Behaviour of the model antibody fluid constrained by rigid spherical obstacles: effects of the obstacle-antibody binding

Yu. Kalyuzhnyi; T. Patsahan

doi:10.5488/CMP.29.13403

Authors

Yu. Kalyuzhnyi University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI-1000 Ljubljana, Slovenia; Yukhnovskii Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine, 1 Svientsitskii Str., 79011 Lviv, Ukraine https://orcid.org/0000-0002-0631-9982
T. Patsahan Yukhnovskii Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine, 1 Svientsitskii Str., 79011 Lviv, Ukraine; Institute of Applied Mathematics and Fundamental Sciences, Lviv Polytechnic National University, 12 S. Bandera Str., 79013 Lviv, Ukraine https://orcid.org/0000-0002-7870-2219

DOI:

https://doi.org/10.5488/CMP.29.13403

Keywords:

monoclonal antibodies, macromolecular crowding, patchy particle model, thermodynamic perturbation theory, percolation, phase separation

Abstract

We study a simplified model of monoclonal antibodies confined in a patchy random porous medium. Antibodies are represented as Y-shaped particles composed of seven tangential hard spheres with attractive patches on the terminal beads, while the matrix consists of randomly distributed hard-sphere obstacles bearing adhesive sites. The model captures antibody behavior in crowded biological environments with strong short-range antibodymatrix attractions. The theoretical approach combines Wertheim’s multidensity thermodynamic perturbation theory, the Flory-Stockmayer theory of polymerization, and scaled particle theory for fluids in porous media. We analyze thermodynamic properties, percolation thresholds, and phase behavior, and compare the selected results with new computer simulations. The interplay between antibody-antibody and antibody-matrix interactions produces a complex phase behavior, including re-entrant phase separation with a closed-loop coexistence region at higher temperatures and conventional liqui-gas separation at lower temperatures.

References

Das N., Khan T., Halder B., Ghosh S., Sen P., Int. J. Biol. Macromol., 2024, 281, 136248. DOI: https://doi.org/10.1016/j.ijbiomac.2024.136248

Kalyuzhnyi Yu. V., Vlachy V., J. Phys.: Condens. Matter, 2018, 30, No. 48, 485101. DOI: https://doi.org/10.1088/1361-648X/aae914

Kastelic M., Dill K. A., Kalyuzhnyi Yu. V., Vlachy V., J. Mol. Liq., 2018, 270, 234–242. DOI: https://doi.org/10.1016/j.molliq.2017.11.106

Kastelic M., Vlachy V., J. Phys. Chem. B, 2018, 122, No. 21, 5400–5408. DOI: https://doi.org/10.1021/acs.jpcb.7b11458

Vlachy V., Kalyuzhnyi Yu. V., Hribar-Lee B., Dill K. A., Biomolecules, 2023, 13, No. 12, 1703. DOI: https://doi.org/10.3390/biom13121703

Hvozd T., Kalyuzhnyi Yu. V., Vlachy V., J. Mol. Liq., 2024, 402, 124740. DOI: https://doi.org/10.1016/j.molliq.2024.124740

Kalyuzhnyi Yu. V., Vlachy V., J. Mol. Liq., 2022, 365, 120006. DOI: https://doi.org/10.1016/j.molliq.2022.120006

Hvozd T., Kalyuzhnyi Yu. V., Vlachy V., Soft Matter, 2020, 16, No. 36, 8432–8443. DOI: https://doi.org/10.1039/D0SM01014F

Hvozd T., Kalyuzhnyi Yu. V., Vlachy V., Soft Matter, 2022, 18, No. 47, 9108–9117. DOI: https://doi.org/10.1039/D2SM01258H

Hvozd T., Kalyuzhnyi Yu. V., Vlachy V., Cummings P. T., J. Chem. Phys., 2022, 156, No. 16, 161102. DOI: https://doi.org/10.1063/5.0088716

Hribar-Lee B., Lukšič M., Vlachy V., Annu. Rep. Prog. Chem., Sect. C: Phys. Chem., 2011, 107, 14–46. DOI: https://doi.org/10.1039/c1pc90001c

Wertheim M. S., J. Stat. Phys., 1986, 42, No. 3–4, 459–476. DOI: https://doi.org/10.1007/BF01127721

Wertheim M. S., J. Stat. Phys., 1986, 42, No. 3–4, 477–492. DOI: https://doi.org/10.1007/BF01127722

Wertheim M., J. Chem. Phys., 1987, 87, No. 12, 7323–7331. DOI: https://doi.org/10.1063/1.453326

Holovko M., Patsahan T., Dong W., Pure Appl. Chem., 2012, 85, No. 1, 115–133. DOI: https://doi.org/10.1351/PAC-CON-12-05-06

Patsahan T., Holovko M., Dong W., J. Chem. Phys., 2011, 134, No. 7. DOI: https://doi.org/10.1063/1.3532546

Holovko M., Patsahan T., Dong W., Condens. Matter Phys., 2017, 20, No. 3, 33602. DOI: https://doi.org/10.5488/CMP.20.33602

Kalyuzhnyi Yu. V., Holovko M., Patsahan T., Cummings P., J. Phys. Chem. Lett., 2014, 5, No. 24, 4260–4264. DOI: https://doi.org/10.1021/jz502135f

Bianchi E., Tartaglia P., Zaccarelli E., Sciortino F., J. Chem. Phys., 2008, 128, No. 14, 144504. DOI: https://doi.org/10.1063/1.2888997

Bianchi E., Tartaglia P., La Nave E., Sciortino F., J. Phys. Chem. B, 2007, 111, No. 40, 11765–11769. DOI: https://doi.org/10.1021/jp074281+

de Las Heras D., Tavares J. M., Da Gama M. M. T., Soft Matter, 2011, 7, No. 12, 5615–5626. DOI: https://doi.org/10.1039/c0sm01493a

Tavares J., Teixeira P., Telo da Gama M., Sciortino F., J. Chem. Phys., 2010, 132, No. 23, 234502. DOI: https://doi.org/10.1063/1.3435346

Kalyuzhnyi Yu. V., Patsahan T., Holovko M., Cummings P. T., Nanoscale, 2024, 16, No. 9, 4668–4677. DOI: https://doi.org/10.1039/D3NR02866F

Trokhymchuk A., Pizio O., Holovko M., Sokolowski S., J. Phys. Chem., 1996, 100, No. 42, 17004–17010. DOI: https://doi.org/10.1021/jp961443l

Trokhymchuk A., Pizio O., Holovko M., Sokolowski S., J. Chem. Phys., 1997, 106, No. 1, 200–209. DOI: https://doi.org/10.1063/1.473042

Ilnytsky J., Patrykiejew A., Sokołowski S., Pizio O., J. Phys. Chem. B, 1999, 103, No. 5, 868–871. DOI: https://doi.org/10.1021/jp983302k

Pizio O., Sokołowska Z., Sokołowski S., Czech. J. Phys., 2000, 50, No. 6, 769–783. DOI: https://doi.org/10.1023/A:1022891004122

Rżysko W., Sokołowski S., Pizio O., J. Chem. Phys., 2002, 116, No. 10, 4286–4292. DOI: https://doi.org/10.1063/1.1450556

Kalyuzhnyi Yu. V., Cummings P., J. Chem. Phys., 1995, 103, No. 8, 3265–3267. DOI: https://doi.org/10.1063/1.470259

Kalyuzhnyi Yu. V., Lin C.-T., Stell G., J. Chem. Phys., 1997, 106, No. 5, 1940–1949. DOI: https://doi.org/10.1063/1.473331

Lin C.-T., Kalyuzhnyi Yu. V., Stell G., J. Chem. Phys., 1998, 108, No. 15, 6513–6524. DOI: https://doi.org/10.1063/1.476058

Butovych H., Kalyuzhnyi Yu. V., Patsahan T., Ilnytskyi J., J. Mol. Liq., 2023, 385, 122321. DOI: https://doi.org/10.1016/j.molliq.2023.122321

Jover J., Haslam A., Galindo A., Jackson G., Müller E., J. Chem. Phys., 2012, 137, No. 14. DOI: https://doi.org/10.1063/1.4754275

Espinosa J. R., Garaizar A., Vega C., Frenkel D., Collepardo-Guevara R., J. Chem. Phys., 2019, 150, No. 22. DOI: https://doi.org/10.1063/1.5098551

Espinosa J. R., Joseph J. A., Sanchez-Burgos I., Garaizar A., Frenkel D., Collepardo-Guevara R., PNAS, 2020, 117, No. 24, 13238–13247. DOI: https://doi.org/10.1073/pnas.1917569117

Joseph J. A., Espinosa J. R., Sanchez-Burgos I., Garaizar A., Frenkel D., Collepardo-Guevara R., Biophys. J., 2021, 120, No. 7, 1219–1230. DOI: https://doi.org/10.1016/j.bpj.2021.01.031

Sanchez-Burgos I., Espinosa J. R., Joseph J. A., Collepardo-Guevara R., PLoS Comput. Biol., 2022, 18, No. 2, e1009810. DOI: https://doi.org/10.1371/journal.pcbi.1009810

Plimpton S., J. Comput. Phys., 1995, 117, No. 1, 1–19. DOI: https://doi.org/10.1006/jcph.1995.1039

Thompson A. P., Aktulga H. M., Berger R., Bolintineanu D. S., Brown W. M., Crozier P. S., In’t Veld P. J., Kohlmeyer A., Moore S. G., Nguyen T. D., Shan R., Stevens M. J., Tranchida J., Trott C., Plimpton S. J., Comput. Phys. Commun., 2022, 271, 108171. DOI: https://doi.org/10.1016/j.cpc.2021.108171

Allen M. P., Tildesley D. J., Computer Simulation of Liquids, Oxford University Press, Oxford, 2017. DOI: https://doi.org/10.1093/oso/9780198803195.001.0001