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Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G
Institute for Applied Physics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.ORCID iD: 0000-0002-2682-576X
School of Physics, Clinical and Optometric Sciences, Technological University Dublin, Grangegorman D07 ADY7, Ireland.ORCID iD: 0000-0003-1083-6234
Malmö University, Faculty of Health and Society (HS), Department of Biomedical Science (BMV). Malmö University, Biofilms Research Center for Biointerfaces.ORCID iD: 0000-0001-5106-4360
Institut Max von Laue—Paul Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France.ORCID iD: 0000-0001-9630-1630
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2023 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 158, no 8, article id 084112Article in journal (Refereed) Published
Abstract [en]

We construct a coarse-grained, structure-based, low-resolution, 6-bead flexible model of bovine serum albumin (BSA, PDB: 4F5S), which is a popular example of a globular protein in biophysical research. The model is obtained via direct Boltzmann inversion using all-atom simulations of a single molecule, and its particular form is selected from a large pool of 6-bead coarse-grained models using two suitable metrics that quantify the agreement in the distribution of collective coordinates between all-atom and coarse-grained Brownian dynamics simulations of solutions in the dilute limit. For immunoglobulin G (IgG), a similar structure-based 12-bead model has been introduced in the literature [Chaudhri et al., J. Phys. Chem. B 116, 8045 (2012)] and is employed here to compare findings for the compact BSA molecule and the more anisotropic IgG molecule. We define several modified coarse-grained models of BSA and IgG, which differ in their internal constraints and thus account for a variation of flexibility. We study denser solutions of the coarse-grained models with purely repulsive molecules (achievable by suitable salt conditions) and address the effect of packing and flexibility on dynamic and static behavior. Translational and rotational self-diffusivity is enhanced for more elastic models. Finally, we discuss a number of effective sphere sizes for the BSA molecule, which can be defined from its static and dynamic properties. Here, it is found that the effective sphere diameters lie between 4.9 and 6.1 nm, corresponding to a relative spread of about ±10% around a mean of 5.5 nm.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2023. Vol. 158, no 8, article id 084112
National Category
Condensed Matter Physics Physical Chemistry Biophysics
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URN: urn:nbn:se:mau:diva-58652DOI: 10.1063/5.0132493ISI: 000940890500005PubMedID: 36859072Scopus ID: 2-s2.0-85149269239OAI: oai:DiVA.org:mau-58652DiVA, id: diva2:1743517
Funder
German Research Foundation (DFG), DFG SCHR 700/28-1German Research Foundation (DFG), ANR-21-CE06-0047Available from: 2023-03-15 Created: 2023-03-15 Last updated: 2024-02-27Bibliographically approved

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Roosen-Runge, Felix

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