Closer look into HIV-host interactions: Standard Gibbs energy of binding of the gp120 antigen of HIV-1 to the CD4 receptor and monoclonal antibodies
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Biothermodynamics of viruses, HIV-1, Binding constant, Gibbs energy of binding, Antigen-receptor bindingAbstract
HIV-1, like other viruses, represents an open thermodynamic system. This is why it is important to know its thermodynamic properties. Virus-host interactions are performed at the membrane as antigen-receptor binding. Antigen-receptor binding represents a chemical reaction, similar to protein-ligand interactions. The driving force for antigen-receptor binding is Gibbs energy of binding. Knowing Gibbs energy of binding, it is possible to estimate the rate of virus binding and entry into host cells. In this paper, binding equilibrium constants and standard Gibbs energies of binding between the HIV-1 gp120 antigen and the CD4 receptor have been reported at 4 °C, 22 °C and 37 °C.
References
Arrildt, K. T., Joseph, S. B., & Swanstrom, R. (2012). The HIV-1 env protein: A coat of many colors. Current Hiv/Aids Reports, 9, 52-63.
Balliet, J. W., Berson, J., D’Cruz, C. M., Huang, J., Crane, J., Gilbert, J. M., & Bates, P. (1999). Production and characterization of a soluble, active form of Tva, the subgroup A avian sarcoma and leukosis virus receptor. Journal of Virology, 73(4), 3054-3061.
Balmer, R. (2010). Modern Engineering Thermodynamics: Cambridge, MA: Academic Press.
Bridges, J. P., Vladar, E. K., Huang, H., & Mason, R. J. (2022). Respiratory epithelial cell responses to SARS-CoV-2 in COVID-19. Thorax, 77(2), 203-209.
Casasnovas, J. M., & Springer, T. A. (1995). Kinetics and Thermodynamics of Virus Binding to Receptor: Studies with Rhinovirus, Intercellular Adhesion Molecule-1 (ICAM-1), and Surface Plasmon Resonance. Journal of Biological Chemistry, 270(22), 13216-13224.
Chan, D. C., Fass, D., Berger, J. M., & Kim, P. S. (1997). Core structure of gp41 from the HIV envelope glycoprotein. Cell, 89(2), 263-273.
Cunningham, A. L., Donaghy, H., Harman, A. N., Kim, M., & Turville, S. G. (2010). Manipulation of dendritic cell function by viruses. Current Opinion in Microbiology, 13(4), 524-529.
Degueldre, C. (2021). Single virus inductively coupled plasma mass spectroscopy analysis: A comprehensive study. Talanta, 228, 122211.
Demirel, Y. (2007). Nonequilibrium thermodynamics: transport and rate processes in physical, chemical and biological systems: Elsevier.
Du, X., Li, Y., Xia, Y. L., Ai, S. M., Liang, J., Sang, P., Ji, X. L., & Liu, S. Q. (2016). Insights into protein–ligand interactions: mechanisms, models, and methods. International Journal of Molecular Sciences, 17(2), 144.
Duffy, S. (2018). Why are RNA virus mutation rates so damn high? PLoS Biology, 16(8), e3000003.
Gale, P. (2018). Using thermodynamic parameters to calibrate a mechanistic dose-response for infection of a host by a virus. Microbial Risk Analysis, 8, 1-13.
Gale, P. (2019). Towards a thermodynamic mechanistic model for the effect of temperature on arthropod vector competence for transmission of arboviruses. Microbial Risk Analysis, 12, 27-43.
Gale, P. (2020). How virus size and attachment parameters affect the temperature sensitivity of virus binding to host cells: Predictions of a thermodynamic model for arboviruses and HIV. Microbial Risk Analysis, 15, 100104.
Gale, P. (2022). Using thermodynamic equilibrium models to predict the effect of antiviral agents on infectivity: Theoretical application to SARS-CoV-2 and other viruses. Microbial Risk Analysis, 21, 100198.
Head, R. J., Lumbers, E. R., Jarrott, B., Tretter, F., Smith, G., Pringle, K. G., Islam, S., & Martin, J. H. (2022). Systems analysis shows that thermodynamic physiological and pharmacological fundamentals drive COVID‐19 and response to treatment. Pharmacology Research & Perspectives, 10(1), e00922.
Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., et al. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215-220.
Lavoisier, A., & DeLaplace, P. (1994). Memoir on heat read to the royal academy of sciences, 28 June 1783. Obesity Research, 2(2), 189-202.
Lavoisier, A., & Marquis de Laplace, P. (1783). Mémoire sur la chaleur: Lû à'Académie royale des sciences, le 28 Juin 1783. Paris, France: De l'Imprimerie royale. (English translation: “Memoir on Heat Read to the Royal Academy of Sciences, 28 June 1783”).
Lortat-Jacob, H., Chouin, E., Cusack, S., & van Raaij, M. J. (2001). Kinetic analysis of adenovirus fiber binding to its receptor reveals an avidity mechanism for trimeric receptor-ligand interactions. Journal of Biological Chemistry, 276(12), 9009-9015.
Mahmoudabadi, G., Milo, R., & Phillips, R. (2017). Energetic cost of building a virus. Proceedings of the National Academy of Sciences, 114(22), E4324-E4333.
Molla, A., Paul, A. V., & Wimmer, E. (1991). Cell-free, de novo synthesis of poliovirus. Science, 254(5038), 1647-1651.
Myszka, D. G., Sweet, R. W., Hensley, P., Brigham-Burke, M., Kwong, P. D., Hendrickson, W. A., Wyatt, R., Sodroski, J., & Doyle, M. L. (2000). Energetics of the HIV gp120-CD4 binding reaction. Proceedings of the National Academy of Sciences, 97(16), 9026-9031.
Popovic, M. (2014). Entropy change of open thermodynamic systems in self-organizing processes. Thermal Science, 18(4), 1425-1432.
Popovic, M. (2022a). Beyond COVID-19: Do biothermodynamic properties allow predicting the future evolution of SARS-CoV-2 variants? Microbial Risk Analysis, 22, 100232.
Popovic, M. (2022b). Biothermodynamic Key Opens the Door of Life Sciences: Bridging the Gap between Biology and Thermodynamics. Preprints, 2022, 2022100326.
Popovic, M. (2022c). Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022). Vaccines, 10(12), 2112.
Popovic, M. (2022d). Formulas for death and life: Chemical composition and biothermodynamic properties of Monkeypox (MPV, MPXV, HMPXV) and Vaccinia (VACV) viruses. Thermal Science, 26(6), 142-142.
Popovic, M. (2022e). Omicron BA. 2.75 Sublineage (Centaurus) Follows the Expectations of the Evolution Theory: Less Negative Gibbs Energy of Biosynthesis Indicates Decreased Pathogenicity. Microbiology Research, 13(4), 937-952.
Popovic, M. (2022f). Omicron BA. 2.75 Subvariant of SARS-CoV-2 Is Expected to Have the Greatest Infectivity Compared with the Competing BA. 2 and BA. 5, Due to Most Negative Gibbs Energy of Binding. BioTech, 11(4), 45.
Popovic, M. (2022g). Strain wars 2: Binding constants, enthalpies, entropies, Gibbs energies and rates of binding of SARS-CoV-2 variants. Virology, 570, 35-44.
Popovic, M. (2022h). Strain wars 3: Differences in infectivity and pathogenicity between Delta and Omicron strains of SARS-CoV-2 can be explained by thermodynamic and kinetic parameters of binding and growth. Microbial Risk Analysis, 22, 100217.
Popovic, M. (2022i). Strain Wars 4-Darwinian evolution through Gibbs’ glasses: Gibbs energies of binding and growth explain evolution of SARS-CoV-2 from Hu-1 to BA. 2. Virology, 575, 36-42.
Popovic, M. (2022j). Strain Wars 5: Gibbs energies of binding of BA. 1 through BA. 4 variants of SARS-CoV-2. Microbial Risk Analysis, 22, 100231.
Popovic, M. (2022k). Thermodynamics of Bacteria-Phage Interactions: T4 and Lambda Bacteriophages, and E. Coli Can Coexist in Natural Ecosystems due to the Ratio of their Gibbs Energies of Biosynthesis. Preprints, 2022, 2022110327.
Popovic, M. (2022l). Why doesn't Ebola virus cause pandemics like SARS-CoV-2? Microbial Risk Analysis, 22, 100236.
Popovic, M., & Minceva, M. (2020a). Thermodynamic insight into viral infections 2: empirical formulas, molecular compositions and thermodynamic properties of SARS, MERS and SARS-CoV-2 (COVID-19) viruses. Heliyon, 6(9), e04943.
Popovic, M., & Minceva, M. (2020b). A thermodynamic insight into viral infections: do viruses in a lytic cycle hijack cell metabolism due to their low Gibbs energy? Heliyon, 6(5), e03933.
Popovic, M., & Minceva, M. (2021). Coinfection and interference phenomena are the results of multiple thermodynamic competitive interactions. Microorganisms, 9(10), 2060.
Popovic, M., & Popovic, M. (2022). Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding. Microbial Risk Analysis, 21, 100202.
Robertson, D. L., Hahn, B. H., & Sharp, P. M. (1995). Recombination in AIDS viruses. Journal of Molecular Evolution, 40, 249-259.
Ryu, G., & Shin, H. W. (2021). SARS-CoV-2 infection of airway epithelial cells. Immune Network, 21(1), e3.
Schnittman, S., Lane, H., Roth, J., Burrows, A., Folks, T., Kehrl, J., Koenig, S., Berman, P., & Fauci, A. (1988). Characterization of GP120 binding to CD4 and an assay that measures ability of sera to inhibit this binding. Journal of Immunology, 141(12), 4181-4186.
Schrödinger, E. (1992). What is life?: With mind and matter and autobiographical sketches: Cambridge University Press.
Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 581(7807), 221-224.
Şimşek, B., Özilgen, M., & Utku, F. Ş. (2022). How much energy is stored in SARS‐CoV‐2 and its structural elements? Energy Storage, 4(2), e298.
Tappert, M. M., Porterfield, J. Z., Mehta-D'Souza, P., Gulati, S., & Air, G. M. (2013). Quantitative comparison of human parainfluenza virus hemagglutinin-neuraminidase receptor binding and receptor cleavage. Journal of Virology, 87(16), 8962-8970.
Thali, M., Olshevsky, U., Furman, C., Gabuzda, D., Li, J., & Sodroski, J. (1991). Effects of changes in gp120-CD4 binding affinity on human immunodeficiency virus type 1 envelope glycoprotein function and soluble CD4 sensitivity. Journal of Virology, 65(9), 5007-5012.
Von Bertalanffy, L. (1950). The theory of open systems in physics and biology. Science, 111(2872), 23-29.
Von Bertalanffy, L. (1968). General system theory: Foundations, development, applications: NY: George Braziller Inc.
Von Stockar, U. (2013). Live cells as open non-equilibrium systems. In Urs von Stockar, ed., Biothermodynamics: The Role of Thermodynamics in Biochemical Engineering: Lausanne: EPFL Press, pp. 475-534.
Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281-292.
Wilen, C. B., Tilton, J. C., & Doms, R. W. (2012). HIV: cell binding and entry. Cold Spring Harbor Perspectives in Medicine, 2(8), a006866.
Wimmer, E. (2006). The test‐tube synthesis of a chemical called poliovirus: The simple synthesis of a virus has far‐reaching societal implications. EMBO Reports, 7(S1), S3-S9.
Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367(6483), 1260-1263.
Xu, X. H. N., Wen, Z., & Brownlow, W. J. (2013). Ultrasensitive analysis of binding affinity of HIV receptor and neutralizing antibodies using solution-phase electrochemiluminescence assay. Journal of Electroanalytical Chemistry, 688, 53-60.
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