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1.
Acta Crystallogr F Struct Biol Commun ; 79(Pt 6): 159-165, 2023 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-37227376

RESUMEN

Aldehyde dehydrogenase (ALDH) is widely distributed in nature and its characteristics have been examined. ALDH plays an important role in aldehyde detoxification. Sources of aldehydes include incomplete combustion and emissions from paints, linoleum and varnishes in the living environment. Acetaldehyde is also considered to be carcinogenic and toxic. Thermostable ALDH from the hyperthermophilic archaeon Sulfolobus tokodaii exhibits high activity towards acetaldehyde and has potential applications as a biosensor for acetaldehyde. Thermostable ALDH displays a unique and wide adaptability. Therefore, its crystal structure can provide new insights into the catalytic mechanism and potential applications of ALDHs. However, a crystal structure of a thermostable ALDH exhibiting high activity towards acetaldehyde has not been reported to date. In this study, crystals of recombinant thermostable ALDH from S. tokodaii were prepared and the crystal structure of its holo form was determined. A crystal of the enzyme was prepared and its structure in complex with NADP was determined at a resolution of 2.2 Å. This structural analysis may facilitate further studies on catalytic mechanisms and applications.


Asunto(s)
Sulfolobus , Archaea , Cristalografía por Rayos X , Acetaldehído
2.
J Biol Chem ; 298(3): 101650, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-35101448

RESUMEN

Hydroxynitrile lyase from Linum usitatissimum (LuHNL) is an enzyme involved in the catabolism of cyanogenic glycosides to release hydrogen cyanide upon tissue damage. This enzyme strictly conserves the substrate- and NAD(H)-binding domains of Zn2+-containing alcohol dehydrogenase (ADH); however, there is no evidence suggesting that LuHNL possesses ADH activity. Herein, we determined the ligand-free 3D structure of LuHNL and its complex with acetone cyanohydrin and (R)-2-butanone cyanohydrin using X-ray crystallography. These structures reveal that an A-form NAD+ is tightly but not covalently bound to each subunit of LuHNL. The restricted movement of the NAD+ molecule is due to the "sandwich structure" on the adenine moiety of NAD+. Moreover, the structures and mutagenesis analysis reveal a novel reaction mechanism for cyanohydrin decomposition involving the cyano-zinc complex and hydrogen-bonded interaction of the hydroxyl group of cyanohydrin with Glu323/Thr65 and H2O/Lys162 of LuHNL. The deprotonated Lys162 and protonated Glu323 residues are presumably stabilized by a partially desolvated microenvironment. In summary, the substrate binding geometry of LuHNL provides insights into the differences in activities of LuHNL and ADH, and identifying this novel reaction mechanism is an important contribution to the study of hydroxynitrile lyases.


Asunto(s)
Aldehído-Liasas , Lino , Proteínas de Plantas , Aldehído-Liasas/química , Aldehído-Liasas/metabolismo , Sitios de Unión , Cristalografía por Rayos X , Lino/enzimología , Modelos Moleculares , NAD/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Zinc/química , Zinc/metabolismo
3.
Sci Rep ; 12(1): 166, 2022 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-34997003

RESUMEN

This study evaluated the influence of positive peritoneal cytology (PPC) on the prognosis of patients with stage IA endometrial cancer, and the usefulness of adjuvant chemotherapy in their treatment. We retrospectively analyzed the data of patients with stage IA endometrial cancer admitted in our hospital between 2005 and 2015. Among 989 patients who underwent peritoneal cytology, 135 (13.7%) had PPC. Multivariate analysis extracted several independent risk factors for recurrence in stage IA patients, including those with PPC. Adjuvant chemotherapy did not cause a significant difference in the 5-year relapse-free survival rate in patients with PPC (p = 0.78). Similarly, the 5-year recurrence-free survival rate with or without chemotherapy was not different among type II cancer patients (p = 0.11). However, the baseline risk of 5-year relapse-free survival without chemotherapy in patients with PPC and type II was very low (66.7%). While PPC was an independent risk factor for recurrence in stage IA endometrial cancer, adjuvant chemotherapy did not influence the survival rate in patients with PPC. While it is controversial whether adjuvant chemotherapy should be administered in stage IA uterine cancer with only PPC as a prognostic factor, it should be considered for early-stage patients who have multiple risk factors for recurrence.


Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Neoplasias Endometriales/tratamiento farmacológico , Histerectomía , Peritoneo/patología , Adulto , Anciano , Anciano de 80 o más Años , Protocolos de Quimioterapia Combinada Antineoplásica/efectos adversos , Biopsia , Quimioterapia Adyuvante , Progresión de la Enfermedad , Neoplasias Endometriales/mortalidad , Neoplasias Endometriales/patología , Femenino , Humanos , Histerectomía/efectos adversos , Histerectomía/mortalidad , Persona de Mediana Edad , Metástasis de la Neoplasia , Recurrencia Local de Neoplasia , Estadificación de Neoplasias , Valor Predictivo de las Pruebas , Supervivencia sin Progresión , Estudios Retrospectivos , Medición de Riesgo , Factores de Riesgo , Factores de Tiempo
4.
J Biosci Bioeng ; 131(5): 483-490, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33563496

RESUMEN

Pyridoxal-5'-phosphate-dependent cysteine synthases synthesize l-cysteine from their primary substrates, O-acetyl-l-serine (OAS) and O-phospho-l-serine (OPS), and their secondary substrate, sulfide. The mechanism by which cysteine synthases recognize OPS remains unclear; hence, we investigated the OPS recognition mechanism of the OPS sulfhydrylase obtained from Aeropyrum pernix K1 (ApOPSS) and the OAS sulfhydrylase-B obtained from Escherichia coli (EcOASS-B), using protein engineering methods. From the amino acid sequence alignment data, we found that some OPS sulfhydrylases (OPSSs) had a Tyr corresponding to the Phe225 and Phe141 residues in ApOPSS and EcOASS-B, respectively, and that the Tyr residue could facilitate OPS recognition. The enzymatic activity of the ApOPSS F225Y mutant toward OPS decreased compared with that of the wild-type; the kcat value decreased 2.3-fold during cysteine synthesis. X-ray crystallography results of the complex of ApOPSS F225Y and F225Y/R297A mutants bound to OPS and l-cysteine showed that kcat might have decreased because of the stronger interactions of the reaction product phosphate with Tyr225, Thr203, and Arg297, and that of the l-cysteine with Tyr225. The specific activity of the EcOASS-B F141Y mutant toward OPS increased by 50-fold compared with that of the wild-type. Thus, a Tyr within a cysteine synthase corresponding to the Phe225 in ApOPSS and Phe141 in EcOASS-B could act as a key residue for classifying an unknown cysteine synthase as an OPSS. The elucidation of the substrate recognition system of cysteine synthases would enable us to effectively classify cysteine synthases and develop pathogen-specific drug targets, as OPSS is absent in mammalian hosts.


Asunto(s)
Cisteína Sintasa/química , Cisteína Sintasa/metabolismo , Serina/química , Serina/metabolismo , Aeropyrum/enzimología , Secuencia de Aminoácidos , Cristalografía por Rayos X , Cinética
5.
Sci Rep ; 11(1): 1441, 2021 01 14.
Artículo en Inglés | MEDLINE | ID: mdl-33446912

RESUMEN

After pelvic lymphadenectomy (PLA), pelvic vessels, nerve, and ureter are skeletonized. Internal hernias beneath the skeletonized pelvic structure following pelvic lymphadenectomy (IBSPP) are a rare complication following PLA. To the best of our knowledge, only 12 IBSPP cases have been reported and clinical details on such hernias remain unknown. The aim of the study was to investigate the incident and etiology of IBSPP. 1313 patients who underwent open or laparoscopic pelvic lymphadenectomy were identified from our database. A retrospective review was performed. Mean follow-up period was 33.9 months. A total of 12 patients had IBSPP. Multivariate analysis of laparoscopic surgeries group as compared to open surgeries group, para-aortic lymphadenectomy rate, number of dissected lymph nodes by PLA, antiadhesive material use rate, and blood loss were lower in laparoscopic surgeries group: odd ratio (OR) = 0.13 [95% confidence interval (CI) 0.08-0.19], and OR = 0.70 [95% CI 0.50-0.99], OR = 0.17 [95% CI 0.10-0.28], OR = 0.93 [95% CI 0.92-0.94]. However, no significant difference was observed in the incidence of IBSPP between laparoscopic surgery (1.0%) and open surgery (0.8%). All IBSPP occurred in the right pelvic space. These findings may contribute to the development of prevention methods for this disease.


Asunto(s)
Neoplasias de los Genitales Femeninos , Hernia , Intestino Delgado , Laparoscopía/efectos adversos , Escisión del Ganglio Linfático/efectos adversos , Complicaciones Posoperatorias/epidemiología , Adulto , Femenino , Estudios de Seguimiento , Neoplasias de los Genitales Femeninos/epidemiología , Neoplasias de los Genitales Femeninos/cirugía , Hernia/epidemiología , Hernia/etiología , Humanos , Persona de Mediana Edad , Estudios Retrospectivos
6.
ACS Omega ; 5(43): 27896-27908, 2020 Nov 03.
Artículo en Inglés | MEDLINE | ID: mdl-33163773

RESUMEN

Hydroxynitrile lyase (HNL) catalyzes the reversible synthesis and degradation of cyanohydrins, which are important synthetic intermediates for fine chemical and pharmaceutical industries. Here, we report the discovery of HNL from Parafontaria laminata (PlamHNL) millipedes, purification of the HNL to homogeneity, expression of the gene for the enzyme in heterologous expression hosts, and increase in the reaction rate and enantioselectivity in the synthesis of 2-chloromandelonitrile by protein engineering. The recombinant PlamHNL expressed in Pichia pastoris is glycosylated and has a higher thermostability and pH stability than the nonglycosylated HNL expressed in Escherichia coli. PlamHNL showed a unique wide substrate specificity among other millipede HNLs acting on various cyanohydrins, including 2-chloromandelonitrile, a key intermediate for the antithrombotic agent clopidogrel. We solved the X-ray crystal structure of the PlamHNL and found that the catalytic residues were almost identical to those of HNL from Chamberlinius hualienensis, although the forming binding cavity was different. In order to improve the catalytic activity and stereoselectivity, a computational structure-guided directed evolution approach was performed by an enzyme-substrate docking simulation at all of the residues that were exposed on the surface of the active site. The PlamHNL-N85Y mutant showed higher conversion (91% conversion with 98.2% ee of the product) than the wild type (76% conversion with 90% ee of the product) at pH 3.5 and 25 °C for 30 min of incubation. This study shows the diversity of millipede HNLs and reveals the molecular basis for improvement of the activity and stereoselectivity of the wild-type HNL to increase the reaction rate and enantioselectivity in the synthesis of 2-chloromandelonitrile.

7.
Tohoku J Exp Med ; 251(4): 287-294, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32759554

RESUMEN

In Japan, a bivalent human papillomavirus (HPV) vaccine against carcinogenic HPV16/18 was licensed in 2009, and a quadrivalent vaccines against HPV16/18 and non-carcinogenic HPV6/11 was licensed in 2011. Recently, the next-generation 9-valent vaccine targeting HPV6/11/16/18/31/33/45/52/58 has been approved. Accurate HPV genotyping is essential for HPV vaccine research and surveillance. The Roche Linear Array (LA) has long been a standard assay for HPV genotyping, but its recent product discontinuation notice has urged us to introduce an alternative assay with comparable performance. In the present study, an in-house HPV genotyping assay that employs PCR with PGMY09/11 primers and reverse blotting hybridization (PGMY-CHUV) was compared with LA to assess genotype-specific agreement. A total of 100 cervical precancer specimens were subjected to both PGMY-CHUV and LA. For detection of genotypes included in the 9-valent vaccine, PGMY-CHUV completely agreed with LA for detection of HPV6, HPV11, HPV16, HPV18, HPV33 and HPV45, and showed near-complete agreement for HPV31 and HPV58 (98% and 99%, respectively). Moreover, PGMY-CHUV detected a significantly higher prevalence of HPV52 than LA (22% vs. 14%, P = 0.008 by McNemar's exact test), with 92.0% overall agreement, 63.6% positive agreement and a kappa value of 0.73. Most (87.5%) of HPV52 discordant cases involved mixed infections with HPV35 or HPV58. In conclusion, while the two assays present equivalent data for assessing the effectiveness of the bivalent and quadrivalent vaccines, PGMY-CHUV is more suitable for evaluating the impact of the current 9-valent vaccine because of its superior detection of HPV52 in co-infection cases.


Asunto(s)
Técnicas de Genotipaje , Papillomaviridae/genética , Papillomaviridae/inmunología , Vacunas contra Papillomavirus/inmunología , Adulto , Anciano , Femenino , Genotipo , Humanos , Persona de Mediana Edad , Adulto Joven
8.
Protein Eng Des Sel ; 32(1): 33-40, 2019 09 10.
Artículo en Inglés | MEDLINE | ID: mdl-30715529

RESUMEN

Fungus-derived GH-7 family cellobiohydrolase I (CBHI, EC 3.2.1.91) is one of the most important industrial enzymes for cellulosic biomass saccharification. Talaromyces cellulolyticus is well known as a mesophilic fungus producing a high amount of CBHI. Thermostability enhances the economic value of enzymes by making them more robust. However, CBHI has proven difficult to engineer, a fact that stems in part from its low expression in heterozygous hosts and its complex structure. Here, we report the successful improvement of the thermostability of CBHI from T. cellulolyticus using our homologous expression system and protein engineering method. We examined the key structures that seem to contribute to its thermostability using the 3D structural information of CBHI. Some parts of the structure of the Talaromyces emersonii CBHI were grafted into T. cellulolyticus CBHI and thermostable mutant CBHIs were constructed. The thermostability was primarily because of the improvement in the loop structures, and the positive effects of the mutations for thermostability were additive. By combing the mutations, the constructed thermophilic CBHI exhibits high hydrolytic activity toward crystalline cellulose with an optimum temperature at over 70°C. In addition, the strategy can be applied to the construction of the other thermostable CBHIs.


Asunto(s)
Celulosa 1,4-beta-Celobiosidasa/química , Proteínas Fúngicas/química , Calor , Mutación , Talaromyces/enzimología , Celulosa 1,4-beta-Celobiosidasa/genética , Estabilidad de Enzimas , Proteínas Fúngicas/genética , Estructura Secundaria de Proteína , Talaromyces/genética
9.
Sci Rep ; 8(1): 15883, 2018 Oct 23.
Artículo en Inglés | MEDLINE | ID: mdl-30353139

RESUMEN

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

10.
Sci Rep ; 8(1): 11205, 2018 07 25.
Artículo en Inglés | MEDLINE | ID: mdl-30046040

RESUMEN

The discovery of circulating tumour DNA molecules created a paradigm shift in tumour biomarkers as predictors of recurrence. Non-invasive prenatal testing (NIPT) to detect circulating cell-free foetal DNA in maternal plasma is increasingly recognised as a valuable substitute to perceive foetal copy number variation (CNV). This study aimed to determine whether the copy number detection in plasma samples using NIPT platform could be used as a prognostic biomarker in patients with gynaecological cancer. We conducted a prospective study using samples containing preoperative plasma from 100 women with gynaecological cancers. Samples were randomly rearranged and blindly sequenced using a low-coverage whole-genome sequencing plasma DNA, NIPT platform. The NIPT pipeline identified copy number alterations (CNAs) were counted in plasma as a gain or loss if they exceeded 10 Mb from the expected diploid coverage. Progression-free survival (PFS) and overall survival (OS) were analysed according to the presence of CNA in plasma using Kaplan-Meier analyses. The NIPT pipeline detected 19/100 cases of all gynaecological cancers, including 6/36 ovarian cancers, 3/11 cervical cancers, and 10/53 endometrial cancers. Patients with CNA in plasma had a significantly poorer prognosis in all stages concerning PFS and OS. Therefore, low-coverage sequencing NIPT platform could serve as a predictive marker of patient outcome.


Asunto(s)
Ácidos Nucleicos Libres de Células/sangre , Variaciones en el Número de Copia de ADN/genética , Neoplasias de los Genitales Femeninos/sangre , Secuenciación de Nucleótidos de Alto Rendimiento , Adulto , Anciano , Anciano de 80 o más Años , Ácidos Nucleicos Libres de Células/genética , ADN Tumoral Circulante/sangre , ADN Tumoral Circulante/genética , Femenino , Pruebas Genéticas , Neoplasias de los Genitales Femeninos/clasificación , Neoplasias de los Genitales Femeninos/genética , Neoplasias de los Genitales Femeninos/patología , Humanos , Persona de Mediana Edad , Supervivencia sin Progresión , Análisis de Secuencia de ADN , Secuenciación Completa del Genoma
11.
Nature ; 543(7643): 131-135, 2017 03 02.
Artículo en Inglés | MEDLINE | ID: mdl-28219079

RESUMEN

Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a Mn4CaO5 cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 Å using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ångström compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the QB/non-haem iron and the Mn4CaO5 cluster. The changes around the QB/non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 Å from the Mn4CaO5 cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique µ4-oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 Å between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously.


Asunto(s)
Cristalografía/métodos , Electrones , Rayos Láser , Luz , Oxígeno/química , Oxígeno/efectos de la radiación , Complejo de Proteína del Fotosistema II/química , Complejo de Proteína del Fotosistema II/efectos de la radiación , Biocatálisis/efectos de la radiación , Cianobacterias/química , Transporte de Electrón/efectos de la radiación , Análisis de Fourier , Manganeso/química , Manganeso/metabolismo , Modelos Moleculares , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/metabolismo , Proteínas de Hierro no Heme/efectos de la radiación , Oxígeno/metabolismo , Complejo de Proteína del Fotosistema II/metabolismo , Protones , Temperatura , Factores de Tiempo , Agua/química , Agua/metabolismo
12.
Gynecol Minim Invasive Ther ; 6(3): 132-134, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-30254898

RESUMEN

Dilation and curettage is one of the treatment options for cesarean scar pregnancy, however, it sometimes requires a salvage therapy. Few reports discuss the methods of evaluating cesarean scar pregnancy before therapeutic procedures. We aimed to present a case study in which a three-step approach using a combination of preoperational sonohysterography, hysteroscopy, and laparoscopy was performed to evaluate cesarean scar pregnancy. A 33-year-old, G2P2, Japanese female with a history of two elective cesarean sections was diagnosed with viable cesarean scar pregnancy. We used the three-step approach right after undergoing bilateral uterine artery embolization and confirmed that there was a low possibility of fatal complications and we performed dilation and curettage. These steps could be done safely even if the cesarean scar pregnancy was viable. To perform safer curettage on cesarean scar pregnancy patients, these three steps seem to be useful.

13.
Sci Rep ; 6: 33861, 2016 Sep 22.
Artículo en Inglés | MEDLINE | ID: mdl-27653664

RESUMEN

We identified drug seeds for treating Huntington's disease (HD) by combining in vitro single molecule fluorescence spectroscopy, in silico molecular docking simulations, and in vivo fly and mouse HD models to screen for inhibitors of abnormal interactions between mutant Htt and physiological Ku70, an essential DNA damage repair protein in neurons whose function is known to be impaired by mutant Htt. From 19,468 and 3,010,321 chemicals in actual and virtual libraries, fifty-six chemicals were selected from combined in vitro-in silico screens; six of these were further confirmed to have an in vivo effect on lifespan in a fly HD model, and two chemicals exerted an in vivo effect on the lifespan, body weight and motor function in a mouse HD model. Two oligopeptides, hepta-histidine (7H) and Angiotensin III, rescued the morphological abnormalities of primary neurons differentiated from iPS cells of human HD patients. For these selected drug seeds, we proposed a possible common structure. Unexpectedly, the selected chemicals enhanced rather than inhibited Htt aggregation, as indicated by dynamic light scattering analysis. Taken together, these integrated screens revealed a new pathway for the molecular targeted therapy of HD.

14.
Extremophiles ; 20(3): 275-82, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26936147

RESUMEN

TTHA0829 from Thermus thermophilus HB8 has a molecular mass of 22,754 Da and is composed of 210 amino acid residues. The expression of TTHA0829 is remarkably elevated in the latter half of logarithmic growth phase. TTHA0829 can form either a tetrameric or dimeric structure, and main-chain folding provides an N-terminal cystathionine-ß-synthase (CBS) domain and a C-terminal aspartate-kinase chorismate-mutase tyrA (ACT) domain. Both CBS and ACT are regulatory domains to which a small ligand molecule can bind. The CBS domain is found in proteins from organisms belonging to all kingdoms and is observed frequently as two or four tandem copies. This domain is considered as a small intracellular module with a regulatory function and is typically found adjacent to the active (or functional) site of several enzymes and integral membrane proteins. The ACT domain comprises four ß-strands and two α-helices in a ßαßßαß motif typical of intracellular small molecule binding domains that help control metabolism, solute transport and signal transduction. We discuss the possible role of TTHA0829 based on its structure and expression pattern. The results imply that TTHA0829 acts as a cell-stress sensor or a metabolite acceptor.


Asunto(s)
Aspartato Quinasa/química , Proteínas Bacterianas/química , Corismato Mutasa/química , Cistationina betasintasa/química , Thermus thermophilus/genética , Aspartato Quinasa/genética , Aspartato Quinasa/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Corismato Mutasa/genética , Corismato Mutasa/metabolismo , Cistationina betasintasa/genética , Cistationina betasintasa/metabolismo , Dominios Proteicos , Thermus thermophilus/enzimología
15.
Bioorg Med Chem ; 23(22): 7274-81, 2015 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-26515040

RESUMEN

1α,25-Dihydroxyvitamin D3 exerts its actions by binding to vitamin D receptor (VDR). We are continuing the study related to the alteration of pocket structure of VDR by 22-alkyl substituent of ligands and the relationships between the alteration and agonistic/antagonistic activity. Previously we reported that compounds 2 (22-H), 3 (22S-Et), and 4 (22S-Bu) are VDR agonist, partial agonist and antagonist, respectively. Here, we describe the synthesis and biological evaluation of 22S-hexyl analog 5 (22S-Hex), which was designed to be a stronger VDR antagonist than 4. Unexpectedly, 5 showed partial agonistic but not antagonistic activity when bound to VDR, indicating that it is not necessarily true that the bulkier the side chain is, the stronger the antagonistic activity will be. X-ray crystallographic analysis of the VDR-ligand-binding domain (VDR-LBD) accommodating compound 5 indicated that the partial agonist activity of 5 is dependent on the mixed population of the agonistic and antagonistic conformations. Binding of compound 5 may not bring the complex into the only antagonistic conformation due to the large conformational change of the VDR-LBD. From this study it was found that fine tuning of agonistic/antagonistic activity for VDR is possible by 22-alkyl chain length of ligands.


Asunto(s)
Calcitriol/análogos & derivados , Receptores de Calcitriol/química , Animales , Sitios de Unión , Células COS , Calcitriol/síntesis química , Calcitriol/metabolismo , Chlorocebus aethiops , Cristalografía por Rayos X , Genes Reporteros , Humanos , Ligandos , Conformación Molecular , Simulación de Dinámica Molecular , Unión Proteica , Estructura Terciaria de Proteína , Receptores de Calcitriol/agonistas , Receptores de Calcitriol/antagonistas & inhibidores , Receptores de Calcitriol/genética , Receptores de Calcitriol/metabolismo , Activación Transcripcional
16.
FEBS J ; 282(13): 2540-52, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25879162

RESUMEN

UNLABELLED: ß-Galactosidase (EC 3.2.1.23) from Bacillus circulans ATCC 31382, designated BgaD, exhibits high transglycosylation activity to produce galacto-oligosaccharides. BgaD has been speculated to have a multiple domain architecture including a F5/8-type C domain or a discoidin domain in the C-terminal peptide region from amino acid sequence analysis. Here, we solved the first crystal structure of the C-terminal deletion mutant BgaD-D, consisting of sugar binding, Glyco_hydro, catalytic and bacterial Ig-like domains, at 2.5 Å. In the asymmetric unit, two molecules of BgaD-D were identified and the value of VM was estimated to be 5.0 Å(3) · Da(-1). It has been speculated that BgaD-D consists of four domains. From the structural analysis, however, we clarified that BgaD-D consists of five domains. We identified a new domain structure comprised of ß-sheets in BgaD. The catalytic domain exhibits a TIM barrel structure with a small pocket suited for accommodating the disaccharides. Detailed structural information for the amino acid residues related to activity and substrate specificity was clarified in the catalytic domain. Furthermore, using the structural information, we successfully constructed some thermostable mutants via protein engineering method. DATABASE: Coordinates for the BgaD-D structure have been deposited in the Protein Data Bank under accession code 4YPJ.


Asunto(s)
Bacillus/enzimología , beta-Galactosidasa/química , Dominio Catalítico , Cristalización , Mutación , Estructura Terciaria de Proteína
17.
Acta Crystallogr F Struct Biol Commun ; 70(Pt 7): 854-9, 2014 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25005077

RESUMEN

One of the ß-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Šin space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability.


Asunto(s)
Proteínas Arqueales/química , Pyrococcus furiosus/química , beta-Glucosidasa/química , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Cristalografía por Rayos X , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Calor , Modelos Moleculares , Peso Molecular , Mutación , Multimerización de Proteína , Estabilidad Proteica , Estructura Cuaternaria de Proteína , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Pyrococcus furiosus/enzimología , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , beta-Glucosidasa/genética , beta-Glucosidasa/metabolismo
18.
J Med Chem ; 57(10): 4073-87, 2014 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-24773565

RESUMEN

Vitamin D receptor (VDR) ligands are therapeutic agents that are used for the treatment of psoriasis, osteoporosis, and secondary hyperparathyroidism and have immense potential as therapeutic agents for autoimmune diseases, cancers, and cardiovascular diseases. However, the major side effect of VDR ligands, the development of hypercalcemia, limits their expanded use. To develop tissue-selective VDR modulators, we have designed vitamin D analogues with an adamantane ring at the side chain terminal, which would interfere with helix 12, the activation function 2, and modulate the VDR potency. Here we report 25- or 26-adamantyl-23,23,24,24-tetradehydro-19-norvitamin D derivatives (ADTK1-4, 4b,a and 5a,b). These compounds showed high VDR affinities (90% at maximum), partial agonistic activities (EC50 10(-9)-10(-8) M with 40-80% efficacy) in transactivation, and tissue-selective activity in target gene expressions. We investigate the structure-activity relationships of these compounds on the basis of their X-ray crystal structures.


Asunto(s)
Adamantano/análogos & derivados , Receptores de Calcitriol/agonistas , Vitamina D/análogos & derivados , Cristalografía por Rayos X , Células HEK293 , Humanos , Receptores de Calcitriol/química , Relación Estructura-Actividad
19.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 3): 877-88, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24598756

RESUMEN

ß-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Šusing protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Mutación , Pyrococcus furiosus/enzimología , Pyrococcus furiosus/genética , Termodinámica , beta-Glucosidasa/química , beta-Glucosidasa/genética , Rastreo Diferencial de Calorimetría , Cristalización , Cristalografía por Rayos X , Oligosacáridos/química , Oligosacáridos/genética , Ingeniería de Proteínas/métodos , Multimerización de Proteína , Subunidades de Proteína/química , Subunidades de Proteína/genética
20.
J Med Chem ; 56(17): 6745-60, 2013 Sep 12.
Artículo en Inglés | MEDLINE | ID: mdl-23944708

RESUMEN

The vitamin D receptor (VDR), a member of the nuclear receptor superfamily, functions as a ligand-dependent transcription factor for various genes. Hereditary vitamin D-resistant rickets (HVDRR), an autosomal recessive disease, is caused by mutations in the VDR. In particular, the missense mutations R274L and W286R in the ligand-binding domain of the VDR can severely reduce or even eliminate natural hormone responsiveness. Here, we report a crystal structure analysis of the R270L and W282R mutants of rat VDR (human R274L and W286R, respectively) in complex with the natural hormone and synthetic ligands. We also studied the folding properties of the mutant proteins by using circular dichroism spectra. Our study indicates that these mutations result in only local structural modifications. We discuss why these mutations disrupt the VDR function and provide clues to develop effective ligands for the treatment of HVDRR.


Asunto(s)
Calcitriol/metabolismo , Raquitismo Hipofosfatémico Familiar/metabolismo , Mutación , Receptores de Calcitriol/química , Enlace de Hidrógeno , Ligandos , Espectroscopía de Resonancia Magnética , Espectrometría de Masas , Receptores de Calcitriol/genética , Receptores de Calcitriol/metabolismo
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