scholarly journals Characterization of the Heme Pocket Structure and Ligand Binding Kinetics of Non-symbiotic Hemoglobins from the Model Legume Lotus japonicus

2017 ◽  
Vol 8 ◽  
Author(s):  
Laura Calvo-Begueria ◽  
Bert Cuypers ◽  
Sabine Van Doorslaer ◽  
Stefania Abbruzzetti ◽  
Stefano Bruno ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Lotus Japonicus ◽  
Binding Kinetics ◽  
Model Legume ◽  
Heme Pocket ◽  
Kinetics Of

scholarly journals Flavonoids and Isoflavonoids Biosynthesis in the Model Legume Lotus japonicus; Connections to Nitrogen Metabolism and Photorespiration

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 774 ◽  
Author(s):  
Margarita García-Calderón ◽  
Carmen M. Pérez-Delgado ◽  
Peter Palove-Balang ◽  
Marco Betti ◽  
Antonio J. Márquez
Keyword(s):  
Abiotic Stress ◽  
Nitrogen Metabolism ◽  
Lotus Japonicus ◽  
Regulatory Proteins ◽  
Phenylpropanoid Metabolism ◽  
Biological Processes ◽  
Model Legume ◽  
Different Types ◽  
Made In

Phenylpropanoid metabolism represents an important metabolic pathway from which originates a wide number of secondary metabolites derived from phenylalanine or tyrosine, such as flavonoids and isoflavonoids, crucial molecules in plants implicated in a large number of biological processes. Therefore, various types of interconnection exist between different aspects of nitrogen metabolism and the biosynthesis of these compounds. For legumes, flavonoids and isoflavonoids are postulated to play pivotal roles in adaptation to their biological environments, both as defensive compounds (phytoalexins) and as chemical signals in symbiotic nitrogen fixation with rhizobia. In this paper, we summarize the recent progress made in the characterization of flavonoid and isoflavonoid biosynthetic pathways in the model legume Lotus japonicus (Regel) Larsen under different abiotic stress situations, such as drought, the impairment of photorespiration and UV-B irradiation. Emphasis is placed on results obtained using photorespiratory mutants deficient in glutamine synthetase. The results provide different types of evidence showing that an enhancement of isoflavonoid compared to standard flavonol metabolism frequently occurs in Lotus under abiotic stress conditions. The advance produced in the analysis of isoflavonoid regulatory proteins by the use of co-expression networks, particularly MYB transcription factors, is also described. The results obtained in Lotus japonicus plants can be also extrapolated to other cultivated legume species, such as soybean, of extraordinary agronomic importance with a high impact in feeding, oil production and human health.

scholarly journals Spectroscopic analyses of the binding kinetics of 15d-PGJ2 to the PPARγ ligand-binding domain by multi-wavelength global fitting

2006 ◽  
Vol 393 (3) ◽  
pp. 749-755 ◽  
Author(s):  
Takuma Shiraki ◽  
Takashi S. Kodama ◽  
Sayaka Shiki ◽  
Tatsuo Nakagawa ◽  
Hisato Jingami
Keyword(s):  
Ligand Binding ◽  
Intermediate State ◽  
Covalent Binding ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Binding Kinetics ◽  
Multi Wavelength ◽  
Lipid Metabolites ◽  
Kinetics Of ◽  
Global Fitting

PPARγ (peroxisome proliferator-activated receptor γ) is a nuclear receptor that is activated by natural lipid metabolites, including 15d-PGJ2 (15-deoxy-Δ12,14-prostaglandin J2). We previously reported that several oxidized lipid metabolites covalently bind to PPARγ through a Michael-addition to activate transcription. To separate the ligand-entering (dock) and covalent-binding (lock) steps in PPARγ activation, we investigated the binding kinetics of 15d-PGJ2 to the PPARγ LBD (ligand-binding domain) by stopped-flow spectroscopy. We analysed the spectral changes of 15d-PGJ2 by multi-wavelength global fitting based on a two-step chemical reaction model, in which an intermediate state represents the 15d-PGJ2–PPARγ complex without covalent binding. The extracted spectrum of the intermediate state in wild-type PPARγ was quite similar to the observed spectrum of 15d-PGJ2 in the C285S mutant, which cannot be activated by 15d-PGJ2, indicating that the complex remains in the inactive, intermediate state in the mutant. Thus ‘lock’ rather than ‘dock’ is one of the critical steps in PPARγ activation by 15d-PGJ2.

scholarly journals Functional consequences of haem orientational disorder in sperm-whale and yellow-fin-tuna myoglobins

1987 ◽  
Vol 243 (1) ◽  
pp. 205-210 ◽  
Author(s):  
H S Aojula ◽  
M T Wilson ◽  
I E G Morrison
Keyword(s):  
Ligand Binding ◽  
Kinetic Parameters ◽  
Sperm Whale ◽  
Binding Kinetics ◽  
Orientational Disorder ◽  
Binding Properties ◽  
Functional Consequences ◽  
Kinetics Of ◽  
Sperm Whale Myoglobin ◽  
O2 Dissociation

Ligand-binding kinetics of native and reconstituted sperm-whale myoglobin were studied in relation to haem orientational disorder by rapid kinetic methods. In addition, native yellow-fin-tuna myoglobin with significant amount of haem disorder was also used. The O2 dissociation and association rates were found for the proteins with different degrees of haem disorder, and these results suggest that the isomers are characterized by almost identical kinetic parameters. Rates of CO recombination after photolysis were also identical for the two orientational isomers. The results clearly indicate that the rotation of the haem about the alpha-gamma meso axis has little or no effect on the ligand-binding properties of these myoglobins.

Characterization of binding kinetics of A2AR to Gαs protein by surface plasmon resonance

2021 ◽  
Author(s):  
Kirsten Swonger Koretz ◽  
Claire E. McGraw ◽  
Steven Stradley ◽  
Ahmed Elbaradei ◽  
Noah Malmstadt ◽  
...  
Keyword(s):  
Surface Plasmon Resonance ◽  
Surface Plasmon ◽  
Plasmon Resonance ◽  
Binding Kinetics ◽  
Kinetics Of

Ligand Binding Kinetics of the Quorum Sensing Regulator PqsR

Biochemistry ◽  
2013 ◽  
Vol 52 (25) ◽  
pp. 4433-4438 ◽  
Author(s):  
Martin Welch ◽  
James T. Hodgkinson ◽  
Jeremy Gross ◽  
David R. Spring ◽  
Thomas Sams
Keyword(s):  
Quorum Sensing ◽  
Ligand Binding ◽  
Binding Kinetics ◽  
Kinetics Of

scholarly journals Spontaneous Root-Nodule Formation in the Model Legume Lotus japonicus: A Novel Class of Mutants Nodulates in the Absence of Rhizobia

2006 ◽  
Vol 19 (4) ◽  
pp. 373-382 ◽  
Author(s):  
Leïla Tirichine ◽  
Euan K. James ◽  
Niels Sandal ◽  
Jens Stougaard
Keyword(s):  
Root Nodule ◽  
Lotus Japonicus ◽  
Nodule Development ◽  
Nodule Formation ◽  
Wild Type ◽  
Model Legume ◽  
Isolation And Characterization ◽  
Mutant Lines ◽  
Spontaneous Nodules

Root-nodule development in legumes is an inducible developmental process initially triggered by perception of lipochitin-oligosaccharide signals secreted by the bacterial microsymbiont. In nature, rhizobial colonization and invasion of the legume root is therefore a prerequisite for formation of nitrogen-fixing root nodules. Here, we report isolation and characterization of chemically induced spontaneously nodulating mutants in a model legume amenable to molecular genetics. Six mutant lines of Lotus japonicus were identified in a screen for spontaneous nodule development under axenic conditions, i.e., in the absence of rhizobia. Spontaneous nodules do not contain rhizobia, bacteroids, or infection threads. Phenotypically, they resemble ineffective white nodules formed by some bacterial mutants on wild-type plants or certain plant mutants inoculated with wild-type Mesorhizobium loti. Spontaneous nodules formed on mutant lines show the ontogeny and characteristic histological features described for rhizobia-induced nodules on wild-type plants. Physiological responses to nitrate and ethylene are also maintained, as elevated levels inhibit spontaneous nodulation. Activation of the nodule developmental program in spontaneous nodules was shown for the early nodulin genes Enod2 and Nin, which are both upregulated in spontaneous nodules as well as in rhizobial nodules. Both monogenic recessive and dominant spontaneous nodule formation (snf) mutations were isolated in this mutant screen, and map positions were determined for three loci. We suggest that future molecular characterization of these mutants will identify key plant determinants involved in regulating nodulation and provide new insight into plant organ development.

scholarly journals Characterization of a Humanized Monoclonal Antibody Recognizing Clumping Factor A Expressed by Staphylococcus aureus

2005 ◽  
Vol 73 (8) ◽  
pp. 5229-5232 ◽  
Author(s):  
Paul J. Domanski ◽  
Pratiksha R. Patel ◽  
Arnold S. Bayer ◽  
Li Zhang ◽  
Andrea E. Hall ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Monoclonal Antibody ◽  
Infective Endocarditis ◽  
Binding Kinetics ◽  
Vancomycin Therapy ◽  
Latex Beads ◽  
Humanized Monoclonal Antibody ◽  
Kinetics Of ◽  
Therapeutic Model

ABSTRACT We report the humanization and characterization of monoclonal antibody (MAb) T1-2 or tefibazumab, a monoclonal antibody that recognizes clumping factor A expressed on the surface of Staphylococcus aureus. We demonstrate that the binding kinetics of MAb T1-2 is indistinguishable compared to that of its murine parent. Furthermore, MAb T1-2 is shown to enhance the opsonophagocytic uptake of ClfA-coated latex beads, protect against an intravenous challenge in a prophylactic model of rabbit infective endocarditis, and enhance the efficacy of vancomycin therapy in a therapeutic model of established infective endocarditis.

scholarly journals Lotus japonicus karrikin receptors display divergent ligand-binding specificities and organ-dependent redundancy

PLoS Genetics ◽  
2020 ◽  
Vol 16 (12) ◽  
pp. e1009249
Author(s):  
Samy Carbonnel ◽  
Salar Torabi ◽  
Maximilian Griesmann ◽  
Elias Bleek ◽  
Yuhong Tang ◽  
...  
Keyword(s):  
Ligand Binding ◽  
System Development ◽  
Lotus Japonicus ◽  
Binding Pocket ◽  
Hypocotyl Growth ◽  
Model Legume ◽  
Root System Development ◽  
Organ Specific ◽  
Synthetic Ligand

Karrikins (KARs), smoke-derived butenolides, are perceived by the α/β-fold hydrolase KARRIKIN INSENSITIVE2 (KAI2) and thought to mimic endogenous, yet elusive plant hormones tentatively called KAI2-ligands (KLs). The sensitivity to different karrikin types as well as the number of KAI2 paralogs varies among plant species, suggesting diversification and co-evolution of ligand-receptor relationships. We found that the genomes of legumes, comprising a number of important crops with protein-rich, nutritious seed, contain two or more KAI2 copies. We uncover sub-functionalization of the two KAI2 versions in the model legume Lotus japonicus and demonstrate differences in their ability to bind the synthetic ligand GR24ent-5DS in vitro and in genetic assays with Lotus japonicus and the heterologous Arabidopsis thaliana background. These differences can be explained by the exchange of a widely conserved phenylalanine in the binding pocket of KAI2a with a tryptophan in KAI2b, which arose independently in KAI2 proteins of several unrelated angiosperms. Furthermore, two polymorphic residues in the binding pocket are conserved across a number of legumes and may contribute to ligand binding preferences. The diversification of KAI2 binding pockets suggests the occurrence of several different KLs acting in non-fire following plants, or an escape from possible antagonistic exogenous molecules. Unexpectedly, L. japonicus responds to diverse synthetic KAI2-ligands in an organ-specific manner. Hypocotyl growth responds to KAR1, KAR2 and rac-GR24, while root system development responds only to KAR1. This differential responsiveness cannot be explained by receptor-ligand preferences alone, because LjKAI2a is sufficient for karrikin responses in the hypocotyl, while LjKAI2a and LjKAI2b operate redundantly in roots. Instead, it likely reflects differences between plant organs in their ability to transport or metabolise the synthetic KLs. Our findings provide new insights into the evolution and diversity of butenolide ligand-receptor relationships, and open novel research avenues into their ecological significance and the mechanisms controlling developmental responses to divergent KLs.

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