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Journal articles on the topic 'Reaction affinity'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 February 2022

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1

Pekař, Miloslav. "Affinity and Reaction Rates: Reconsideration of Theoretical Background and Modelling Results." Zeitschrift für Naturforschung A 64, no. 5-6 (June 1, 2009): 289–99. http://dx.doi.org/10.1515/zna-2009-5-602.

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Abstract The phenomenological affinity approach to chemical kinetics based on mass-action rate expression is revised. It is shown that the reaction rate is not an unambiguous function of affinity and that in ideal mixtures with only elementary reactions thermodynamic coupling, i. e. a positive reaction rate and negative affinity of some reaction step at the same time, is not possible. Neither does thermodynamic coupling occur in a non-ideal system of elementary reactions where the mass-action rate equation is written with activities in place of concentrations. The non-ideality and/or non-equality of reaction orders to stoichiometric coefficients lead to more complex affinity-rate relationships than commonly given which puts no explicit restrictions on affinity and rate signs. Theoretical considerations are completed with results of numerical modelling made on several simple mechanisms. Various combinations of affinity and rate signs and complex affinity-rate profiles were obtained. Modelling results support the idea that affinity is much more a result of the time evolution of a reacting system and corresponding time profiles of concentrations than the actual cause of reaction rates.

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2

Rakitzis, E. T. "Utilization of the free energy of the reversible binding of protein and modifying agent towards the rate-enhancement of protein covalent modification." Biochemical Journal 269, no. 3 (August 1, 1990): 835–38. http://dx.doi.org/10.1042/bj2690835.

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An analysis is presented of the catalytic factors responsible for the rate-enhancement that may be observed when a protein modification reaction is compared with a reaction of the same modifying agent with a model micromolecular compound exhibiting the same reactive group as the protein under study. It is seen that affinity-mediated rate-enhancement of protein modification is realized by the loss of activation entropy. On the assumption that attainment of maximal affinity-mediated rate-enhancement presents with an activation entropy of the protein modification reaction equal to zero, whereas the activation enthalpy of the reaction remains unchanged, it is shown that the value for maximal affinity-mediated rate-enhancement is equal to e-delta s++/R. Accordingly, protein modification reactions may be differentiated into (i) reactions the rate-enhancement of which (relative to the reaction of the same modifying agent with a model compound) is primarily entropy-controlled and (ii) reactions the rate-enhancement of which is primarily enthalpy-controlled. It is seen that modifying agents of low reactivity towards model compounds, but with a high, i.e. highly negative, activation entropy are better suited as prospective affinity-based protein-modifying agents, since the potential affinity-mediated rate-enhancement, and hence the selectivity, of these compounds is necessarily high. Kinetic and thermodynamic constants of the reaction of modifying agents with proteins, and with model compounds, and values of maximal affinity-mediated rate-enhancement, based on published data of the reaction of several modifying agents with model compounds, are presented and discussed.

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3

Hall, Denver G. "Reaction Rate, Activities and Affinity — Further Comments." Zeitschrift für Physikalische Chemie 153, Part_1_2 (January 1987): 213–16. http://dx.doi.org/10.1524/zpch.1987.153.part_1_2.213.

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4

PATTISON, D. R. M., C. DE CAPITANI, and F. GAIDIES. "Petrological consequences of variations in metamorphic reaction affinity." Journal of Metamorphic Geology 29, no. 9 (July 18, 2011): 953–77. http://dx.doi.org/10.1111/j.1525-1314.2011.00950.x.

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5

Pekař, Miloslav. "Affinity and Reaction Rates: Reconsideration of Experimental Data." Helvetica Chimica Acta 90, no. 10 (October 2007): 1897–916. http://dx.doi.org/10.1002/hlca.200790198.

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6

Caoili, Salvador Eugenio C. "On the Meaning of Affinity Limits in B-Cell Epitope Prediction for Antipeptide Antibody-Mediated Immunity." Advances in Bioinformatics 2012 (November 14, 2012): 1–17. http://dx.doi.org/10.1155/2012/346765.

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B-cell epitope prediction aims to aid the design of peptide-based immunogens (e.g., vaccines) for eliciting antipeptide antibodies that protect against disease, but such antibodies fail to confer protection and even promote disease if they bind with low affinity. Hence, the Immune Epitope Database (IEDB) was searched to obtain published thermodynamic and kinetic data on binding interactions of antipeptide antibodies. The data suggest that the affinity of the antibodies for their immunizing peptides appears to be limited in a manner consistent with previously proposed kinetic constraints on affinity maturation in vivo and that cross-reaction of the antibodies with proteins tends to occur with lower affinity than the corresponding reaction of the antibodies with their immunizing peptides. These observations better inform B-cell epitope prediction to avoid overestimating the affinity for both active and passive immunization; whereas active immunization is subject to limitations of affinity maturation in vivo and of the capacity to accumulate endogenous antibodies, passive immunization may transcend such limitations, possibly with the aid of artificial affinity-selection processes and of protein engineering. Additionally, protein disorder warrants further investigation as a possible supplementary criterion for B-cell epitope prediction, where such disorder obviates thermodynamically unfavorable protein structural adjustments in cross-reactions between antipeptide antibodies and proteins.

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7

Keeble, Anthony H., Paula Turkki, Samuel Stokes, Irsyad N. A. Khairil Anuar, Rolle Rahikainen, Vesa P. Hytönen, and Mark Howarth. "Approaching infinite affinity through engineering of peptide–protein interaction." Proceedings of the National Academy of Sciences 116, no. 52 (December 10, 2019): 26523–33. http://dx.doi.org/10.1073/pnas.1909653116.

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Much of life’s complexity depends upon contacts between proteins with precise affinity and specificity. The successful application of engineered proteins often depends on high-stability binding to their target. In recent years, various approaches have enabled proteins to form irreversible covalent interactions with protein targets. However, the rate of such reactions is a major limitation to their use. Infinite affinity refers to the ideal where such covalent interaction occurs at the diffusion limit. Prototypes of infinite affinity pairs have been achieved using nonnatural reactive groups. After library-based evolution and rational design, here we establish a peptide–protein pair composed of the regular 20 amino acids that link together through an amide bond at a rate approaching the diffusion limit. Reaction occurs in a few minutes with both partners at low nanomolar concentration. Stopped flow fluorimetry illuminated the conformational dynamics involved in docking and reaction. Hydrogen–deuterium exchange mass spectrometry gave insight into the conformational flexibility of this split protein and the process of enhancing its reaction rate. We applied this reactive pair for specific labeling of a plasma membrane target in 1 min on live mammalian cells. Sensitive and specific detection was also confirmed by Western blot in a range of model organisms. The peptide–protein pair allowed reconstitution of a critical mechanotransmitter in the cytosol of mammalian cells, restoring cell adhesion and migration. This simple genetic encoding for rapid irreversible reaction should provide diverse opportunities to enhance protein function by rapid detection, stable anchoring, and multiplexing of protein functionality.

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8

Girr, Philipp, Jessica Kilper, Anne-Christin Pohland, and Harald Paulsen. "The pigment binding behaviour of water-soluble chlorophyll protein (WSCP)." Photochemical & Photobiological Sciences 19, no. 5 (2020): 695–712. http://dx.doi.org/10.1039/d0pp00043d.

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9

Alison-Youel, Sarah D. "Observation and Analysis of Affinity Law Deviations through Tested Performance of Liquefied Gas Reaction Turbines." International Journal of Rotating Machinery 2008 (2008): 1–5. http://dx.doi.org/10.1155/2008/737285.

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Liquefied gas reaction turbines are subject to the hydraulic affinity laws. Particularly for liquefied hydrocarbon gas-driven turbines, deviations from the affinity laws are encountered. In the case of reaction turbines, where the geometry is fixed, the affinity law relationships between flow, head, and rotational speed are relevant. Field experience confirms that the affinity law relationships are adequate, but that the predictions made also tend to deviate from real turbine performance. Part of the deviations seen may be attributed to the nonideal fluid; however, further examination is warranted. This paper presents an investigation into the affinity law relationships between head, flow, and rotational speed in conjunction with actual turbine performance. The three basic affinity law relationships are combined to form the most general performance equation. This equation subsequently incorporates both the affinity law relationships and the conservation of energy principal. Application of real turbine test data shows that this general performance equation presents a more accurate representation of turbine performance than the affinity law relationships alone.

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10

Sakamoto, Keiichi, Satoru Yoshino, Makoto Takemoto, Kazuhiro Sugaya, Hitomi Kubo, Tomoe Komoriya, Shinnosuke Kamei, and Shigeki Furukawa. "Synthesis of arylsulfanyl-subphthalocyanines and their ring expansion reaction." Journal of Porphyrins and Phthalocyanines 19, no. 05 (May 2015): 688–94. http://dx.doi.org/10.1142/s1088424615500194.

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For dye-sensitized solar cells, phthalocyanines require strong absorption of far-red light between 700 and 850 nm because of their high electron transfer efficiency. Nevertheless phthalocyanines lack of affinity to basal plats, they inhibit utilization as dye-sensitized solar cell photosensitizer. Then, subphthalocyanines are used as precursors to prepare asymmetric 3:1 type phthalocyanines using a ring-enlargement technique to give affinity to basal plates. As subphthalocyanines having arylsulfanyl substituents used as a precursor, asymmetric phthalocyanines are expected to have good affinity to basal plates. Spectroscopic properties and electron transfer abilities to synthesize non-peripheral arylsulfanyl-subphthalocyanines were estimated. In addition to prepare as trial, asymmetric 3:1 type phthalocyanine, hexakis[(4-methylphenyl)thio]phthalocyanine, was synthesized from corresponding subphthalocyanine.

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11

Karlsson, Elin, Cristina Paissoni, Amanda M. Erkelens, Zeinab A. Tehranizadeh, Frieda A. Sorgenfrei, Eva Andersson, Weihua Ye, Carlo Camilloni, and Per Jemth. "Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins." Journal of Biological Chemistry 295, no. 51 (October 16, 2020): 17698–712. http://dx.doi.org/10.1074/jbc.ra120.015645.

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Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we map native contacts in the transition states of the low-affinity ancestral and high-affinity human NCBD/CID interactions. We show that the coupled binding and folding mechanism is overall similar but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex and more heterogeneous transient interactions, including electrostatic pairings, and an increased disorder for the human complex. Adaptation to new binding partners may be facilitated by this ability to exploit multiple alternative transient interactions while retaining the overall binding and folding pathway.

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12

Ryu, Do Hyun, Gang Zhou, and E. J. Corey. "Nonparallelism between Reaction Rate and Dienophile−Catalyst Affinity in Catalytic Enantioselective Diels−Alder Reactions." Organic Letters 7, no. 8 (April 2005): 1633–36. http://dx.doi.org/10.1021/ol0503236.

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13

Hao, Lihua, and Qiang Zhao. "Using fluoro modified RNA aptamers as affinity ligands on magnetic beads for sensitive thrombin detection through affinity capture and thrombin catalysis." Analytical Methods 8, no. 3 (2016): 510–16. http://dx.doi.org/10.1039/c5ay02665b.

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14

Pekař, Miloslav. "Thermodynamics and foundations of mass-action kinetics." Progress in Reaction Kinetics and Mechanism 30, no. 1-2 (June 2005): 3–113. http://dx.doi.org/10.3184/007967405777874868.

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A critical overview is given of phenomenological thermodynamic approaches to reaction rate equations of the type based on the law of mass-action. The review covers treatments based on classical equilibrium and irreversible (linear) thermodynamics, extended irreversible, rational and continuum thermodynamics. Special attention is devoted to affinity, the applications of activities in chemical kinetics and the importance of chemical potential. The review shows that chemical kinetics survives as the touchstone of these various thermody-namic theories. The traditional mass-action law is neither demonstrated nor proved and very often is only introduced post hoc into the framework of a particular thermodynamic theory, except for the case of rational thermodynamics. Most published “thermodynamic'’ kinetic equations are too complicated to find application in practical kinetics and have merely theoretical value. Solely rational thermodynamics can provide, in the specific case of a fluid reacting mixture, tractable rate equations which directly propose a possible reaction mechanism consistent with mass conservation and thermodynamics. It further shows that affinity alone cannot determine the reaction rate and should be supplemented by a quantity provisionally called constitutive affinity. Future research should focus on reaction rates in non-isotropic or non-homogeneous mixtures, the applicability of traditional (equilibrium) expressions relating chemical potential to activity in non-equilibrium states, and on using activities and activity coefficients determined under equilibrium in non-equilibrium states.

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15

Dong, Dong, Dong Zheng, Fu-Quan Wang, Xi-Qiang Yang, Na Wang, Yuan-Guang Li, Liang-Hong Guo, and Jing Cheng. "Quantitative Photoelectrochemical Detection of Biological Affinity Reaction: Biotin−Avidin Interaction." Analytical Chemistry 76, no. 2 (December 3, 2003): 499–501. http://dx.doi.org/10.1021/ac035184p.

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16

Boudart, Michel, Daniel G. Löffler, and Juan Carlos Gottifredi. "Comments on the linear relation between reaction rate and affinity." International Journal of Chemical Kinetics 17, no. 10 (October 1985): 1119–23. http://dx.doi.org/10.1002/kin.550171008.

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17

Dutt, A. K. "Reaction Affinity and Entropy Production in a Model Glycolytic Oscillation." Journal of Physical Chemistry A 106, no. 11 (March 2002): 2401–3. http://dx.doi.org/10.1021/jp002999i.

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18

Haigh, Jonathan M., Abid Hussain, Michael L. Mimmack, and Christopher R. Lowe. "Affinity ligands for immunoglobulins based on the multicomponent Ugi reaction." Journal of Chromatography B 877, no. 14-15 (May 2009): 1440–52. http://dx.doi.org/10.1016/j.jchromb.2009.03.010.

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19

Oropallo, Michael A., and Andrea Cerutti. "Germinal center reaction: antigen affinity and presentation explain it all." Trends in Immunology 35, no. 7 (July 2014): 287–89. http://dx.doi.org/10.1016/j.it.2014.06.001.

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20

Dharmatti, Miyatake, Nandakumar, Ueda, Kobayashi, Kiga, Yamamura, and Ito. "Enhancement of Binding Affinity of Folate to Its Receptor by Peptide Conjugation." International Journal of Molecular Sciences 20, no. 9 (April 30, 2019): 2152. http://dx.doi.org/10.3390/ijms20092152.

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(1) Background: The folate receptor (FR) is a target for cancer treatment and detection. Expression of the FR is restricted in normal cells but overexpressed in many types of tumors. Folate was conjugated with peptides for enhancing binding affinity to the FR. (2) Materials and Methods: For conjugation, folate was coupled with propargyl or dibenzocyclooctyne, and 4-azidophenylalanine was introduced in peptides for “click” reactions. We measured binding kinetics including the rate constants of association (ka) and dissociation (kd) of folate-peptide conjugates with purified FR by biolayer interferometry. After optimization of the conditions for the click reaction, we successfully conjugated folate with designed peptides. (3) Results: The binding affinity, indicated by the equilibrium dissociation constant (KD), of folate toward the FR was enhanced by peptide conjugation. The enhanced FR binding affinity by peptide conjugation is a result of an increase in the number of interaction sites. (4) Conclusion: Such peptide-ligand conjugates will be important in the design of ligands with higher affinity. These high affinity ligands can be useful for targeted drug delivery system.

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21

Park, Seonhwa, Gamwoo Kim, Jeongwook Seo, and Haesik Yang. "Ultrasensitive Protease Sensors Using Selective Affinity Binding, Selective Proteolytic Reaction, and Proximity-Dependent Electrochemical Reaction." Analytical Chemistry 88, no. 24 (November 30, 2016): 11995–2000. http://dx.doi.org/10.1021/acs.analchem.6b03255.

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22

Tobisu, Mamoru, Masayuki Oshita, Sachiko Yoshioka, Aki Kitajima, and Naoto Chatani. "GaCl3-catalyzed reactions utilizing isocyanides as a C1 source." Pure and Applied Chemistry 78, no. 2 (January 1, 2006): 275–80. http://dx.doi.org/10.1351/pac200678020275.

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Two GaCl3-catalyzed reactions, which utilize isocyanides as a one-carbon unit, are described: a [4+1] cycloaddition of α,β-unsaturated carbonyl compounds with isocyanides, and an insertion reaction of isocyanides into a C-O bond of ketals and acetals. The relatively low affinity of GaCl3 toward heteroatoms enables the successful catalysis.

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23

Ishii, K., S. Futaki, H. Uchiyama, K. Nagasawa, and T. Andoh. "Mechanism of inhibition of mammalian DNA topoisomerase I by heparin." Biochemical Journal 241, no. 1 (January 1, 1987): 111–19. http://dx.doi.org/10.1042/bj2410111.

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We have previously shown that heparin is a potent inhibitor of a mammalian DNA topoisomerase I. We have now investigated the mechanism of its inhibition. This was carried out first by scrutinizing the structural features of heparin molecules responsible for the inhibition. Commercial heparin preparation was fractionated by antithrombin III-Sepharose into non-adsorbed, low-affinity and high-affinity fractions, of which only the high-affinity fraction of heparin is known to contain a specific oligosaccharide sequence responsible for the binding to antithrombin III. These fractions all exhibited essentially similar inhibitory activities. Furthermore, when chemically sulphated to an extent comparable with or higher than heparin, otherwise inactive glycosaminoglycans such as heparan sulphate, chondroitin 4-sulphate, dermatan sulphate and neutral polysaccharides such as dextran and amylose were converted into potent inhibitors. Sulphated dermatan sulphate, one of the model compounds, was further shown to bind competitively to the same sites on the enzyme as heparin. These observations strongly suggested that topoisomerase inhibition by heparin is attributable primarily, if not entirely, to the highly sulphated polyanionic nature of the molecules. In a second series of experiments we examined whether heparin inhibits only one or both of the topoisomerase reactions, i.e. nicking and re-joining. It was demonstrated that both reactions were inhibited by heparin, but the nicking reaction was more severely affected than was the re-joining reaction.

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24

Patston, PA, and M. Schapira. "Low-affinity heparin stimulates the inactivation of plasminogen activator inhibitor-1 by thrombin." Blood 84, no. 4 (August 15, 1994): 1164–72. http://dx.doi.org/10.1182/blood.v84.4.1164.1164.

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Abstract The influence of heparin on the reaction between thrombin and plasminogen activator inhibitor-1 (PAI-1) has been examined. With a 50- fold excess of PAI-1, the rate constant for the inhibition of thrombin was 458 mol/L-1s-1, which increased to 5,000 mol/L-1s-1 in the presence of 25 micrograms/mL unfractionated heparin or heparin with low affinity for antithrombin. The effect of low affinity heparin was then examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, using close to equimolar concentrations of reactants. Thrombin and PAI-1 formed a stable stoichiometric complex in the absence of heparin, which did not dissociate after the addition of 25 micrograms/mL low-affinity heparin. In contrast, when low-affinity heparin was added at the beginning of the reaction, there was an initial increase in PAI-1- thrombin complex formation, but this was rapidly followed by substantial proteolytic cleavage of unreacted PAI-1 and of the thrombin- PAI-1 complex. The idea that the relative concentrations of thrombin and PAI-1, and the presence of low affinity heparin, could influence the products of the reaction was examined in detail. Quantitative zymographic analysis of tissue plasminogen activator and PAI-1 activities and chromogenic substrate assay of thrombin activity showed that low-affinity heparin stimulated the inactivation of PAI-1 by an equimolar amount of thrombin, but caused only a minimal stimulation of thrombin inhibition. It is concluded that low-affinity heparin stimulates thrombin inhibition when PAI-1 is in excess, but, unexpectedly, that low-affinity heparin enhances PAI-1 inactivation when thrombin is equimolar to PAI-1.

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25

Patston, PA, and M. Schapira. "Low-affinity heparin stimulates the inactivation of plasminogen activator inhibitor-1 by thrombin." Blood 84, no. 4 (August 15, 1994): 1164–72. http://dx.doi.org/10.1182/blood.v84.4.1164.bloodjournal8441164.

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The influence of heparin on the reaction between thrombin and plasminogen activator inhibitor-1 (PAI-1) has been examined. With a 50- fold excess of PAI-1, the rate constant for the inhibition of thrombin was 458 mol/L-1s-1, which increased to 5,000 mol/L-1s-1 in the presence of 25 micrograms/mL unfractionated heparin or heparin with low affinity for antithrombin. The effect of low affinity heparin was then examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, using close to equimolar concentrations of reactants. Thrombin and PAI-1 formed a stable stoichiometric complex in the absence of heparin, which did not dissociate after the addition of 25 micrograms/mL low-affinity heparin. In contrast, when low-affinity heparin was added at the beginning of the reaction, there was an initial increase in PAI-1- thrombin complex formation, but this was rapidly followed by substantial proteolytic cleavage of unreacted PAI-1 and of the thrombin- PAI-1 complex. The idea that the relative concentrations of thrombin and PAI-1, and the presence of low affinity heparin, could influence the products of the reaction was examined in detail. Quantitative zymographic analysis of tissue plasminogen activator and PAI-1 activities and chromogenic substrate assay of thrombin activity showed that low-affinity heparin stimulated the inactivation of PAI-1 by an equimolar amount of thrombin, but caused only a minimal stimulation of thrombin inhibition. It is concluded that low-affinity heparin stimulates thrombin inhibition when PAI-1 is in excess, but, unexpectedly, that low-affinity heparin enhances PAI-1 inactivation when thrombin is equimolar to PAI-1.

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26

Carposu, Maria, Lucia Odochian, St Dima, M. Dumitras, and Magda Petrovanu. "Thermokinetic study of the inactivation reaction of 1-methyl phthalazinium ylids." Journal of the Serbian Chemical Society 68, no. 6 (2003): 447–54. http://dx.doi.org/10.2298/jsc0306447c.

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The present paper consists in a thermokinetic study on the dimerization reactions of 1-methylphthalazinium ylids with ?NO2 (ylid 1) and respectively, ?O?CH3 (ylid 2) substituents in the p position of the benzoyl radical bound to the ylidic carbanion. From experimental data, the reaction order and rate constants have been calculated. The reaction order n = 2 confirmed the ylids? dimerization reactions, while the values of the rate constants, k2 = 3.093x10-2L/mol s and, respectively, 2.16 x?10-1 L/mol s for the dimerization of ylids 1 and 2 made evident the higher reactivity of ylid 2 versus ylid 1. The same conclusion is also supported by the results of the thermodynamic study based on the chemical affinity of the two reactions, when Ao dim,1 < Aodim,2.

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27

Stoler-Barak, Liat, Adi Biram, Natalia Davidzohn, Yoseph Addadi, Ofra Golani, and Ziv Shulman. "B cell dissemination patterns during the germinal center reaction revealed by whole-organ imaging." Journal of Experimental Medicine 216, no. 11 (September 6, 2019): 2515–30. http://dx.doi.org/10.1084/jem.20190789.

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Germinal centers (GCs) are sites wherein B cells proliferate and mutate their immunoglobulins in the dark zone (DZ), followed by affinity-based selection in the light zone (LZ). Here, we mapped the location of single B cells in the context of intact lymph nodes (LNs) throughout the GC response, and examined the role of BCR affinity in dictating their position. Imaging of entire GC structures and proximal single cells by light-sheet fluorescence microscopy revealed that individual B cells that previously expressed AID are located within the LN cortex, in an area close to the GC LZ. Using in situ photoactivation, we demonstrated that B cells migrate from the LZ toward the GC outskirts, while DZ B cells are confined to the GC. B cells expressing very-low-affinity BCRs formed GCs but were unable to efficiently disperse within the follicles. Our findings reveal that BCR affinity regulates B cell positioning during the GC response.

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28

Koenderink, Jan B., Herman G. P. Swarts, H. Christiaan Stronks, Harm P. H. Hermsen, Peter H. G. M. Willems, and Jan Joep H. H. M. De Pont. "Chimeras of X+,K+-ATPases." Journal of Biological Chemistry 276, no. 15 (January 16, 2001): 11705–11. http://dx.doi.org/10.1074/jbc.m010804200.

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In this study we reveal regions of Na+,K+-ATPase and H+,K+-ATPase that are involved in cation selectivity. A chimeric enzyme in which transmembrane hairpin M5-M6 of H+,K+-ATPase was replaced by that of Na+,K+-ATPase was phosphorylated in the absence of Na+and showed no K+-dependent reactions. Next, the part originating from Na+,K+-ATPase was gradually increased in the N-terminal direction. We demonstrate that chimera HN16, containing the transmembrane segments one to six and intermediate loops of Na+,K+-ATPase, harbors the amino acids responsible for Na+specificity. Compared with Na+,K+-ATPase, this chimera displayed a similar apparent Na+affinity, a lower apparent K+affinity, a higher apparent ATP affinity, and a lower apparent vanadate affinity in the ATPase reaction. This indicates that theE2K form of this chimera is less stable than that of Na+,K+-ATPase, suggesting that it, like H+,K+-ATPase, de-occludes K+ions very rapidly. Comparison of the structures of these chimeras with those of the parent enzymes suggests that the C-terminal 187 amino acids and the β-subunit are involved in K+occlusion. Accordingly, chimera HN16 is not only a chimeric enzyme in structure, but also in function. On one hand it possesses the Na+-stimulated ATPase reaction of Na+,K+-ATPase, while on the other hand it has the K+occlusion properties of H+,K+-ATPase.

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29

Syvänen, Ann-Christine, Marina Bengtström, Tenhunen Jukka, and Hans Söderlund. "Quantification of polymerase chain reaction products by affinity-based hybrid collection." Nucleic Acids Research 16, no. 23 (1988): 11327–38. http://dx.doi.org/10.1093/nar/16.23.11327.

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30

Tyapochkin, Eduard, Vidya Prasanna Kumar, Paul F. Cook, and Guangping Chen. "Reaction product affinity regulates activation of human sulfotransferase 1A1 PAP sulfation." Archives of Biochemistry and Biophysics 506, no. 2 (February 2011): 137–41. http://dx.doi.org/10.1016/j.abb.2010.11.018.

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31

Wijewickreme, Arosha N., David D. Kitts, and Timothy D. Durance. "Reaction Conditions Influence the Elementary Composition and Metal Chelating Affinity of Nondialyzable Model Maillard Reaction Products." Journal of Agricultural and Food Chemistry 45, no. 12 (December 1997): 4577–83. http://dx.doi.org/10.1021/jf970041n.

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32

Rubinstein, S., and H. Breitbart. "Role of spermine in mammalian sperm capacitation and acrosome reaction." Biochemical Journal 278, no. 1 (August 15, 1991): 25–28. http://dx.doi.org/10.1042/bj2780025.

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The binding properties of seminal polyamines to ram spermatozoa and their possible role in sperm capacitation and the acrosome reaction were studied. Binding and release of [14C]spermine from ram spermatozoa occurred at a rate faster than in somatic cells and were not energy-dependent. Release of bound spermine was further facilitated by heparin, a constituent of the female reproductive tract which was reported to induce capacitation and the acrosome reaction. High- and low-affinity polyamine-binding sites were identified, of which the high-affinity site was specific to polyamines with three or more amino groups. We also found that spermine inhibited the acrosome reaction and propose that it is the major seminal decapacitating factor. Since precise timing of capacitation and the acrosome reaction are critical for successful fertilization, it is suggested that the role of seminal spermine is to prevent premature capacitation and the acrosome reaction.

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33

MEYER–HERMANN, MICHAEL. "A CONCERTED ACTION OF B CELL SELECTION MECHANISMS." Advances in Complex Systems 10, no. 04 (December 2007): 557–80. http://dx.doi.org/10.1142/s0219525907001276.

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Mathematical modeling of complex biological systems has been shown to lead to contradictory results. Two completely different approaches are compared using a highly dynamic system of the adaptive immune response with medical relevance. In germinal centers, high affinity antibodies are newly generated from antigen-activated B cell clones. The encoded antibody is mutated and high affinity clones for a specific antigen are selected to survive, giving rise to affinity maturation of antibodies. Here, the general assumption that competition for antigen held on follicular dendritic cells is responsible for affinity maturation is shown to be unlikely. This finding is based on the investigation of eight different selection mechanisms. A realistic model on selection mechanisms leading to affinity maturation is developed. It is found that negative selection of B cell, a B cell refractory time for binding antigen, and competition for T cell help, have strongest impact on affinity maturation. Antigen consumption is demonstrated to have impact on the kinetics of the germinal center in the late phase of the reaction and is hypothesized to be responsible for the termination of the reaction. These results are consistently found with agent-based and ordinary differential equation approaches and can, thus be considered to be robust. Experimental tests of the predicted selection mechanisms are proposed.

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Sagami, H., Y. Morita, T. Korenaga, and K. Ogura. "Purification of geranylgeranyl diphosphate synthase from bovine brain." Acta Biochimica Polonica 41, no. 3 (September 30, 1994): 293–302. http://dx.doi.org/10.18388/abp.1994_4718.

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Geranylgeranyl diphosphate (GGPP) synthase was purified to homogeneity from bovine brain in a one-step affinity column procedure. For the construction of the affinity column, a farnesyl diphosphate (FPP) analog, O-(6-amino-1-hexyl)-P-farnesylmethyl phosphonophosphate, was synthesized and linked to the spacer of the matrix of Affigel 10 via the amino group. The native enzyme appeared to be homooligomer (150-195 kDa) with a molecular mass of the monomer of 37.5 kDa. The pI for the enzyme was 6.2. The Km values for dimethylallyl diphosphate (DMAPP), geranyl diphosphate (GPP) and FPP were estimated to be 33 microM, 0.80 microM and 0.74 microM, respectively. The Km value for isopentenyl diphosphate (IPP) in the presence of both IPP and FPP mixture was 2 microM. The ratio of the reaction velocity for formation of GGPP from DMAPP, GPP or FPP was 0.004:0.145:1. The intermediate FPP was formed in the reaction with GPP as an allylic primer. FPP synthase catalyzing the formation of FPP from DMAPP and IPP was also purified to homogeneity from the same organ by a similar affinity chromatography procedure using a GPP analog, O-(6-amino-1-hexyl)-P-geranylmethyl phosphonophosphate as a ligand. The enzyme was a homodimer with a monomeric molecular mass of 40.0 kDa. These results indicate that GGPP, a lipid precursor for the biosynthesis of a majority of prenylated proteins, is synthesized from DMAPP and IPP by the action of FPP synthase catalyzing the reactions C5-->C15 followed by the action of GGPP synthase catalyzing the reaction C15-->C20.

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35

Schwickert, Tanja A., Gabriel D. Victora, David R. Fooksman, Alice O. Kamphorst, Monica R. Mugnier, Alexander D. Gitlin, Michael L. Dustin, and Michel C. Nussenzweig. "A dynamic T cell–limited checkpoint regulates affinity-dependent B cell entry into the germinal center." Journal of Experimental Medicine 208, no. 6 (May 16, 2011): 1243–52. http://dx.doi.org/10.1084/jem.20102477.

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The germinal center (GC) reaction is essential for the generation of the somatically hypermutated, high-affinity antibodies that mediate adaptive immunity. Entry into the GC is limited to a small number of B cell clones; however, the process by which this limited number of clones is selected is unclear. In this study, we demonstrate that low-affinity B cells intrinsically capable of seeding a GC reaction fail to expand and become activated in the presence of higher-affinity B cells even before GC coalescence. Live multiphoton imaging shows that selection is based on the amount of peptide–major histocompatibility complex (pMHC) presented to cognate T cells within clusters of responding B and T cells at the T–B border. We propose a model in which T cell help is restricted to the B cells with the highest amounts of pMHC, thus allowing for a dynamic affinity threshold to be imposed on antigen-binding B cells.

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36

Tamizifar, Maryam, and Gang Sun. "Control of surface radical graft polymerization on polyester fibers by using Hansen solubility parameters as a measurement of the affinity of chemicals to materials." RSC Advances 7, no. 22 (2017): 13299–303. http://dx.doi.org/10.1039/c6ra27186c.

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Several key interactive and controlling elements of the graft polymerization reaction of polyester fibers were identified, and corresponding affinity characters of each reaction component were quantified by using Hansen solubility theory.

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SUZUKI, MASUO, and HAKUAI INOUE. "EFFECTIVE KINETIC THEORY OF COMPLEX CHEMICAL REACTION SYSTEMS AND THERMODYNAMICS: GENERAL THEORY OF THE FORWARD AND REVERSE REACTION RATES." International Journal of Modern Physics B 05, no. 19 (November 20, 1991): 3029–48. http://dx.doi.org/10.1142/s0217979291001188.

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In this paper a new precise definition of the forward and reverse reaction rates of complex reaction processes is proposed. To apply the definition to reaction systems a general branching law, which yields the recursion formula on the forward and reverse reaction rates, is derived and general rate expressions are presented for complex reaction systems in the steady state. Based on these newly defined reaction rates, the thermodynamic relation between reaction rates and the affinity holds in chemical reaction processes of any order.

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38

Liu, Jingxin, Mohammed A. A. Abdullah, Liwei Yang, and Jun Wang. "Fast Affinity Induced Reaction Sensor Based on a Fluorogenic Click Reaction for Quick Detection of Protein Biomarkers." Analytical Chemistry 92, no. 1 (December 2, 2019): 647–53. http://dx.doi.org/10.1021/acs.analchem.9b04502.

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39

Goenka, Radhika, Andrew H. Matthews, Bochao Zhang, Patrick J. O’Neill, Jean L. Scholz, Thi-Sau Migone, Warren J. Leonard, William Stohl, Uri Hershberg, and Michael P. Cancro. "Local BLyS production by T follicular cells mediates retention of high affinity B cells during affinity maturation." Journal of Experimental Medicine 211, no. 1 (December 23, 2013): 45–56. http://dx.doi.org/10.1084/jem.20130505.

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We have assessed the role of B lymphocyte stimulator (BLyS) and its receptors in the germinal center (GC) reaction and affinity maturation. Despite ample BLyS retention on B cells in follicular (FO) regions, the GC microenvironment lacks substantial BLyS. This reflects IL-21–mediated down-regulation of the BLyS receptor TACI (transmembrane activator and calcium modulator and cyclophilin ligand interactor) on GC B cells, thus limiting their capacity for BLyS binding and retention. Within the GC, FO helper T cells (TFH cells) provide a local source of BLyS. Whereas T cell–derived BLyS is dispensable for normal GC cellularity and somatic hypermutation, it is required for the efficient selection of high affinity GC B cell clones. These findings suggest that during affinity maturation, high affinity clones rely on TFH-derived BLyS for their persistence.

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Helbo, Signe, and Angela Fago. "Allosteric modulation by S-nitrosation in the low-O2 affinity myoglobin from rainbow trout." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 300, no. 1 (January 2011): R101—R108. http://dx.doi.org/10.1152/ajpregu.00374.2010.

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Myoglobin (Mb) serves in the facilitated diffusion and storage of O2 in heart and skeletal muscle, where it also regulates O2 consumption via nitric oxide (NO) scavenging or generation. S-nitrosation at reactive cysteines may generate S-nitroso Mb (Mb-SNO) and contribute further to NO homeostasis. In being a monomer, Mb is commonly believed to lack allosteric control of heme reactivity. Here, we test whether in rainbow trout, a fast swimmer living in well-aerated water, the Mb-O2 affinity is regulated by ionic cofactors and S-nitrosation. O2 equilibria showed the lowest O2 affinity ever reported among vertebrate Mbs (P50 = 4.92 ± 0.29 mmHg, 25°C), a small overall heat of oxygenation (Δ H = −12.03 kcal/mol O2), and no effect of chloride, pH, or lactate. Although the reaction with 4,4′-dithiodipyridine (4-PDS) showed 1.3–1.9 accessible thiols per heme, the reaction of Mb with S-nitroso cysteine (Cys-NO) and S-nitrosoglutathione (GSNO) to generate Mb-SNO yielded ∼0.3–0.6 and ∼0.1 SNO/heme, respectively, suggesting S-nitrosation at only one cysteine (likely Cys10). At ∼60% S-nitrosation, trout Mb-SNO showed a higher O2 affinity (P50 = 2.23 ± 0.19 mmHg, 20°C) than unmodified Mb (3.36 ± 0.11 mmHg, 20°C). Total SNO levels measured by chemiluminescence in trout myocardial preparations decreased after hypoxia, but not significantly, indicating that transnitrosation reactions between thiols may occur in vivo. Our data reveal a novel, S-nitrosation-dependent allosteric mechanism in this low-affinity Mb that may contribute to targeted O2-linked SNO release in the hypoxic fish heart and be of importance in preserving cardiac function during intense exercise.

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Pekař, Miloslav. "Thermodynamic Driving Forces and Chemical Reaction Fluxes; Reflections on the Steady State." Molecules 25, no. 3 (February 6, 2020): 699. http://dx.doi.org/10.3390/molecules25030699.

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Molar balances of continuous and batch reacting systems with a simple reaction are analyzed from the point of view of finding relationships between the thermodynamic driving force and the chemical reaction rate. Special attention is focused on the steady state, which has been the core subject of previous similar work. It is argued that such relationships should also contain, besides the thermodynamic driving force, a kinetic factor, and are of a specific form for a specific reacting system. More general analysis is provided by means of the non-equilibrium thermodynamics of linear fluid mixtures. Then, the driving force can be expressed either in the Gibbs energy (affinity) form or on the basis of chemical potentials. The relationships can be generally interpreted in terms of force, resistance and flux.

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Chen, Chien-Yuan, Kun-Hsien Li, and Yen-Ho Chu. "Reaction-Based Detection of Chemical Warfare Agent Mimics with Affinity Ionic Liquids." Analytical Chemistry 90, no. 14 (June 25, 2018): 8320–25. http://dx.doi.org/10.1021/acs.analchem.8b01763.

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43

Beckmann, Henning S. G., Heiko M. Möller, and Valentin Wittmann. "High-affinity multivalent wheat germ agglutinin ligands by one-pot click reaction." Beilstein Journal of Organic Chemistry 8 (June 1, 2012): 819–26. http://dx.doi.org/10.3762/bjoc.8.91.

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A series of six mono-, di-, and trivalent N,N’-diacetylchitobiose derivatives was conveniently prepared by employing a one-pot procedure for Cu(II)-catalyzed diazo transfer and Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) starting from commercially available amines. These glycoclusters were probed for their binding potencies to the plant lectin wheat germ agglutinin (WGA) from Triticum vulgaris by an enzyme-linked lectin assay (ELLA) employing covalently immobilized N-acetylglucosamine (GlcNAc) as a reference ligand. IC50 values were in the low micromolar/high nanomolar range, depending on the linker between the two disaccharides. Binding enhancements β up to 1000 for the divalent ligands and 2800 for a trivalent WGA ligand, compared to N,N’-diacetylchitobiose as the corresponding monovalent ligand, were observed. Molecular modeling studies, in which the chitobiose moieties were fitted into crystallographically determined binding sites of WGA, correlate the binding enhancements of the multivalent ligands with their ability to bind to the protein in a chelating mode. The best WGA ligand is a trivalent cluster with an IC50 value of 220 nM. Calculated per mol of contained chitobiose, this is the best WGA ligand known so far.

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44

Wang, Chwan-Hang, and Shu-Yuan Tschen. "Affinity capture-polymerase chain reaction for quantitation of hepatitis B virus DNA." Nucleic Acids Research 22, no. 22 (1994): 4837–39. http://dx.doi.org/10.1093/nar/22.22.4837.

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45

Unarska, M., P. A. Davies, M. P. Esnouf, and B. J. Bellhouse. "Comparative study of reaction kinetics in membrane and agarose bead affinity systems." Journal of Chromatography A 519, no. 1 (October 1990): 53–67. http://dx.doi.org/10.1016/0021-9673(90)85134-h.

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46

Freidin, Alexander B., Igor K. Korolev, Sergey P. Aleshchenko, and Elena N. Vilchevskaya. "Chemical affinity tensor and chemical reaction front propagation: theory and FE-simulations." International Journal of Fracture 202, no. 2 (October 26, 2016): 245–59. http://dx.doi.org/10.1007/s10704-016-0155-1.

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47

Chen, Chen, Graziella El Khoury, and Christopher R. Lowe. "Affinity ligands for glycoprotein purification based on the multi-component Ugi reaction." Journal of Chromatography B 969 (October 2014): 171–80. http://dx.doi.org/10.1016/j.jchromb.2014.07.035.

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48

Han, Shuhua, Xuejun Zhang, Gangdou Wang, Hui Guan, Gabriela Garcia, Ping Li, Lili Feng, and Biao Zheng. "FTY720 suppresses humoral immunity by inhibiting germinal center reaction." Blood 104, no. 13 (December 15, 2004): 4129–33. http://dx.doi.org/10.1182/blood-2004-06-2075.

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Abstract FTY720 is a novel immunosuppressant that is highly effective in inhibiting rejection of allografts and autoimmunity in various animal models. It has been shown that the sphingosine 1 phosphate (S1P) receptors are the direct molecular targets of FTY720. However, the mechanisms responsible for inhibiting specific immune responses by FTY720 are not well resolved. In particular, there is no available information on whether or how this compound affects humoral immunity. We have investigated the effect of FTY720 treatment on B-cell response during the immune response to a well-defined T-dependent antigen. Our data demonstrated that germinal center reaction was significantly reduced in peripheral lymphoid tissues of mice treated with FTY720. In addition, FTY720 treatment inhibited the production of high-affinity, class-switched antibodies, but not the production of low-affinity, immunoglobulin M (IgM) antibody. Consistently, FTY720 did not have a significant effect on antibody response to a T-independent antigen. Our results may have important implications in application of FTY720 in immune regulation. (Blood. 2004; 104:4129-4133)

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Whedon, Samuel D., Marissa K. Parker, Elizabeth L. Tyson, Tobias Ritterhoff, Patrick M. M. Shelton, and Champak Chatterjee. "A clickable glutamine (CliQ) derivative for the traceless reversible modification of peptides and proteins." Chemical Communications 55, no. 14 (2019): 2043–45. http://dx.doi.org/10.1039/c8cc09404g.

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LLORÉNS, Mónica, C. Juan NUÑO, and Francisco MONTERO. "Transient times in linear metabolic pathways under constant affinity constraints." Biochemical Journal 327, no. 2 (October 15, 1997): 493–98. http://dx.doi.org/10.1042/bj3270493.

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In the early seventies, Easterby began the analytical study of transition times for linear reaction schemes [Easterby (1973) Biochim. Biophys. Acta 293, 552-558]. In this pioneer work and in subsequent papers, a state function (the transient time) was used to measure the period before the stationary state, for systems constrained to work under both constant and variable input flux, was reached. Despite the undoubted usefulness of this quantity to describe the time-dependent features of these kinds of systems, its application to the study of chemical reactions under other constraints is questionable. In the present work, a generalization of these magnitudes to linear metabolic pathways functioning under a constant-affinity constraint is carried out. It is proved that classical definitions of transient times do not reflect the actual properties of the transition to the steady state in systems evolving under this restriction. Alternatively, a more adequate framework for interpretation of the transient times for systems with both constant and variable input flux is suggested. Within this context, new definitions that reflect more accurately the transient characteristics of constant affinity systems are stated. Finally, the meaning of these transient times is discussed.

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