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1.
STAR Protoc ; 5(2): 102996, 2024 Jun 21.
Artículo en Inglés | MEDLINE | ID: mdl-38573861

RESUMEN

Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor that can be targeted for inducing potent adjuvant effects. Mincle can recognize trehalose dimycolate and related glycolipids. Here, we present a protocol to identify the ligand binding mode of Mincle. We describe steps for preparing labeled Mincle ectodomain, data acquisition, and analysis of nuclear magnetic resonance experiments using non-detergent sulfobetaine-195. This protocol can be applied to other protein-ligand interactions that have aggregation problems for complex formation. For complete details on the use and execution of this protocol, please refer to Furukawa et al.1.


Asunto(s)
Lectinas Tipo C , Lectinas Tipo C/metabolismo , Lectinas Tipo C/química , Ligandos , Sitios de Unión , Humanos , Espectroscopía de Resonancia Magnética/métodos , Unión Proteica , Receptores Inmunológicos/química , Receptores Inmunológicos/metabolismo , Proteínas de la Membrana/química , Proteínas de la Membrana/metabolismo , Resonancia Magnética Nuclear Biomolecular/métodos
2.
Sci Rep ; 13(1): 18098, 2023 10 23.
Artículo en Inglés | MEDLINE | ID: mdl-37872180

RESUMEN

The effects of seed dispersers on plant fitness (seed dispersal effectiveness, SDE) have been evaluated based on the number (quantity) and recruitment probability (quality) of dispersed seeds. Although seeds of most zoochorous species are dispersed by two or more animal species, which may interact with each other, SDE has often been studied assuming a one-plant and one-animal species system. We compared the SDE of Japanese walnut (Juglans ailanthifolia) between squirrel-only and squirrel-mouse sites in natural forests of Hokkaido, Japan, and found that the SDE from the red squirrel (Sciurus vulgaris), considered a primary seed disperser, was altered by an alternative seed disperser species, the Japanese wood mouse (Apodemus speciosus). Seed removal rates at the squirrel-mouse site were significantly higher than those at the squirrel-only site, and both dispersed seeds and seedlings were less aggregated, with a strongly repulsive relationship with adult conspecific trees at the squirrel-mouse site. Seedlings established themselves at a location with fewer medium-sized trees (< 10 cm DBH) at the squirrel-mouse site. These results suggest that the interactive effect of the rodent species affects the SDE of Japanese walnut.


Asunto(s)
Conducta Alimentaria , Juglans , Sciuridae , Dispersión de Semillas , Animales , Ratones , Plantones , Semillas , Japón , Conducta Animal
3.
Protein Expr Purif ; 212: 106361, 2023 12.
Artículo en Inglés | MEDLINE | ID: mdl-37652393

RESUMEN

DiRAS3, also called ARHI, is a RAS (sub)family small GTPase protein that shares 50-60% sequence identity with H-, K-, and N-RAS, with substitutions in key conserved G-box motifs and a unique 34 amino acid extension at its N-terminus. Unlike the RAS proto-oncogenes, DiRAS3 exhibits tumor suppressor properties. DiRAS3 function has been studied through genetics and cell biology, but there has been a lack of understanding of the biochemical and biophysical properties of the protein, likely due to its instability and poor solubility. To overcome this solubility issue, we engineered a DiRAS3 variant (C75S/C80S), which significantly improved soluble protein expression in E. coli. Recombinant DiRAS3 was purified by Ni-NTA and size exclusion chromatography (SEC). Concentration dependence of the SEC chromatogram indicated that DiRAS3 exists in monomer-dimer equilibrium. We then produced truncations of the N-terminal (ΔN) and both (ΔNC) extensions to the GTPase domain. Unlike full-length DiRAS3, the SEC profiles showed that ΔNC is monomeric while ΔN was monomeric with aggregation, suggesting that the N and/or C-terminal tail(s) contribute to dimerization and aggregation. The 1H-15N HSQC NMR spectrum of ΔNC construct displayed well-dispersed peaks similar to spectra of other GTPase domains, which enabled us to demonstrate that DiRAS3 has a GTPase domain that can bind GDP and GTP. Taken together, we conclude that, despite the substitutions in the G-box motifs, DiRAS3 can switch between nucleotide-bound states and that the N- and C-terminal extensions interact transiently with the GTPase domain in intra- and inter-molecular fashions, mediating weak multimerization of this unique small GTPase.


Asunto(s)
Proteínas de Unión al GTP Monoméricas , Proteínas ras , Escherichia coli/genética , Aminoácidos , Biofisica
4.
Structure ; 31(9): 1077-1085.e5, 2023 09 07.
Artículo en Inglés | MEDLINE | ID: mdl-37348496

RESUMEN

Mincle (macrophage-inducible C-type lectin, CLEC4E) is a C-type lectin immune-stimulatory receptor for cord factor, trehalose dimycolate (TDM), which serves as a potent component of adjuvants. The recognition of glycolipids by Mincle, especially their lipid parts, is poorly understood. Here, we performed nuclear magnetic resonance analysis, revealing that titration of trehalose harboring a linear short acyl chain showed a chemical shift perturbation of hydrophobic residues next to the Ca-binding site. Notably, there were split signals for Tyr201 upon complex formation, indicating two binding modes for the acyl chain. In addition, most Mincle residues close to the Ca-binding site showed no observable signals, suggesting their mobility on an ∼ ms scale even after complex formation. Mutagenesis study supported two putative lipid-binding modes for branched acyl-chain TDM binding. These results provide novel insights into the plastic-binding modes of Mincle toward a wide range of glycol- and glycerol-lipids, important for rational adjuvant development.


Asunto(s)
Glucolípidos , Lectinas Tipo C , Sitios de Unión , Factores Cordón/química , Factores Cordón/metabolismo , Glucolípidos/química , Glucolípidos/metabolismo , Lectinas Tipo C/química , Mutagénesis , Humanos
5.
Cancer Diagn Progn ; 2(2): 258-262, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35399171

RESUMEN

Background: Langerhans cell histiocytosis (LCH) is a rare disease, especially in adults. It is often associated with non-fatal bone and skin lesions and has relatively good radiosensitivity. In contrast, brain and lymph node metastases from LCH lesions are considered to be less sensitive to radiotherapy. Case Report: At our institution, 30 Gy radiotherapy was used to treat bone lesions with dural invasion in a patient with adult-onset LCH. The patient was treated with chemotherapy and radiotherapy for 21 years since the initial diagnosis. After radiotherapy, the tumor shrank rapidly, and a complete response was achieved 1 year after treatment. The patient survived without local recurrence. Conclusion: Here, we report the details of this case, along with a review of the literature. We suggest that even with invasion of the tissues around the bone lesions in LCH, local recurrence can be prevented by middle radiation doses.

6.
Nat Commun ; 12(1): 1848, 2021 03 23.
Artículo en Inglés | MEDLINE | ID: mdl-33758193

RESUMEN

Neuroligin 3 (NLGN3) and neurexins (NRXNs) constitute a canonical transsynaptic cell-adhesion pair, which has been implicated in autism. In autism spectrum disorder (ASD) development of sociality can be impaired. However, the molecular mechanism underlying NLGN3-mediated social development is unclear. Here, we identify non-canonical interactions between NLGN3 and protein tyrosine phosphatase δ (PTPδ) splice variants, competing with NRXN binding. NLGN3-PTPδ complex structure revealed a splicing-dependent interaction mode and competition mechanism between PTPδ and NRXNs. Mice carrying a NLGN3 mutation that selectively impairs NLGN3-NRXN interaction show increased sociability, whereas mice where the NLGN3-PTPδ interaction is impaired exhibit impaired social behavior and enhanced motor learning, with imbalance in excitatory/inhibitory synaptic protein expressions, as reported in the Nlgn3 R451C autism model. At neuronal level, the autism-related Nlgn3 R451C mutation causes selective impairment in the non-canonical pathway. Our findings suggest that canonical and non-canonical NLGN3 pathways compete and regulate the development of sociality.


Asunto(s)
Trastorno del Espectro Autista/genética , Proteínas de Unión al Calcio/metabolismo , Moléculas de Adhesión Celular Neuronal/metabolismo , Proteínas de la Membrana/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Moléculas de Adhesión de Célula Nerviosa/metabolismo , Neuronas/metabolismo , Proteínas Tirosina Fosfatasas Clase 2 Similares a Receptores/metabolismo , Secuencia de Aminoácidos , Animales , Trastorno del Espectro Autista/metabolismo , Escala de Evaluación de la Conducta , Proteínas de Unión al Calcio/química , Proteínas de Unión al Calcio/genética , Moléculas de Adhesión Celular Neuronal/química , Moléculas de Adhesión Celular Neuronal/genética , Modelos Animales de Enfermedad , Femenino , Células HEK293 , Humanos , Masculino , Proteínas de la Membrana/química , Proteínas de la Membrana/genética , Ratones , Ratones Noqueados , Ratones Transgénicos , Mutación , Proteínas del Tejido Nervioso/química , Proteínas del Tejido Nervioso/genética , Moléculas de Adhesión de Célula Nerviosa/química , Moléculas de Adhesión de Célula Nerviosa/genética , Dominios Proteicos , Empalme de Proteína , Proteínas Tirosina Fosfatasas Clase 2 Similares a Receptores/química , Proteínas Tirosina Fosfatasas Clase 2 Similares a Receptores/genética , Proteínas Recombinantes , Transducción de Señal/genética , Transducción de Señal/fisiología , Conducta Social , Sinapsis/genética
7.
Dev Dyn ; 250(8): 1140-1159, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-33683772

RESUMEN

BACKGROUND: How bats deviate heterochronically from other mammals remains largely unresolved, reflecting the lack of a quantitative staging framework allowing comparison among species. The standard event system (SES) is an embryonic staging system allowing quantitative detection of interspecific developmental variations. Here, the first SES-based staging system for bats, using Asian parti-colored bat (Vespertilio sinensis) is introduced. General aspects of normal embryonic development and the three-dimensional development of the bat cochlea were described for the first time. Recoding the embryonic staging tables of 18 previously reported bat species and Mus musculus into the SES system, quantitative developmental comparisons were performed. RESULTS: It was found that limb bud development of V. sinensis is relatively late among 19 bat species and late limb development is a shared trait of vespertilionid bats. The inner ear cochlear canal forms before the semicircular canal in V. sinensis while the cochlear canal forms after the semicircular canal in non-volant mammals. CONCLUSIONS: The present approach using the SES system provides a powerful framework to detect the peculiarities of bat development. Incorporating the timing of gene expression patterns into the SES framework will further contribute to the understanding of the evolution of specialized features in bats.


Asunto(s)
Quirópteros/embriología , Cóclea/embriología , Organogénesis/fisiología , Animales , Femenino , Ratones , Fenotipo , Embarazo
8.
J Biochem ; 168(4): 427-434, 2020 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-32470136

RESUMEN

The malaria parasite (Plasmodium sp.) contains a plastid-derived organelle called the apicoplast, which is essential for the growth of the parasite. In this organelle, a redox system comprising plant-type ferredoxin (Fd) and Fd: NADP(H) oxidoreductase (FNR) supplies reducing power for the crucial metabolic pathways. Electron transfer between Plasmodium falciparum Fd (PfFd) and FNR (PfFNR) is performed with higher affinity and specificity than those of plant Fd and FNR. We investigated the structural basis for such superior protein-protein interaction by focussing on the Plasumodium-specific regions of PfFd. Significant contribution of the C-terminal region of PfFd for the electron transfer with PfFNR was revealed by exchanging the C-terminal three residues between plant Fd and PfFd. Further site-directed mutagenesis of the PfFd C-terminal residues indicated that the presence of aromatic residue at Positions 96 and 97 contributes to the lower Km for PfFNR. Physical binding analyses using fluorescence and calorimetric measurements supported the results. A mutation from Asp to Tyr at position 97 of PfFd was recently reported to be strongly associated with P. falciparum resistance to artemisinin, the front line anti-malarial drug. Thus, the enhanced interaction of PfFd D97Y protein with PfFNR could be involved in artemisinin resistance of human malaria parasites.


Asunto(s)
Artemisininas/farmacología , Ferredoxina-NADP Reductasa/metabolismo , Ferredoxinas/metabolismo , Malaria Falciparum/parasitología , Plasmodium falciparum/efectos de los fármacos , Plasmodium falciparum/enzimología , Proteínas Protozoarias/metabolismo , Secuencia de Aminoácidos , Antimaláricos/farmacología , Cristalografía por Rayos X/métodos , Resistencia a Medicamentos , Ferredoxinas/química , Humanos , Malaria Falciparum/tratamiento farmacológico , Malaria Falciparum/metabolismo , Modelos Moleculares , Mutagénesis Sitio-Dirigida/métodos , Plasmodium falciparum/parasitología , Proteínas Protozoarias/química , Homología de Secuencia
9.
Cells ; 9(2)2020 02 24.
Artículo en Inglés | MEDLINE | ID: mdl-32102436

RESUMEN

Konjac ceramide (kCer) is a plant-type ceramide composed of various long-chain bases and a-hydroxyl fatty acids. The presence of d4t,8t-sphingadienine is essential for semaphorin 3A (Sema3A)-like activity. Herein, we examined the three neuropilin 1 (Nrp1) domains (a1a2, b1b2, or c), and found that a1a2 binds to d4t,8t-kCer and possesses Sema3A-like activity. kCer binds to Nrp1 with a weak affinity of mM dissociation constant (Kd). We wondered whether bovine serum albumin could influence the ligand-receptor interaction that a1a2 has with a single high affinity binding site for kCer (Kd in nM range). In the present study we demonstrated the influence of bovine serum albumin. Thermal denaturation indicates that the a1a2 domain may include intrinsically disordered region (IDR)-like flexibility. A potential interaction site on the a1 module was explored by molecular docking, which revealed a possible Nrp1 activation mechanism, in which kCer binds to Site A close to the Sema3A-binding region of the a1a2 domain. The a1 module then accesses a2 as the IDR-like flexibility becomes ordered via kCer-induced protein rigidity of a1a2. This induces intramolecular interaction between a1 and a2 through a slight change in protein secondary structure.


Asunto(s)
Glucosilceramidas/farmacología , Neuropilina-1/metabolismo , Sitios de Unión , Línea Celular Tumoral , Glucosilceramidas/química , Humanos , Inmunoprecipitación , Modelos Moleculares , Neuropilina-1/química , Dominios Proteicos , Semaforina-3A/metabolismo
10.
Mol Ecol Resour ; 20(2): 444-456, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31736261

RESUMEN

Multiple male mating (MMM) causes sperm competition, which may play an important role in the evolution of reproductive traits. The frequency of multiple paternity (MP), where multiple males sire offspring within a single litter, has been used as an index of MMM frequency. However, MP frequency is necessarily lower than MMM frequency. The magnitude of the difference between MMM and MP frequency depends on litter size (LS) and fertilization probability skew (FPS), and this difference may be meaningfully large in animals with small LSs. In this study, we propose a method to estimate MMM frequency using an individual-based model with three variables (MP frequency, LS and FPS). We incorporated observed paternity skew data to infer a possible range of FPS that cannot be measured in free-living populations and tested the validity of our method using a data set from a grey-sided vole (Myodes rufocanus) population and from hypothetical populations. MP was found in 50 out of 215 litters (23.3%) in the grey-sided vole population, while MMM frequency was estimated in 67 of 215 litters (31.2%), with a certainty range of 59-88 (27.4%-40.9%). The point estimation of MMM frequency was realized, and the certainty range was limited within the practical range. The use of observed paternity skew was very effective at narrowing the certainty range of the estimate. Our method could contribute to a deeper understanding of the ecology of MMM in free-living populations.


Asunto(s)
Arvicolinae/fisiología , Conducta Sexual Animal , Animales , Arvicolinae/genética , Femenino , Masculino , Paternidad , Reproducción
11.
Membranes (Basel) ; 9(11)2019 Oct 30.
Artículo en Inglés | MEDLINE | ID: mdl-31671562

RESUMEN

Water gas shift reaction of carbon monoxide (CO) with membrane reactors should be a promising method for hydrogen mass-production because of its high CO conversion, high hydrogen purity and low carbon dioxide emission. For developing such membrane reactors, we need hydrogen permselective membranes with high hydrogen permeance with order of 10-6 mol m-2 s-1 Pa-1 at 573 K and high steam durability. In this study, we have optimized the kind of substrates, precursors, vapor concentration, and chemical vapor deposition (CVD) time using the counter-diffusion CVD method for developing such membranes. The developed membrane prepared from hexamethyldisiloxane has a hydrogen permeance of 1.29 × 10-6 mol m-2 s-1 Pa-1 at 573 K and high steam durability. We also conducted water gas shift reactions with membrane reactors installed the developed silica membranes. The results indicated that reactions proceed efficiently with the conversion around 95-97%, hydrogen purity around 94%, and hydrogen recovery around 60% at space velocity (SV) 7000.

12.
FEBS Open Bio ; 9(12): 2126-2136, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31665566

RESUMEN

Ferredoxin-NADP+ reductase (FNR) in plants receives electrons from ferredoxin (Fd) at the end of the photosynthetic electron transfer chain and converts NADP+ to NADPH. The interaction between Fd and FNR in plants was previously shown to be attenuated by NADP(H). Here, we investigated the molecular mechanism of this phenomenon using maize FNR and Fd, as the three-dimensional structure of this complex is available. NADPH, NADP+ , and 2'5'-ADP differentially affected the interaction, as revealed through kinetic and physical binding analyses. Site-directed mutations of FNR which change the affinity for NADPH altered the affinity for Fd in the opposite direction to that for NADPH. We propose that the binding of NADP(H) causes a conformational change of FNR which is transferred to the Fd-binding region through different domains of FNR, resulting in allosteric changes in the affinity for Fd.


Asunto(s)
Ferredoxina-NADP Reductasa/genética , Ferredoxina-NADP Reductasa/metabolismo , NADP/metabolismo , Secuencia de Aminoácidos/genética , Transporte de Electrón/genética , Transporte de Electrón/fisiología , Ferredoxina-NADP Reductasa/fisiología , Ferredoxinas/metabolismo , Cinética , Modelos Moleculares , Oxidación-Reducción , Fotosíntesis/genética , Conformación Proteica , Zea mays/genética , Zea mays/metabolismo
13.
BMC Gastroenterol ; 18(1): 189, 2018 Dec 27.
Artículo en Inglés | MEDLINE | ID: mdl-30587141

RESUMEN

BACKGROUND: Intramucosal, histologically mixed-type, low-grade (LG), well-differentiated gastric tubular adenocarcinomas (tub1s; LG-tub1s) have larger mean diameters and exhibit a higher frequency of the gastric mucin phenotype (G-phenotype) than pure LG-tub1s. In proportion to their increases in diameter, G-phenotype differentiated-type early gastric cancer (EGC) tumours reportedly grow to eventually contain (an) undifferentiated-type component(s) and LG-tub1s, which are included in differentiated-type EGCs, reportedly exhibit changes in their glandular architectural and cytological atypia grades from LG to high-grade (HG) and can grow to contain a moderately differentiated tubular adenocarcinoma (tub2) component and undifferentiated components. Because they generally show a higher frequency of malignancy relative to tumours with a higher atypia grade and lower differentiation degree, it is suggested that, among mixed-type LG-tub1s, G-phenotype LG-tub1s containing an HG-tub2 component (LG-tub1s > HG-tub2) with undifferentiated components might lead to late-onset metastasis to lymph nodes even after a successful endoscopic submucosal dissection (ESD). We aimed to clarify the endoscopic and clinicopathological features of these G-phenotype LG-tub1s > HG-tub2. METHODS: Of the 13,217 oesophagogastroduodenoscopies performed at our institutions between September 2008 and March 2016, 185 EGC lesions were evaluated in this retrospective observational study. Among these EGC lesions, 60 intramucosal LG-tub1s were divided into 53 tub1 (44 pure LG-tub1s and nine LG-tub1s containing HG-tub1) lesions and seven LG-tub1 > tub2 (LG-tub1 containing LG- and HG-tub2) lesions. RESULTS: The frequencies of the superficial depressed type (P = 0.026), reddish colour (P = 0.006), HG of contained tub2s (P = 0.006), and G-phenotype (P = 0.028) were significantly higher in the LG-tub1 > tub2 group than those in the tub1 group. However, the largest lesion of the LG-tub1 > tub2 group had a superficial flat appearance, an isochromatic colour, an HG-tub2 and an undifferentiated component, and a large diameter greater than 30 mm, and it exhibited a G-phenotype. CONCLUSIONS: Intramucosal G-phenotype LG-tub1s > HG-tub2 are potential premalignant stomach neoplasms that may have specific endoscopic and clinicopathological features. However, G-phenotype LG-tub1s > HG-tub2 with undifferentiated component, which potentially show higher malignancy than those without undifferentiated components might change from a reddish to isochromatic colour. Accurately diagnosing, treating, and following-up G-phenotype LG-tub1s > HG-tub2 might decrease the number of patients who experience late-onset metastasis after ESD.


Asunto(s)
Adenocarcinoma/patología , Metástasis Linfática , Neoplasias Gástricas/patología , Adenocarcinoma/microbiología , Adenocarcinoma/cirugía , Anciano , Anciano de 80 o más Años , Resección Endoscópica de la Mucosa , Endoscopía del Sistema Digestivo , Femenino , Mucinas Gástricas/metabolismo , Helicobacter pylori/aislamiento & purificación , Humanos , Masculino , Persona de Mediana Edad , Clasificación del Tumor , Fenotipo , Estudios Retrospectivos , Neoplasias Gástricas/microbiología , Neoplasias Gástricas/cirugía
14.
Nat Commun ; 9(1): 3964, 2018 09 27.
Artículo en Inglés | MEDLINE | ID: mdl-30262834

RESUMEN

Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Neurexins (Nrxns) and heparan sulfate proteoglycans have been identified as presynaptic ligands for LRRTMs. Specifically, LRRTM1 and LRRTM2 bind to the Nrxn splice variant lacking an insert at the splice site 4 (S4). Here, we report the crystal structure of the Nrxn1ß-LRRTM2 complex at 3.4 Å resolution. The Nrxn1ß-LRRTM2 interface involves Ca2+-mediated interactions and overlaps with the Nrxn-neuroligin interface. Together with structure-based mutational analyses at the molecular and cellular levels, the present structural analysis unveils the mechanism of selective binding between Nrxn and LRRTM1/2 and its modulation by the S4 insertion of Nrxn.


Asunto(s)
Moléculas de Adhesión Celular Neuronal/química , Proteínas de la Membrana/química , Proteínas del Tejido Nervioso/química , Moléculas de Adhesión de Célula Nerviosa/química , Sinapsis/metabolismo , Secuencia de Aminoácidos , Animales , Proteínas de Unión al Calcio , Moléculas de Adhesión Celular Neuronal/metabolismo , Células HEK293 , Humanos , Proteínas de la Membrana/metabolismo , Ratones , Proteínas Mutantes/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Moléculas de Adhesión de Célula Nerviosa/metabolismo , Unión Proteica
15.
J Biochem ; 164(3): 231-237, 2018 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-29688515

RESUMEN

The malaria parasite (Plasmodium falciparum) possesses a plastid-derived, essential organelle called the apicoplast, which contains a redox system comprising plant-type ferredoxin (Fd) and Fd-NADP+ reductase (FNR). This system supplies reducing power for the crucial metabolic pathways in this organelle. Electron transfer between P. falciparum Fd (PfFd) and FNR (PfFNR) is performed with higher affinity and specificity than that of plant Fd and FNR. To investigate the mechanism for such superior protein-protein interaction, we searched for the Fd interaction sites on the surface of PfFNR. Basic amino acid residues on the FAD binding side of PfFNR were comprehensively substituted to acidic amino acids by site-directed mutagenesis. Kinetic analysis of electron transfer to PfFd and plant Fds, physical binding to immobilized PfFd and thermodynamics of the PfFd binding using these PfFNR mutants revealed that several basic amino acid residues including those in Plasmodium-specific insertion region are important for the interaction with PfFd. Majority of these basic residues are Plasmodium-specific and not conserved among plant and cyanobacteria FNRs. These results suggest that the interaction mode of Fd and FNR is diverged during evolution so that PfFd: PfFNR interaction meets the physiological requirement in the cells of Plasmodium species.


Asunto(s)
Aminoácidos/metabolismo , Ferredoxina-NADP Reductasa/metabolismo , Ferredoxinas/metabolismo , Plasmodium falciparum/metabolismo , Proteínas Protozoarias/metabolismo , Aminoácidos/química , Animales , Sitios de Unión , Transporte de Electrón , Cinética , Mutagénesis Sitio-Dirigida , Unión Proteica , Proteínas Protozoarias/química , Proteínas Protozoarias/genética , Termodinámica
16.
Molecules ; 22(10)2017 Oct 10.
Artículo en Inglés | MEDLINE | ID: mdl-28994732

RESUMEN

Due to their lower production cost compared with monoclonal antibodies, single-chain variable fragments (scFvs) have potential for use in several applications, such as for diagnosis and treatment of a range of diseases, and as sensor elements. However, the usefulness of scFvs is limited by inhomogeneity through the formation of dimers, trimers, and larger oligomers. The scFv protein is assumed to be in equilibrium between the closed and open states formed by assembly or disassembly of VH and VL domains. Therefore, the production of an scFv with equilibrium biased to the closed state would be critical to overcome the problem in inhomogeneity of scFv for industrial or therapeutic applications. In this study, we obtained scFv clones stable against GA-pyridine, an advanced glycation end-product (AGE), by using a combination of a phage display system and random mutagenesis. Executing the bio-panning at 37 °C markedly improved the stability of scFvs. We further evaluated the radius of gyration by small-angle X-ray scattering (SAXS), obtained compact clones, and also visualized open.


Asunto(s)
Productos Finales de Glicación Avanzada/inmunología , Compuestos de Piridinio/inmunología , Anticuerpos de Cadena Única/biosíntesis , Secuencia de Aminoácidos , Biblioteca de Péptidos , Dominios Proteicos , Multimerización de Proteína , Estabilidad Proteica , Anticuerpos de Cadena Única/química
17.
J Biol Chem ; 292(51): 21128-21136, 2017 12 22.
Artículo en Inglés | MEDLINE | ID: mdl-29046357

RESUMEN

Before entering host cells, herpes simplex virus-1 uses its envelope glycoprotein B to bind paired immunoglobulin-like type 2 receptor α (PILRα) on immune cells. PILRα belongs to the Siglec (sialic acid (SA)-binding immunoglobulin-like lectin)-like family, members of which bind SA. PILRα is the only Siglec member to recognize not only the sialylated O-linked sugar T antigen (sTn) but also its attached peptide region. We previously determined the crystal structure of PILRα complexed with the sTn-linked glycopeptide of glycoprotein B, revealing the simultaneous recognition of sTn and peptide by the receptor. However, the contribution of each glycopeptide component to PILRα binding was largely unclear. Here, we chemically synthesized glycopeptide derivatives and determined the thermodynamic parameters of their interaction with PILRα. We show that glycopeptides with different sugar units linking SA and peptides (i.e. "GlcNAc-type" and "deoxy-GlcNAc-type" glycopeptides) have lower affinity and more enthalpy-driven binding than the wild type (i.e. GalNAc-type glycopeptide). The crystal structures of PILRα complexed with these glycopeptides highlighted the importance of stereochemical positioning of the O4 atom of the sugar moiety. These results provide insights both for understanding the unique O-glycosylated peptide recognition by the PILRα and for the rational design of herpes simplex virus-1 entry inhibitors.


Asunto(s)
Glicoproteínas de Membrana/metabolismo , Modelos Moleculares , Fragmentos de Péptidos/metabolismo , Receptores Inmunológicos/metabolismo , Proteínas del Envoltorio Viral/metabolismo , Acetilgalactosamina/análogos & derivados , Acetilgalactosamina/química , Acetilgalactosamina/metabolismo , Sitios de Unión , Calorimetría , Cristalografía por Rayos X , Escherichia coli/metabolismo , Humanos , Cinética , Ligandos , Glicoproteínas de Membrana/química , Glicoproteínas de Membrana/genética , Fragmentos de Péptidos/síntesis química , Fragmentos de Péptidos/química , Fragmentos de Péptidos/genética , Polisacáridos/síntesis química , Polisacáridos/química , Polisacáridos/metabolismo , Conformación Proteica , Dominios y Motivos de Interacción de Proteínas , Receptores Inmunológicos/química , Receptores Inmunológicos/genética , Proteínas Recombinantes , Estereoisomerismo , Termodinámica , Proteínas del Envoltorio Viral/síntesis química , Proteínas del Envoltorio Viral/química
18.
Ecology ; 97(12): 3402-3413, 2016 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-27912025

RESUMEN

Taylor's law (TL) asserts that the variance in a species' population density is a power-law function of its mean population density: log(variance) = a + b × log(mean). TL is widely verified. We show here that empirical time series of density of the Hokkaido gray-sided vole, Myodes rufocanus, sampled 1962-1992 at 85 locations, satisfied temporal and spatial forms of TL. The slopes (b ± standard error) of the temporal and spatial TL were estimated to be 1.613 ± 0.141 and 1.430 ± 0.132, respectively. A previously verified autoregressive Gompertz model of the dynamics of these populations generated time series of density which reproduced the form of temporal and spatial TLs, but with slopes that were significantly steeper than the slopes estimated from data. The density-dependent components of the Gompertz model were essential for the temporal TL. Adding to the Gompertz model assumptions that populations with higher mean density have reduced variance of density-independent perturbations and that density-independent perturbations are spatially correlated among populations yielded simulated time series that satisfactorily reproduced the slopes from data. The slopes (b ± standard error) of the enhanced simulations were 1.619 ± 0.199 for temporal TL and 1.575 ± 0.204 for spatial TL.


Asunto(s)
Distribución Animal/fisiología , Arvicolinae/fisiología , Modelos Biológicos , Animales , Simulación por Computador , Japón , Dinámica Poblacional , Factores de Tiempo
19.
Sci Rep ; 6: 37887, 2016 11 24.
Artículo en Inglés | MEDLINE | ID: mdl-27883072

RESUMEN

Transcription activator-like effector (TALE) nuclease (TALEN) is widely used as a tool in genome editing. The DNA binding part of TALEN consists of a tandem array of TAL-repeats that form a right-handed superhelix. Each TAL-repeat recognises a specific base by the repeat variable diresidue (RVD) at positions 12 and 13. TALEN comprising the TAL-repeats with periodic mutations to residues at positions 4 and 32 (non-RVD sites) in each repeat (VT-TALE) exhibits increased efficacy in genome editing compared with a counterpart without the mutations (CT-TALE). The molecular basis for the elevated efficacy is unknown. In this report, comparison of the physicochemical properties between CT- and VT-TALEs revealed that VT-TALE has a larger amplitude motion along the superhelical axis (superhelical motion) compared with CT-TALE. The greater superhelical motion in VT-TALE enabled more TAL-repeats to engage in the target sequence recognition compared with CT-TALE. The extended sequence recognition by the TAL-repeats improves site specificity with limiting the spatial distribution of FokI domains to facilitate their dimerization at the desired site. Molecular dynamics simulations revealed that the non-RVD mutations alter inter-repeat hydrogen bonding to amplify the superhelical motion of VT-TALE. The TALEN activity is associated with the inter-repeat hydrogen bonding among the TAL repeats.


Asunto(s)
Edición Génica , Mutación , Nucleasas de los Efectores Tipo Activadores de la Transcripción/genética , Nucleasas de los Efectores Tipo Activadores de la Transcripción/metabolismo , Cromatografía en Gel , ADN/metabolismo , Dispersión Dinámica de Luz , Enlace de Hidrógeno , Simulación de Dinámica Molecular , Secuencias Repetitivas de Aminoácido , Termodinámica , Nucleasas de los Efectores Tipo Activadores de la Transcripción/química
20.
Gastroenterol Res Pract ; 2016: 3028456, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27127502

RESUMEN

Backgrounds. Magnifying endoscopy with narrow-band imaging (NBI-ME) is useful for diagnosing differentiated early gastric cancer (D-EGC). D-EGC is classified as high- or low-grade based on its glandular architectural and cytological atypia. Low-grade, well-differentiated tubular adenocarcinoma (LG-tub1) mixed with high-grade tub1 (HG-tub1) and/or other histological types (M-LG-tub1) may indicate a primitive high-risk malignant lesion compared to histologically simple-type LG-tub1 (S-LG-tub1). Because LG-tub1 is occasionally difficult to diagnose due to its unclear demarcation under conventional white light endoscopy, early precise diagnoses are important. Methods. We compared NBI-ME and postendoscopic submucosal dissection histological findings for 30 S-LG-tub1 and 15 M-LG-tub1 lesions. We classified the NBI-ME findings of S-LG-tub1 (and not D-EGC) into four patterns. The differential diagnosis between M-LG-tub1 and S-LG-tub1 depended on the presence of more than one of these patterns without or with other patterns (referred to as "limited-to-four-pattern [LFP] sign-positive" and "sign-negative", resp.). Result. The sensitivity, specificity, accuracy, positive and negative predictive values, and intraobserver and interobserver agreement, using the "LFP sign" for the differential diagnosis between M-LG-tub1 and S-LG-tub1, were 87.9%, 91.7%, 88.9%, 96.7%, 73.3%, and k = 0.842 and k = 0.737, respectively. Conclusion. NBI-ME may be useful in differentiating between high-risk M-LG-tub1 and low-risk S-LG-tub1.

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