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1.
Sensors (Basel) ; 24(9)2024 Apr 24.
Artículo en Inglés | MEDLINE | ID: mdl-38732818

RESUMEN

This study comprehensively investigates how rain and drizzle affect the object-detection performance of non-contact safety sensors, which are essential for the operation of unmanned aerial vehicles and ground vehicles in adverse weather conditions. In contrast to conventional sensor-performance evaluation based on the amount of precipitation, this paper proposes spatial transmittance and particle density as more appropriate metrics for rain environments. Through detailed experiments conducted under a variety of precipitation conditions, it is shown that sensor performance is significantly affected by the density of small raindrops rather than the total amount of precipitation. This finding challenges traditional sensor-evaluation metrics in rainfall environments and suggests a paradigm shift toward the use of spatial transmittance as a universal metric for evaluating sensor performance in rain, drizzle, and potentially other adverse weather scenarios.

2.
Biochem Biophys Res Commun ; 718: 150080, 2024 Jul 23.
Artículo en Inglés | MEDLINE | ID: mdl-38735137

RESUMEN

Catalytic promiscuity of enzymes plays a pivotal role in driving the evolution of plant specialized metabolism. Chalcone synthase (CHS) catalyzes the production of 2',4,4',6'-tetrahydroxychalcone (THC), a common precursor of plant flavonoids, from p-coumaroyl-coenzyme A (-CoA) and three malonyl-CoA molecules. CHS has promiscuous product specificity, producing a significant amount of p-coumaroyltriacetic lactone (CTAL) in vitro. However, mechanistic aspects of this CHS promiscuity remain to be clarified. Here, we show that the product specificity of soybean CHS (GmCHS1) is altered by CoA, a reaction product, which selectively inhibits THC production (IC50, 67 µM) and enhances CTAL production. We determined the structure of a ternary GmCHS1/CoA/naringenin complex, in which CoA is bound to the CoA-binding tunnel via interactions with Lys55, Arg58, and Lys268. Replacement of these residues by alanine resulted in an enhanced THC/CTAL production ratio, suggesting the role of these residues in the CoA-mediated alteration of product specificity. In the ternary complex, a mobile loop ("the K-loop"), which contains Lys268, was in a "closed conformation" placing over the CoA-binding tunnel, whereas in the apo and binary complex structures, the K-loop was in an "open conformation" and remote from the tunnel. We propose that the production of THC involves a transition of the K-loop conformation between the open and closed states, whereas synthesis of CTAL is independent of it. In the presence of CoA, an enzyme conformer with the closed K-loop conformation becomes increasingly dominant, hampering the transition of K-loop conformations to result in decreased THC production and increased CTAL production.


Asunto(s)
Aciltransferasas , Glycine max , Aciltransferasas/química , Aciltransferasas/metabolismo , Aciltransferasas/genética , Glycine max/enzimología , Especificidad por Sustrato , Coenzima A/metabolismo , Coenzima A/química , Modelos Moleculares , Conformación Proteica , Chalconas/química , Chalconas/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Proteínas de Plantas/genética
3.
Chembiochem ; 25(7): e202300796, 2024 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-38225831

RESUMEN

Neryl diphosphate (C10) synthase (NDPS1), a homodimeric soluble cis-prenyltransferase from tomato, contains four disulfide bonds, including two inter-subunit S-S bonds in the N-terminal region. Mutagenesis studies demonstrated that the S-S bond formation affects not only the stability of the dimer but also the catalytic efficiency of NDPS1. Structural polymorphs in the crystal structures of NDPS1 complexed with its substrate and substrate analog were identified by employing massive data collections and hierarchical clustering analysis. Heterogeneity of the C-terminal region, including the conserved RXG motifs, was observed in addition to the polymorphs of the binding mode of the ligands. One of the RXG motifs covers the active site with an elongated random coil when the ligands are well-ordered. Conversely, the other RXG motif was located away from the active site with a helical structure. The heterogeneous C-terminal regions suggest alternating structural transitions of the RXG motifs that result in closed and open states of the active sites. Site-directed mutagenesis studies demonstrated that the conserved glycine residue cannot be replaced. We propose that the putative structural transitions of the order/disorder of N-terminal regions and the closed/open states of C-terminal regions may cooperate and be important for the catalytic mechanism of NDPS1.


Asunto(s)
Solanum lycopersicum , Solanum lycopersicum/genética , Transferasas/metabolismo , Dominios Proteicos , Mutagénesis Sitio-Dirigida
4.
Genes Cells ; 29(1): 17-38, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-37984375

RESUMEN

Irgb6 is a priming immune-related GTPase (IRG) that counteracts Toxoplasma gondii. It is known to be recruited to the low virulent type II T. gondii parasitophorous vacuole (PV), initiating cell-autonomous immunity. However, the molecular mechanism by which immunity-related GTPases become inactivated after the parasite infection remains obscure. Here, we found that Thr95 of Irgb6 is prominently phosphorylated in response to low virulent type II T. gondii infection. We observed that a phosphomimetic T95D mutation in Irgb6 impaired its localization to the PV and exhibited reduced GTPase activity in vitro. Structural analysis unveiled an atypical conformation of nucleotide-free Irgb6-T95D, resulting from a conformational change in the G-domain that allosterically modified the PV membrane-binding interface. In silico docking corroborated the disruption of the physiological membrane binding site. These findings provide novel insights into a T. gondii-induced allosteric inactivation mechanism of Irgb6.


Asunto(s)
Toxoplasma , Toxoplasma/metabolismo , Fosforilación , GTP Fosfohidrolasas/genética , GTP Fosfohidrolasas/metabolismo , Vacuolas/metabolismo
5.
Acta Crystallogr D Struct Biol ; 79(Pt 10): 909-924, 2023 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-37747037

RESUMEN

In macromolecular structure determination using X-ray diffraction from multiple crystals, the presence of different structures (structural polymorphs) necessitates the classification of the diffraction data for appropriate structural analysis. Hierarchical clustering analysis (HCA) is a promising technique that has so far been used to extract isomorphous data, mainly for single-structure determination. Although in principle the use of HCA can be extended to detect polymorphs, the absence of a reference to define the threshold used to group the isomorphous data sets (the `isomorphic threshold') poses a challenge. Here, unit-cell-based and intensity-based HCAs have been applied to data sets for apo trypsin and inhibitor-bound trypsin that were mixed post data acquisition to investigate the efficacy of HCA in classifying polymorphous data sets. Single-step intensity-based HCA successfully classified polymorphs with a certain `isomorphic threshold'. In data sets for several samples containing an unknown degree of structural heterogeneity, polymorphs could be identified by intensity-based HCA using the suggested `isomorphic threshold'. Polymorphs were also detected in single crystals using data collected using the continuous helical scheme. These findings are expected to facilitate the determination of multiple structural snapshots by exploiting automated data collection and analysis.


Asunto(s)
Cristalografía por Rayos X , Tripsina , Difracción de Rayos X , Estructura Molecular , Análisis por Conglomerados
6.
Protein Sci ; 32(9): e4745, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37550885

RESUMEN

Antibodies are used for many therapeutic and biotechnological purposes. Because the affinity of an antibody to the antigen is critical for clinical efficacy of pharmaceuticals, many affinity maturation strategies have been developed. Although we previously reported an affinity maturation strategy in which the association rate of the antibody toward its antigen is improved by introducing a cluster of arginine residues into the framework region of the antibody, the detailed molecular mechanism responsible for this improvement has been unknown. In this study, we introduced five arginine residues into an anti-hen egg white lysozyme antibody (HyHEL10) Fab fragment to create the R5-mutant and comprehensively characterized the interaction between antibody and antigen using thermodynamic analysis, X-ray crystallography, and molecular dynamics (MD) simulations. Our results indicate that introduction of charged residues strongly enhanced the association rate, as previously reported, and the antibody-antigen complex structure was almost the same for the R5-mutant and wild-type Fabs. The MD simulations indicate that the mutation increased conformational diversity in complementarity-determining region loops and thereby enhanced the association rate. These observations provide the molecular basis of affinity maturation by R5 mutation.


Asunto(s)
Complejo Antígeno-Anticuerpo , Antígenos , Conformación Proteica , Antígenos/química , Complejo Antígeno-Anticuerpo/química , Regiones Determinantes de Complementariedad/genética , Regiones Determinantes de Complementariedad/química , Fragmentos Fab de Inmunoglobulinas/genética , Fragmentos Fab de Inmunoglobulinas/química , Cristalografía por Rayos X
7.
J Biochem ; 174(4): 335-344, 2023 Sep 29.
Artículo en Inglés | MEDLINE | ID: mdl-37384427

RESUMEN

The sesaminol triglucoside (STG)-hydrolyzing ß-glucosidase from Paenibacillus sp. (PSTG1), which belongs to glycoside hydrolase family 3 (GH3), is a promising catalyst for the industrial production of sesaminol. We determined the X-ray crystal structure of PSTG1 with bound glycerol molecule in the putative active site. PSTG1 monomer contained typical three domains of GH3 with the active site in domain 1 (TIM barrel). In addition, PSTG1 contained an additional domain (domain 4) at the C-terminus that interacts with the active site of the other protomer as a lid in the dimer unit. Interestingly, the interface of domain 4 and the active site forms a hydrophobic cavity probably for recognizing the hydrophobic aglycone moiety of substrate. The short flexible loop region of TIM barrel was found to be approaching the interface of domain 4 and the active site. We found that n-heptyl-ß-D-thioglucopyranoside detergent acts as an inhibitor for PSTG1. Thus, we propose that the recognition of hydrophobic aglycone moiety is important for PSTG1-catalyzed reactions. Domain 4 might be a potential target for elucidating the aglycone recognition mechanism of PSTG1 as well as for engineering PSTG1 to create a further excellent enzyme to degrade STG more efficiently to produce sesaminol.


Asunto(s)
Glicósido Hidrolasas , beta-Glucosidasa , beta-Glucosidasa/química , beta-Glucosidasa/metabolismo , Glicósido Hidrolasas/química , Glicósido Hidrolasas/metabolismo , Furanos/metabolismo , Cristalografía por Rayos X , Especificidad por Sustrato
8.
Elife ; 112022 09 06.
Artículo en Inglés | MEDLINE | ID: mdl-36065637

RESUMEN

Kinesin superfamily proteins are microtubule-based molecular motors driven by the energy of ATP hydrolysis. Among them, the kinesin-4 family is a unique motor that inhibits microtubule dynamics. Although mutations of kinesin-4 cause several diseases, its molecular mechanism is unclear because of the difficulty of visualizing the high-resolution structure of kinesin-4 working at the microtubule plus-end. Here, we report that KLP-12, a C. elegans kinesin-4 ortholog of KIF21A and KIF21B, is essential for proper length control of C. elegans axons, and its motor domain represses microtubule polymerization in vitro. The crystal structure of the KLP-12 motor domain complexed with tubulin, which represents the high-resolution structural snapshot of the inhibition state of microtubule-end dynamics, revealed the bending effect of KLP-12 for tubulin. Comparison with the KIF5B-tubulin and KIF2C-tubulin complexes, which represent the elongation and shrinking forms of microtubule ends, respectively, showed the curvature of tubulin introduced by KLP-12 is in between them. Taken together, KLP-12 controls the proper length of axons by modulating the curvature of the microtubule ends to inhibit the microtubule dynamics.


From meter-long structures that allow nerve cells to stretch across a body to miniscule 'hairs' required for lung cells to clear mucus, many life processes rely on cells sporting projections which have the right size for their role. Networks of hollow filaments known as microtubules shape these structures and ensure that they have the appropriate dimensions. Controlling the length of microtubules is therefore essential for organisms, yet how this process takes place is still not fully elucidated. Previous research has shown that microtubules continue to grow when their end is straight but stop when it is curved. A family of molecular motors known as kinesin-4 participate in this process, but the exact mechanisms at play remain unclear. To investigate, Tuguchi, Nakano, Imasaki et al. focused on the KLP-12 protein, a kinesin-4 equivalent which helps to controls the length of microtubules in the tiny worm Caenorhabditis elegans. They performed genetic manipulations and imaged the interactions between KLP-12 and the growing end of a microtubule using X-ray crystallography. This revealed that KLP-12 controls the length of neurons by inhibiting microtubule growth. It does so by modulating the curvature of the growing end of the filament to suppress its extension. A 'snapshot' of KLP-12 binding to a microtubule at the resolution of the atom revealed exactly how the protein helps to bend the end of the filament to prevent it from growing further. These results will help to understand how nerve cells are shaped. This may also provide insights into the molecular mechanisms for various neurodegenerative disorders caused by problems with the human equivalents of KLP-12, potentially leading to new therapies.


Asunto(s)
Cinesinas , Tubulina (Proteína) , Animales , Caenorhabditis elegans/genética , Microtúbulos/metabolismo , Modelos Estructurales , Tubulina (Proteína)/metabolismo
9.
Acta Crystallogr F Struct Biol Commun ; 78(Pt 6): 241-251, 2022 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-35647681

RESUMEN

In situ diffraction data collection using crystallization plates has been utilized for macromolecules to evaluate crystal quality without requiring additional sample treatment such as cryocooling. Although it is difficult to collect complete data sets using this technique due to the mechanical limitation of crystal rotation, recent advances in methods for data collection from multiple crystals have overcome this issue. At SPring-8, an in situ diffraction measurement system was constructed consisting of a goniometer for a plate, an articulated robot and plate storage. Using this system, complete data sets were obtained utilizing the small-wedge measurement method. Combining this system with an acoustic liquid handler to prepare protein-ligand complex crystals by applying fragment compounds to trypsin crystals for in situ soaking, binding was confirmed for seven out of eight compounds. These results show that the system functioned properly to collect complete data for structural analysis and to expand the capability for ligand screening in combination with a liquid dispenser.


Asunto(s)
Ligandos , Cristalización/métodos , Cristalografía por Rayos X , Recolección de Datos , Sustancias Macromoleculares
10.
Elife ; 112022 06 28.
Artículo en Inglés | MEDLINE | ID: mdl-35762204

RESUMEN

Microtubules are dynamic polymers consisting of αß-tubulin heterodimers. The initial polymerization process, called microtubule nucleation, occurs spontaneously via αß-tubulin. Since a large energy barrier prevents microtubule nucleation in cells, the γ-tubulin ring complex is recruited to the centrosome to overcome the nucleation barrier. However, a considerable number of microtubules can polymerize independently of the centrosome in various cell types. Here, we present evidence that the minus-end-binding calmodulin-regulated spectrin-associated protein 2 (CAMSAP2) serves as a strong nucleator for microtubule formation by significantly reducing the nucleation barrier. CAMSAP2 co-condensates with αß-tubulin via a phase separation process, producing plenty of nucleation intermediates. Microtubules then radiate from the co-condensates, resulting in aster-like structure formation. CAMSAP2 localizes at the co-condensates and decorates the radiating microtubule lattices to some extent. Taken together, these in vitro findings suggest that CAMSAP2 supports microtubule nucleation and growth by organizing a nucleation centre as well as by stabilizing microtubule intermediates and growing microtubules.


Cells are able to hold their shape thanks to tube-like structures called microtubules that are made of hundreds of tubulin proteins. Microtubules are responsible for maintaining the uneven distribution of molecules throughout the cell, a phenomenon known as polarity that allows cells to differentiate into different types with various roles. A protein complex called the γ-tubulin ring complex (γ-TuRC) is necessary for microtubules to form. This protein helps bind the tubulin proteins together and stabilises microtubules. However, recent research has found that in highly polarized cells such as neurons, which have highly specialised regions, microtubules can form without γ-TuRC. Searching for the proteins that could be filling in for γ-TuRC in these cells some evidence has suggested that a group known as CAMSAPs may be involved, but it is not known how. To characterize the role of CAMSAPs, Imasaki, Kikkawa et al. studied how one of these proteins, CAMSAP2, interacts with tubulins. To do this, they reconstituted both CAMSAP2 and tubulins using recombinant biotechnology and mixed them in solution. These experiments showed that CAMSAP2 can help form microtubules by bringing together their constituent proteins so that they can bind to each other more easily. Once microtubules start to form, CAMSAP2 continues to bind to them, stabilizing them and enabling them to grow to full size. These results shed light on how polarity is established in cells such as neurons, muscle cells, and epithelial cells. Additionally, the ability to observe intermediate structures during microtubule formation can provide insights into the processes that these structures are involved in.


Asunto(s)
Espectrina , Tubulina (Proteína) , Proteínas Asociadas a Microtúbulos/metabolismo , Centro Organizador de los Microtúbulos/metabolismo , Microtúbulos/metabolismo , Espectrina/metabolismo , Tubulina (Proteína)/metabolismo
11.
J Synchrotron Radiat ; 29(Pt 2): 593, 2022 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-35254325

RESUMEN

A figure in the article by Baba et al. [(2021), J. Synchrotron Rad. 28, 1284-1295] is corrected.

12.
J Org Chem ; 87(6): 4468-4475, 2022 03 18.
Artículo en Inglés | MEDLINE | ID: mdl-35199522

RESUMEN

The enantioselective kinetic resolution of ß-unfunctionalized primary alcohols with benzoyl chloride was carried out in the presence of a catalytic amount of a novel chiral 1,2-diamine derived from (S)-proline. Several valuable chiral 2-substituted propan-1-ols were obtained with good enantioselectivities. Density functional theory calculations revealed that the noncovalent interaction, such as CH-π interaction, is crucial for the enantioselectivity of the resolution. This study was conducted through an interplay between experiment and computation.


Asunto(s)
Alcoholes , Diaminas , Catálisis , Cinética , Estereoisomerismo
13.
FEBS J ; 289(15): 4602-4621, 2022 08.
Artículo en Inglés | MEDLINE | ID: mdl-35133719

RESUMEN

Most cis-prenyltransferases (cPTs) use all-trans-oligoprenyl diphosphate, such as (E,E)-farnesyl diphosphate (FPP, C15 ), but scarcely accept dimethylallyl diphosphate (DMAPP, C5 ), as an allylic diphosphate primer in consecutive cis-condensations of isopentenyl diphosphate. Consequently, naturally occurring cis-1,4-polyisoprenoids contain a few trans-isoprene units at their ω-end. However, some Solanum plants have distinct cPTs that primarily use DMAPP as a primer to synthesize all-cis-oligoprenyl diphosphates, such as neryl diphosphate (NPP, C10 ). However, the mechanism underlying the allylic substrate preference of cPTs remains unclear. In this study, we determined the crystal structure of NDPS1, an NPP synthase from tomato, and investigated critical residues for primer substrate preference through structural comparisons of cPTs. Highly conserved Gly and Trp in the primer substrate-binding region of cPTs were discovered to be substituted for Ile/Leu and Phe, respectively, in DMAPP-preferring cPTs. An I106G mutant of NDPS1 exhibited a low preference for DMAPP, but a higher preference for FPP. However, an I106G/F276W mutant preferred not only DMAPP but also all-trans-oligoprenyl diphosphates, with 15-fold higher catalytic efficiency than WT. Surprisingly, the mutant synthesized longer polyisoprenoids (~C50 ). Furthermore, one of the helix domains that constitute the hydrophobic cleft for accommodating elongating prenyl chains was also demonstrated to be critical in primer substrate preference. An NDPS1 I106G/F276W mutant with a chimeric helix domain swapped with that of a medium-chain cPT synthesizing C50-60 polyisoprenoids showed over 94-fold increase in catalytic efficiency for all primer substrates tested, resulting in longer products (~C70 ). These NDPS1 mutants could be used in the enzymatic synthesis of nonnatural all-cis-polyisoprenoids.


Asunto(s)
Transferasas Alquil y Aril , Difosfatos , Catálisis , Transferasas/química
14.
Mol Clin Oncol ; 16(2): 38, 2022 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-35003736

RESUMEN

Mass screening based on prostate-specific antigen (PSA) reduces mortality in prostate cancer. However, the effectiveness of this screening in the elderly has not been demonstrated. In the city of Yokosuka, Japan, PSA screening has been conducted since 2001 and the present study examined the real-world status of PSA-based population screening in the elderly. It retrospectively evaluated 1,117 prostate cancer patients >75 years of age. The patients were divided into two groups: The screened group comprising patients diagnosed by PSA-based population screening or workplace screening and PSA follow-up patients at urology clinics; and the non-screened group comprising patients detected by other methods. Overall survival (OS), cancer-specific survival (CSS) and factors contributing to shorter CSS between the groups were compared. In patients >75 years of age, the screened group had significantly longer OS (171 vs. 154 months; P=0.019) and CSS (median not reached; P=0.020) but screening was not an independent factor associated with prolonged OS or CSS on multivariate analysis. The factors contributing to shorten CSS in the elderly were ≥T3 (odds ratio: 3.301 [1.704-6.369], P<0.001), M1 (odds ratio: 4.856 [2.809-8.393], P<0.001) and Gleason score ≥8 (odds ratio: 4.691 [2.479-8.876], P<0.001). In those with metastasis, PSA screening was not associated with prolonged OS or CSS. Real-world data 15 years after introducing PSA-based population screening was not an independent factor for both OS and CSS in multivariate analyses for patients >75 years of age.

15.
FEBS Open Bio ; 12(3): 560-570, 2022 03.
Artículo en Inglés | MEDLINE | ID: mdl-35038379

RESUMEN

Noroviruses have been identified as major causative agents of acute nonbacterial gastroenteritis in humans. Histo-blood group antigens (HBGAs) are thought to play a major role among the host cellular factors influencing norovirus infection. Genogroup I, genotype 9 (GI.9) is the most recently identified genotype within genogroup I, whose representative strain is the Vancouver 730 norovirus. However, the molecular interactions between host antigens and the GI.9 capsid protein have not been investigated in detail. In this study, we demonstrate that the GI.9 norovirus preferentially binds Lewis antigens over blood group A, B, and H antigens, as revealed by an HBGA binding assay using virus-like particles. We determined the crystal structures of the protruding domain of the GI.9 capsid protein in the presence or absence of Lewis antigens. Our analysis demonstrated that Lewis fucose (α1-3/4 fucose) represents a key moiety for the GI.9 protein-HBGA interaction, thus suggesting that Lewis antigens might play a critical role during norovirus infection. In addition to previously reported findings, our observations may support the future design of antiviral agents and vaccines against noroviruses.


Asunto(s)
Antígenos de Grupos Sanguíneos , Norovirus , Sitios de Unión , Antígenos de Grupos Sanguíneos/química , Antígenos de Grupos Sanguíneos/metabolismo , Cristalografía por Rayos X , Fucosa/química , Fucosa/metabolismo , Humanos , Modelos Moleculares , Norovirus/química , Norovirus/genética , Norovirus/metabolismo , Unión Proteica
16.
Jpn J Radiol ; 40(4): 404-411, 2022 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-34739655

RESUMEN

PURPOSE: To assess prebiopsy characteristics influencing the occurrence of pneumothorax after first puncture of ultrasound (US)-guided lung biopsy with coaxial technique. MATERIALS AND METHODS: From January 2007 to September 2018, 180 peripheral lung lesions in 174 patients who underwent B-mode US-guided lung biopsy with coaxial technique at single institution were included in this study. Technical success was defined as the ability to make a diagnosis using the acquired sample with/without an adverse event of pneumothorax. Statistical analyses of prebiopsy characteristics were performed to identify the most important cutpoint and to evaluate the effect on diagnostic accuracy. RESULTS: Of the 180 lesions (mean size, 37 mm ± 26.2; mean pleural contact length, 38.2 mm ± 34.4), technical success rate was 97.2% (175/180 lesions) and diagnostic accuracy rate was 91.6% (165/180 lesions). Pneumothorax occurred immediately after first puncture for seven of 180 lesions. Classification and regression tree analysis and Fisher's exact test showed the proportion of the pneumothorax immediately after first puncture was higher in lesions with pleural contact length less than 9.78 mm (p = 0.002). No significant difference was shown between the pneumothorax and non-pneumothorax after first puncture in technical success and final diagnosis success rate. CONCLUSION: Pleural contact length affects the occurrence of pneumothorax after first puncture of US-guided lung biopsy with coaxial technique.


Asunto(s)
Neumotórax , Humanos , Biopsia Guiada por Imagen/efectos adversos , Pulmón/diagnóstico por imagen , Pulmón/patología , Neumotórax/diagnóstico por imagen , Neumotórax/etiología , Punciones , Tomografía Computarizada por Rayos X , Ultrasonografía Intervencional
17.
Life Sci Alliance ; 5(1)2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34753804

RESUMEN

The p47 immunity-related GTPase (IRG) Irgb6 plays a pioneering role in host defense against Toxoplasma gondii infection. Irgb6 is recruited to the parasitophorous vacuole membrane (PVM) formed by T. gondii and disrupts it. Despite the importance of this process, the molecular mechanisms accounting for PVM recognition by Irgb6 remain elusive because of lack of structural information on Irgb6. Here we report the crystal structures of mouse Irgb6 in the GTP-bound and nucleotide-free forms. Irgb6 exhibits a similar overall architecture to other IRGs in which GTP binding induces conformational changes in both the dimerization interface and the membrane-binding interface. The membrane-binding interface of Irgb6 assumes a unique conformation, composed of N- and C-terminal helical regions forming a phospholipid binding site. In silico docking of phospholipids further revealed membrane-binding residues that were validated through mutagenesis and cell-based assays. Collectively, these data demonstrate a novel structural basis for Irgb6 to recognize T. gondii PVM in a manner distinct from other IRGs.


Asunto(s)
Interacciones Huésped-Parásitos , Proteínas de Unión al GTP Monoméricas/química , Proteínas de Unión al GTP Monoméricas/metabolismo , Toxoplasma , Toxoplasmosis/metabolismo , Toxoplasmosis/parasitología , Secuencia de Aminoácidos , Animales , Sitios de Unión , Ratones , Modelos Moleculares , Unión Proteica , Conformación Proteica , Dominios y Motivos de Interacción de Proteínas , Relación Estructura-Actividad , Vacuolas
18.
J Synchrotron Radiat ; 28(Pt 5): 1284-1295, 2021 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-34475278

RESUMEN

Intense micro-focus X-ray beamlines available at synchrotron facilities have achieved high-quality data collection even from the microcrystals of membrane proteins. The automatic data collection system developed at SPring-8, named ZOO, has contributed to many structure determinations of membrane proteins using small-wedge synchrotron crystallography (SWSX) datasets. The `small-wedge' (5-20°) datasets are collected from multiple crystals and then merged to obtain the final structure factors. To our knowledge, no systematic investigation on the dose dependence of data accuracy has so far been reported for SWSX, which is between `serial crystallography' and `rotation crystallography'. Thus, herein, we investigated the optimal dose conditions for experimental phasing with SWSX. Phase determination using anomalous scattering signals was found to be more difficult at higher doses. Furthermore, merging more homogeneous datasets grouped by hierarchical clustering with controlled doses mildly reduced the negative factors in data collection, such as `lack of signal' and `radiation damage'. In turn, as more datasets were merged, more probable phases could be obtained across a wider range of doses. Therefore, our findings show that it is essential to choose a lower dose than 10 MGy for de novo structure determination by SWSX. In particular, data collection using a dose of 5 MGy proved to be optimal in balancing the amount of signal available while reducing the amount of damage as much as possible.


Asunto(s)
Cristalografía por Rayos X/métodos , Proteínas de la Membrana/química , Proteínas de la Membrana/efectos de la radiación , Muramidasa/química , Muramidasa/efectos de la radiación , Modelos Moleculares , Dosis de Radiación , Traumatismos por Radiación , Dispersión de Radiación , Sincrotrones
19.
Org Lett ; 23(15): 5714-5718, 2021 08 06.
Artículo en Inglés | MEDLINE | ID: mdl-34254813

RESUMEN

Maleimides are often used as electrophiles in conventional reactions; however, their application as nucleophiles is limited to only a few reactions, and reactions utilizing α-aminomaleimides as asymmetric Michael donors have not been reported to date. Thus, in this work, asymmetric Michael addition of α-aminomaleimides as Michael donors to ß-nitrostyrenes was conducted for the first time using an organocatalyst derived from a Cinchona alkaloid. Density functional theory investigations were crucial to improve the enantioselectivity of the adduct.


Asunto(s)
Alcaloides de Cinchona/química , Maleimidas/química , Estirenos/química , Reacción de Cicloadición , Estructura Molecular
20.
Proc Natl Acad Sci U S A ; 118(11)2021 03 16.
Artículo en Inglés | MEDLINE | ID: mdl-33674463

RESUMEN

Biomolecular assemblies govern the physiology of cells. Their function often depends on the changes in molecular arrangements of constituents, both in the positions and orientations. While recent advancements of fluorescence microscopy including super-resolution microscopy have enabled us to determine the positions of fluorophores with unprecedented accuracy, monitoring the orientation of fluorescently labeled molecules within living cells in real time is challenging. Fluorescence polarization microscopy (FPM) reports the orientation of emission dipoles and is therefore a promising solution. For imaging with FPM, target proteins need labeling with fluorescent probes in a sterically constrained manner, but because of difficulties in the rational three-dimensional design of protein connection, a universal method for constrained tagging with fluorophore was not available. Here, we report POLArIS, a genetically encoded and versatile probe for molecular orientation imaging. Instead of using a direct tagging approach, we used a recombinant binder connected to a fluorescent protein in a sterically constrained manner that can target specific biomolecules of interest by combining with phage display screening. As an initial test case, we developed POLArISact, which specifically binds to F-actin in living cells. We confirmed that the orientation of F-actin can be monitored by observing cells expressing POLArISact with FPM. In living starfish early embryos expressing POLArISact, we found actin filaments radially extending from centrosomes in association with microtubule asters during mitosis. By taking advantage of the genetically encoded nature, POLArIS can be used in a variety of living specimens, including whole bodies of developing embryos and animals, and also be expressed in a cell type/tissue specific manner.


Asunto(s)
Citoesqueleto de Actina/metabolismo , Polarización de Fluorescencia/métodos , Colorantes Fluorescentes/metabolismo , Microscopía Fluorescente/métodos , Microtúbulos/metabolismo , Imagen Molecular/métodos , Estrellas de Mar/embriología , Animales , Embrión no Mamífero/citología , Embrión no Mamífero/metabolismo , Proteínas Fluorescentes Verdes/metabolismo , Células HeLa , Humanos , Células LLC-PK1 , Porcinos
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