are responsible for the transport of iron in vertebrates. The three-dimensional structures of diferric porcine and rabbit serum transferrin have been refined against X-ray diffraction data extending to 2.15 and 2.60 A, respectively. Data for both proteins were collected using synchrotron radiation at temperatures of 277 K. The porcine protein crystallizes in the space group C2, with unit-cell parameters a = 223.8, b = 44.9, c = 78.9 A, beta = 105.4 degrees with one molecule in the asymmetric unit. The structure was solved by molecular-replacement methods using rabbit serum transferrin as the search model. The structure was refined using REFMAC, with a final residual of 13.8% (R(free) = 18.2% for a 5% data sample) for all data to 2.15 A. The final model comprises 5254 protein atoms, two Fe(3+) cations and two CO(3)(2-) anions, one N-acetyl glucosamine moiety and 494 water molecules. The rabbit protein crystallizes in space group P4(3)2(1)2, with unit-cell parameters a = 127.2, c = 144.9 A and one molecule per asymmetric unit. The structure was solved using the method of multiple isomorphous replacement and refined using REFMAC to give a final residual of 18.6% (R(free) = 22.2% for a 5% data sample) for all data to 2.60 A. The final model comprises 5216 protein atoms, two Fe(3+) cations and two CO(3)(2-) anions, a Cl(-) anion and 206 solvent molecules; there is no clear indication of the carbohydrate moiety attached to Asn490 (rabbit serum numbering). Both molecules adopt a bilobal structure typical for members of the transferrin family. Each of the structurally homologous lobes contains two dissimilar domains with a single iron-binding site buried within the interdomain cleft. The porcine serum protein lacks an interdomain disulfide bridge close to the connecting peptide between the lobes, but this seems to have little effect on the overall orientation of the lobes. The N-lobes of both proteins possess lysine residues, one from each of the two domains, that lie in close proximity to one another to form the so-called dilysine trigger. The more acid-labile release of iron from serum transferrins than from lactoferrins is discussed.


Assuntos
Transferrina/química , Animais , Ânions , Sítios de Ligação , Carboidratos/química , Carbonatos/metabolismo , Cristalografia por Raios X , Dissulfetos/química , Ferro/metabolismo , Conformação Proteica , Coelhos , Suínos , Transferrina/metabolismo
15.
J Med Chem ; 44(25): 4393-403, 2001 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-11728185

RESUMO

We have shown that p-arylthio cinnamides can inhibit the interaction of LFA-1 and ICAM-1, which is involved in cell adhesion and the inflammatory process. We now show that 2,3-disubstitution on the aryl portion of the cinnamide results in enhanced activity over mono substitution on the ring. The best 2,3-substituents were chlorine and trifluoromethyl groups. Compounds 39 and 40 which contain two CF3 groups have IC(50) values of 0.5 and 0.1 nM, respectively, in inhibiting JY8 cells expressing LFA-1 on their surface, from adhering to ICAM-1. The structure-activity relationship (SAR) was examined using an NMR based model of the LFA-1 I domain/compound 31 complex. One of our compounds (38) was able to reduce cell migration in two different in vivo experiments.


Assuntos
Cinamatos/síntese química , Indóis/síntese química , Molécula 1 de Adesão Intercelular/metabolismo , Antígeno-1 Associado à Função Linfocitária/metabolismo , Sulfetos/síntese química , Amidas/síntese química , Amidas/química , Amidas/farmacologia , Animais , Linhagem Celular , Quimiotaxia de Leucócito/efeitos dos fármacos , Cinamatos/química , Cinamatos/farmacologia , Enterotoxinas/farmacologia , Eosinófilos/patologia , Indóis/química , Indóis/farmacologia , Espectroscopia de Ressonância Magnética , Camundongos , Modelos Moleculares , Neutrófilos/efeitos dos fármacos , Neutrófilos/fisiologia , Ovalbumina/imunologia , Pneumonia/imunologia , Pneumonia/patologia , Ratos , Staphylococcus aureus , Relação Estrutura-Atividade , Sulfetos/química , Sulfetos/farmacologia
16.
J Med Chem ; 44(23): 3978-84, 2001 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-11689084

RESUMO

The synthesis and structure-activity relationships (SAR) of a series of pyrrolidine-3-carboxylic acids as endothelin antagonists are described. The data shows an increase in selectivity when the methoxy of Atrasentan (ABT-627) is replaced with methyl, and the benzodioxole is replaced with dihydrobenzofuran. Adding a fluorine further increases the binding activity and provides a metabolically stable and orally bioavailable ET(A)-selective antagonist.


Assuntos
Benzofuranos/síntese química , Antagonistas dos Receptores de Endotelina , Pirrolidinas/síntese química , Administração Oral , Animais , Benzofuranos/química , Benzofuranos/farmacologia , Disponibilidade Biológica , Células CHO , Cricetinae , Humanos , Pirrolidinas/química , Pirrolidinas/farmacologia , Ensaio Radioligante , Ratos , Receptor de Endotelina A , Estereoisomerismo , Relação Estrutura-Atividade
17.
Acta Crystallogr D Biol Crystallogr ; 57(Pt 1): 122-33, 2001 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-11134934

RESUMO

An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameter ratio. This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters. The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body. This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC. Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique. TLS refinement is therefore fast and can be used routinely. Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 A, so that individual anisotropic refinement is not feasible. GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups. In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent. Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules. These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied.


Assuntos
Modelos Moleculares , Gliceraldeído-3-Fosfato Desidrogenases/química , Conformação Proteica
18.
Kidney Int ; 57(5): 1818-35, 2000 May.
Artigo em Inglês | MEDLINE | ID: mdl-10792601

RESUMO

BACKGROUND: IgA nephropathy (IgAN) is the most common glomerulonephritis in the world among patients undergoing renal biopsy. Once considered a relatively benign condition, longitudinal follow-up studies have revealed that in fact 9 to 50% of patients progress to end-stage renal disease within 20 years of disease onset. In the three decades since its first description by Jean Berger and Nicole Hinglais, clinical, epidemiologic, and immunologic studies of the pathogenesis of primary (idiopathic) mesangial glomerulonephritis with predominant IgA deposits have characterized the features of IgAN as a distinct glomerular disease entity. However, the basic molecular mechanism(s) underlying abnormal IgA deposition in the mesangium with ensuing extracellular matrix expansion and mesangial cell proliferation remains poorly understood. The task of elucidating the molecular basis of IgAN is made especially challenging by the fact that both environmental and genetic components likely contribute to the development and progression of IgAN. METHODS AND RESULTS: We review here the evidence for genetic factors in the development and progression of IgAN, including a reappraisal of earlier conflicting results from small immunogenetic case-control studies, the evidence for racial differences in the prevalence of IgAN, a detailed summary of all reported occurrences of familial IgAN worldwide, and an exhaustive review of new insights gained through the study of two murine models of hereditary IgAN: the ddY and the uteroglobin-deficient mouse. CONCLUSIONS: With the development of powerful molecular genetic approaches to the study of both Mendelian and complex human genetic diseases, and the successful efforts of investigators to identify and clinically characterize large IgAN multiplex families, we propose that genetic analysis of familial IgAN is the most promising approach to the identification of IgAN disease/susceptibility genes. Alternatively, if the case-control study design is employed to identify associations between particular candidate genes or markers and the development of IgAN, spurious associations caused by the effects of population stratification should be ruled out by confirming the findings using powerful and sensitive family-based methodologies such as the transmission/dysequilibrium test (TDT).


Assuntos
Glomerulonefrite por IGA/genética , Animais , Modelos Animais de Doenças , Genes MHC da Classe II , Predisposição Genética para Doença , Glomerulonefrite por IGA/etnologia , Glomerulonefrite por IGA/etiologia , Humanos , Camundongos , Peptidil Dipeptidase A/genética , Polimorfismo Genético , Receptores de Antígenos de Linfócitos T alfa-beta/genética
19.
Am J Respir Crit Care Med ; 161(5): 1459-64, 2000 May.
Artigo em Inglês | MEDLINE | ID: mdl-10806139

RESUMO

Previous studies have shown that the regular administration of short acting beta-agonists can be associated with adverse effects on airway caliber and bronchial hyperresponsiveness (BHR) and that this may occur through a proinflammatory mechanism. The aim was to explore possible adverse effects of high-dose beta-agonist therapy and to assess any adverse interaction with corticosteroids. We undertook a randomized, crossover study to investigate the effects of 6 wk of treatment with regular terbutaline (1 mg four times a day), regular budesonide (400 microg twice a day), combined treatment, and placebo in subjects with mild to moderate asthma. Major endpoints were PD(15) saline, PD(20) methacholine, and induced sputum differential cell counts. Thirty-four subjects were randomized and 28 completed the study. PD(15) saline decreased on terbutaline alone compared with placebo treatment and on combined treatment compared with budesonide alone (mean fold decrease of 0.57 [95% CI = 0.36, 0.90] and 0.65 [95% CI = 0.43, 0.97], respectively). PD(20) methacholine was not affected by the use of terbutaline either alone or in combination with budesonide. The percentage of eosinophils in induced sputum increased during terbutaline treatment alone compared with placebo (median 8.3% versus 4.4%, p = 0.049). The addition of terbutaline to budesonide did not affect the percentage of eosinophils compared with budesonide treatment alone. These findings support the hypothesis that short-acting beta-agonists have a permissive effect on airway inflammation and that when used in high dose there may be an unfavorable interaction with inhaled corticosteroids.


Assuntos
Agonistas Adrenérgicos beta/uso terapêutico , Anti-Inflamatórios/uso terapêutico , Asma/fisiopatologia , Hiper-Reatividade Brônquica/fisiopatologia , Broncodilatadores/uso terapêutico , Budesonida/uso terapêutico , Escarro/citologia , Terbutalina/uso terapêutico , Administração Tópica , Adolescente , Agonistas Adrenérgicos beta/efeitos adversos , Adulto , Asma/tratamento farmacológico , Asma/patologia , Hiper-Reatividade Brônquica/tratamento farmacológico , Hiper-Reatividade Brônquica/patologia , Testes de Provocação Brônquica , Contagem de Células , Estudos Cross-Over , Método Duplo-Cego , Interações Medicamentosas , Quimioterapia Combinada , Feminino , Volume Expiratório Forçado , Glucocorticoides , Humanos , Masculino , Cloreto de Metacolina , Pessoa de Meia-Idade , Pico do Fluxo Expiratório , Cloreto de Sódio/administração & dosagem , Terbutalina/efeitos adversos
20.
Kidney Int ; 56(5): 1863-71, 1999 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-10571795

RESUMO

BACKGROUND: Focal segmental glomerulosclerosis (FSGS) is the underlying pathologic entity in 5% of adults and 20% of children with end-stage renal disease (ESRD). FSGS is generally considered to be sporadic in origin. METHODS: Recently, we identified 60 families involving 190 individuals with familial FSGS, providing evidence for a subset of families in which a genetic form is segregating. Each family had at least one member with renal biopsy-confirmed FSGS and at least one other member with either renal biopsy-confirmed FSGS or ESRD. RESULTS: Twenty-six families had individuals affected in more than one generation [multigeneration (MG)], and the remaining 34 families had only a single generation (SG) affected. There was equal representation of males and females among affected individuals. Ten percent of MG families were African American, and 52% of SG families were African American. The mean age of presentation was significantly higher in the MG families (32.5 +/- 14.6 years) compared with the SG families (20.1 +/- 12.1 years, P = 0.0001). SG cases had higher levels of proteinuria at presentation (7.0 +/- 5.6 g/24 hr, compared with 3.8 +/- 3.4 g/24 hr, for the MG families, P = 0.002). On renal biopsy, tubulointerstitial damage was more severe in patients in the SG families than in the MG families; however, the level of glomerular damage did not differ between these groups. Fifty percent of the patients had progressed to ESRD by the age of 30 years. Variables measured at presentation that were independently associated with poor renal survival were decreased age, increased serum creatinine, and increased urinary protein excretion. Forty-one patients underwent successful renal transplantation, with a 10-year graft survival rate of 62%. One patient developed clinical and biopsy evidence of recurrence of FSGS in the allograft. CONCLUSION: These data confirm the existence of a non-Alport's form of hereditary glomerulonephritis, which has a morphological pattern of FSGS.


Assuntos
Glomerulosclerose Segmentar e Focal/genética , Adulto , Idoso , Feminino , Glomerulosclerose Segmentar e Focal/complicações , Glomerulosclerose Segmentar e Focal/patologia , Humanos , Falência Renal Crônica/etiologia , Transplante de Rim , Masculino , Pessoa de Meia-Idade
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