Electron Transport from QA to Thymoquinone in a Synechococcus Oxygen-Evolving Photosystem II Preparation: Role of QB and Binding Affinity of Thymoquinone to the QB Site

1993 ◽  
Vol 48 (3-4) ◽  
pp. 174-178 ◽  
Author(s):  
Kazuhiko Satoh ◽  
Yasuhiro Kashino ◽  
Hiroyuki Koike
Keyword(s):  
Binding Affinity ◽  
Turnover Rate ◽  
Side Chain ◽  
Head Group ◽  
Binding Affinities ◽  
Ps Ii ◽  
Thermophilic Cyanobacteria ◽  
High Concentrations ◽  
Oxygen Evolving

Abstract We have recently shown that binding affinities of benzoquinones can be estimated by two methods in photosystem (PS) II particles (K. Satoh et al., Biochim. Biophys. Acta 1102, 45-52 (1992)). Using these methods we calculated the binding affinity of thymoquinone (2-methyl-5-isopropyl-p-benzoquinone) to the QB site and studied how the quinone accepts electrons in oxygen-evolving PS II particles isolated from the thermophilic cyanobacteria, Synechococcus elongatus and S. vulcanus. The results are as follows: (1) The binding constant of thymoqui­ none to the QB site determined by several methods was around 0.33 mᴍ . (2) At low thymoquinone concentrations the quinone was supposed to accept electrons via QB-plastoquinone, whereas at high concentrations the quinone seemed to bind to the QB site and accept an electron directly from Q-A. Lower rates of photoreduction of the quinone at high concentrations were attributed to a slower turnover rate of the quinone at the QB site than that of endogenous plastoquinone. (3) A model for the function of plastoquinone at the QB site, which can explain all the results, was presented. According to this model, the plastoquinone molecule at the QB site is not replaced by another plastoquinone molecule. Instead, it transfers electrons to pool plastoquinone molecules by turning over its head group but remaining its long side chain bound to the PS II complexes.

Role of Side-Chain Bioisosteres in Determining the Binding Affinity of Click Chemistry Derived RGD Peptidomimetics to αvβ3Integrin

2014 ◽  
Vol 2014 (34) ◽  
pp. 7595-7604 ◽  
Author(s):  
Pierangelo Fabbrizzi ◽  
Gloria Menchi ◽  
Silvia Raspanti ◽  
Antonio Guarna ◽  
Andrea Trabocchi
Keyword(s):  
Click Chemistry ◽  
Binding Affinity ◽  
Side Chain

scholarly journals Determination of binding affinities of retinoids to retinoic acid-binding protein and serum albumin

1978 ◽  
Vol 171 (3) ◽  
pp. 711-717 ◽  
Author(s):  
Brahma P. Sani ◽  
Belinda C. Titus ◽  
Chandra K. Banerjee
Keyword(s):  
Retinoic Acid ◽  
Serum Albumin ◽  
Binding Affinity ◽  
Binding Protein ◽  
Side Chain ◽  
Binding Affinities ◽  
Acid Binding Protein ◽  
Relative Binding ◽  
Biological Potency

Binding affinities of retinoic acid and its synthetic analogues to intracellular retinoic acid-binding protein, which is a possible candidate for mediating their biological function, and to serum albumin, the plasma transport protein, were evaluated. A quantitative method involving elimination of interfering serum albumin by immunoprecipitation was developed to measure the binding efficiency of these retinoids, some of which are active in modifying epithelial differentiation and preventing tumorigenesis. Two cyclopentenyl analogues of retinoic acid and 13-cis-retinoic acid showed, like retinoic acid, a binding efficiency of 100% for the cellular binding protein. With the phenyl, dichlorophenyl and trimethylmethoxyphenyl analogues of retinoic acid, the binding efficiency increased as the substituents on the aromatic ring increased; thus the trimethylmethoxyphenyl analogue binds almost as efficiently as retinoic acid itself. However, the trimethylmethoxyphenyl analogue with a sulphur atom on the side chain has a much decreased binding affinity. The correlation noticed between the binding efficiency of these retinoids and their biological activity in differentiation and/or in the control of tumorigenesis particularly enhances the confidence in the present method of determining the relative binding efficiencies. None of the vitamins, hormones and cofactors tested, showed appreciable affinity for the retinoic acid-binding site. Studies on binding of retinoic acid and its analogues to serum albumin indicate that no correlation exists between binding affinity for albumin and their biological potency.

scholarly journals Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5505 ◽  
Author(s):  
Alexander Krah ◽  
Peter J. Bond
Keyword(s):  
Binding Affinity ◽  
Atp Hydrolysis ◽  
Atp Binding ◽  
Evolutionary Analysis ◽  
Binding Affinities ◽  
Wild Type ◽  
Dynamics Simulations ◽  
High Binding Affinity ◽  
Atp Synthases

The ε subunit from ATP synthases acts as an ATP sensor in the bacterial cell to prevent ATP hydrolysis and thus the waste of ATP under conditions of low ATP concentration. However, the ATP binding affinities from various bacterial organisms differ markedly, over several orders of magnitude. For example, the ATP synthases from thermophilic Bacillus PS3 and Escherichia coli exhibit affinities of 4 µM and 22 mM, respectively. The recently reported R103A/R115A double mutant of Bacillus PS3 ATP synthase demonstrated an increased binding affinity by two orders of magnitude with respect to the wild type. Here, we used atomic-resolution molecular dynamics simulations to determine the role of the R103A and R115A single mutations. These lead us to predict that both single mutations also cause an increased ATP binding affinity. Evolutionary analysis reveals R103 and R115 substitutions in the ε subunit from other bacillic organisms, leading us to predict they likely have a higher ATP binding affinity than previously expected.

Relevant role of Leu265 in helix VI of the angiotensin AT1 receptor in agonist binding and activity

2002 ◽  
Vol 80 (5) ◽  
pp. 426-430 ◽  
Author(s):  
Silvana Aparecida Alves Correa ◽  
Lucimar Pereira França ◽  
Claudio Miguel Costa-Neto ◽  
Laerte Oliveira ◽  
Antonio Cechelli Mattos Paiva ◽  
...  
Keyword(s):  
Angiotensin Ii ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Transmembrane Domain ◽  
Inositol Phosphate ◽  
Chinese Hamster ◽  
Side Chain ◽  
Maximum Effect ◽  
Agonist Binding

The finding of critical residues for angiotensin II (AII) binding and receptor signalling in helices V and VI led us to assess if, in this region of the receptor, aliphatic side chains might play a role in the agonist-mediated mechanism. Two mutations of the angiotensin AT1 receptor were designed to explore a possible role of a leucine at two positions, Leu265 and Leu268. Thus two mutants, L265D and L268D, were prepared through single substitutions of Leu265, located in the C-terminal region of transmembrane VI (TM-VI), and Leu268, in the adjoining region of the third extracellular loop (EC-3), for an aspartyl residue, and were stably transfected into Chinese hamster ovary (CHO) cells. Ligand-binding experiments and the functional assays determining inositol phosphate (IP) production were performed in these cells expressing these mutants. No significant changes were found in the binding affinity for the ligands, AII, DuP753, and [Sar1Leu8]AII in the mutant L268D. Moreover, the relative potency and the maximum effect on IP production of this mutant were similar to those of the wild-type receptor. In contrast, L265D mutant AT1 receptor, located within the transmembrane domain, markedly decreased binding affinity and ability to stimulate phosphatidylinositol turnover. Our results suggest that the hydrophobic side chain of Leu265, at the C-terminal portion of the AT1's TM-VI, but not Leu268, which belongs to the EC-3 loop, might interact with the AII molecule. On the other side, the aliphatic side chain of Leu265 may be involved in the formation of the ligand binding sites through allosteric effects, thus helping to stabilize the receptor structure around the agonist binding site for full activity.Key words: angiotensin II, AT1 receptor, site-directed mutagenesis.

scholarly journals The role of cysteine residues in the allosteric modulation of the chromophore phototransformations of biphotochromic fluorescent protein SAASoti

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. V. Gavshina ◽  
N. K. Marynich ◽  
M. G. Khrenova ◽  
I. D. Solovyev ◽  
A. P. Savitsky
Keyword(s):  
Fluorescent Protein ◽  
Thermal Relaxation ◽  
Site Directed Mutagenesis ◽  
Side Chain ◽  
Cysteine Residues ◽  
Monomeric Form ◽  
Dynamic Simulations ◽  
High Concentrations ◽  
Mutant Forms

AbstractBiphotochromic fluorescent protein SAASoti contains five cysteine residues in its sequence and a V127T point mutation transforms it to the monomeric form, mSAASoti. These cysteine residues are located far from the chromophore and might control its properties only allosterically. The influence of individual, double and triple cysteine substitutions of mSAASoti on fluorescent parameters and phototransformation reactions (irreversible green-to-red photoconversion and reversible photoswitching) is studied. A set of mSAASoti mutant forms (C21N, C117S, C71V, C105V, C175A, C21N/C71V, C21N/C175A, C21N/C71G/C175A) is obtained by site-directed mutagenesis. We demonstrate that the C21N variant exists in a monomeric form up to high concentrations, the C71V substitution accelerates photoconversion to the red form and the C105V variant has the maximum photoswitching rate. All C175A-containing variants demonstrate different photoswitching kinetics and decreased photostability during subsequent switching cycles compared with other considered systems. Classical molecular dynamic simulations reveal that the F177 side chain located in the vicinity of the chromophore is considerably more flexible in the mSAASoti compared with its C175A variant. This might be the explanation of the experimentally observed slowdown the thermal relaxation rate, i.e., trans–cis isomerization of the chromophore in mSAASoti upon C175A substitution.

scholarly journals Munc18-1 Regulates Early and Late Stages of Exocytosis via Syntaxin-independent Protein Interactions

2005 ◽  
Vol 16 (2) ◽  
pp. 470-482 ◽  
Author(s):  
Leonora F. Ciufo ◽  
Jeff W. Barclay ◽  
Robert D. Burgoyne ◽  
Alan Morgan
Keyword(s):  
Binding Affinity ◽  
Protein Interactions ◽  
Membrane Trafficking ◽  
Release Kinetics ◽  
Binding Affinities ◽  
Sm Proteins ◽  
Kinetics Of ◽  
Late Stages ◽  
Independent Protein

Sec1/Munc18 (SM) proteins are involved in various intracellular membrane trafficking steps. Many SM proteins bind to appropriate syntaxin homologues involved in these steps, suggesting that SM proteins function as syntaxin chaperones. Organisms with mutations in SM genes, however, exhibit defects in either early (docking) or late (fusion) stages of exocytosis, implying that SM proteins may have multiple functions. To gain insight into the role of SM proteins, we introduced mutations modeled on those identified in Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae into mammalian Munc18-1. As expected, several mutants exhibited reduced binding to syntaxin1A. However, three mutants displayed wild-type syntaxin binding affinities, indicating syntaxin-independent defects. Expression of these mutants in chromaffin cells either increased the rate and extent of exocytosis or altered the kinetics of individual release events. This latter effect was associated with a reduced Mint binding affinity in one mutant, implying a potential mechanism for the observed alteration in release kinetics. Furthermore, this phenotype persisted when the mutation was combined with a second mutation that greatly reduced syntaxin binding affinity. These results clarify the data on the function of SM proteins in mutant organisms and indicate that Munc18-1 controls multiple stages of exocytosis via both syntaxin-dependent and -independent protein interactions.

Docking Studies of Curcumin and Analogues with Various Phosphodiesterase 4 Subtypes

2020 ◽  
Vol 17 (2) ◽  
pp. 248-260 ◽  
Author(s):  
Yau Xin Yi ◽  
Anand Gaurav ◽  
Gabriel A. Akowuah
Keyword(s):  
Binding Affinity ◽  
Structural Information ◽  
Docking Studies ◽  
Side Chain ◽  
Data Set ◽  
Docking Analysis ◽  
Phosphodiesterase 4 ◽  
Curcumin Derivatives ◽  
Anti Inflammatory

Introduction: The primary aim of this study is to understand the binding of curcumin and its analogues to different PDE4 subtypes and identify the role of PDE4 subtype inhibition in the anti-inflammatory property of curcumin. Docking analysis has been used to acquire the above mentioned structural information and this has been further used for designing of curcumin derivatives with better anti-inflammatory activity. Materials and Methods: Curcumin and its analogues were subjected to docking using PDE4A, PDE4B, PDE4C and PDE4D as the targets. A data set comprising 18 analogues of curcumin, was used as ligands for docking of PDE4 subtypes. Curcumin was used as the standard for comparison. Docking was performed using AutoDock Vina 1.1.2 software integrated in LigandScout 4.1. During this process water molecules were removed from proteins, charges were added and receptor structures were minimised by applying suitable force fields. The docking scores were compared, and the selectivity of compounds for PDE4B over PDE4D was calculated as well. Results: All curcumin analogues used in the study showed good binding affinity with all PDE4 subtypes, with evident selectivity towards PDE4B subtype. Analogue A11 provides the highest binding affinity among all ligands. Conclusion: Curcumin and analogues have moderate to strong affinity towards all PDE4 subtypes and have evident selectivity towards PDE4B. The Oxygen atom of the methoxy group plays a key role in PDE4B binding and any alterations could interfere with the binding. Tetrahydropyran side chain and heterocyclic rings are also suggested to be helpful in PDE4B binding.

The Role of the Initiator System in the Synthesis of Acidic Multifunctional Nanoparticles Designed for Molecular Imprinting of Proteins

2020 ◽  
Vol 65 (1) ◽  
pp. 28-41
Author(s):  
Marwa Aly Ahmed ◽  
Júlia Erdőssy ◽  
Viola Horváth
Keyword(s):  
Acrylic Acid ◽  
Binding Affinity ◽  
Molecular Imprinting ◽  
Low Temperatures ◽  
Ammonium Persulfate ◽  
Sodium Bisulfite ◽  
Multifunctional Nanoparticles ◽  
High Affinity ◽  
Initiator System

Multifunctional nanoparticles have been shown earlier to bind certain proteins with high affinity and the binding affinity could be enhanced by molecular imprinting of the target protein. In this work different initiator systems were used and compared during the synthesis of poly (N-isopropylacrylamide-co-acrylic acid-co-N-tert-butylacrylamide) nanoparticles with respect to their future applicability in molecular imprinting of lysozyme. The decomposition of ammonium persulfate initiator was initiated either thermally at 60 °C or by using redox activators, namely tetramethylethylenediamine or sodium bisulfite at low temperatures. Morphology differences in the resulting nanoparticles have been revealed using scanning electron microscopy and dynamic light scattering. During polymerization the conversion of each monomer was followed in time. Striking differences were demonstrated in the incorporation rate of acrylic acid between the tetramethylethylenediamine catalyzed initiation and the other systems. This led to a completely different nanoparticle microstructure the consequence of which was the distinctly lower lysozyme binding affinity. On the contrary, the use of sodium bisulfite activation resulted in similar nanoparticle structural homogeneity and protein binding affinity as the thermal initiation.

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