title: Influence of structure properties on protein-protein interactions-QSAR modeling of changes in diffusion coefficients.
abstract: Information about protein-protein interactions provides valuable knowledge about the phase behavior of protein solutions during the biopharmaceutical production process. Up to date it is possible to capture their overall impact by an experimentally determined potential of mean force. For the description of this potential, the second virial coefficient B22, the diffusion interaction parameter kD, the storage modulus G', or the diffusion coefficient D is applied. In silico methods do not only have the potential to predict these parameters, but also to provide deeper understanding of the molecular origin of the protein-protein interactions by correlating the data to the protein's three-dimensional structure. This methodology furthermore allows a lower sample consumption and less experimental effort. Of all in silico methods, QSAR modeling, which correlates the properties of the molecule's structure with the experimental behavior, seems to be particularly suitable for this purpose. To verify this, the study reported here dealt with the determination of a QSAR model for the diffusion coefficient of proteins. This model consisted of diffusion coefficients for six different model proteins at various pH values and NaCl concentrations. The generated QSAR model showed a good correlation between experimental and predicted data with a coefficient of determination R2 = 0.9 and a good predictability for an external test set with R2 = 0.91. The information about the properties affecting protein-protein interactions present in solution was in agreement with experiment and theory. Furthermore, the model was able to give a more detailed picture of the protein properties influencing the diffusion coefficient and the acting protein-protein interactions. Biotechnol. Bioeng. 2017;114: 821-831. © 2016 Wiley Periodicals, Inc.
authors: Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131 Karlsruhe, Germany.
authors: Katharina Christin
authors: KC
authors: Bauer
authors: Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131 Karlsruhe, Germany.
authors: Frank
authors: F
authors: Hämmerling
authors: Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131 Karlsruhe, Germany.
authors: Jörg
authors: J
authors: Kittelmann
authors: Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131 Karlsruhe, Germany.
authors: Cathrin
authors: C
authors: Dürr
authors: Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131 Karlsruhe, Germany.
authors: Fabian
authors: F
authors: Görlich
authors: Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Engler-Bunte-Ring 3, 76131 Karlsruhe, Germany.
authors: Jürgen
authors: J
authors: Hubbuch
mesh_terms: D019295:Computational Biology; D004058:Diffusion; D057927:Hydrophobic and Hydrophilic Interactions; D008962:Models, Theoretical; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism / Q000502:physiology*; D021281:Quantitative Structure-Activity Relationship; D055672:Static Electricity
chemical_list: D011506:Proteins
keywords:  quantitative structure-activity relationship; PDB; electrostatic interactions; hydrophobic interactions; protein shape; protein size