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Influence of structure properties on protein–protein interactions—QSAR modeling of changes in diffusion coefficients
Author(s) -
Bauer Katharina Christin,
Hämmerling Frank,
Kittelmann Jörg,
Dürr Cathrin,
Görlich Fabian,
Hubbuch Jürgen
Publication year - 2017
Publication title -
biotechnology and bioengineering
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.136
H-Index - 189
eISSN - 1097-0290
pISSN - 0006-3592
DOI - 10.1002/bit.26210
Subject(s) - quantitative structure–activity relationship , virial coefficient , diffusion , chemistry , in silico , biological system , thermodynamics , correlation coefficient , protein structure , chemical physics , computational chemistry , mathematics , physics , stereochemistry , statistics , biochemistry , biology , gene
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 coefficientB 22, the diffusion interaction parameterk D , 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 determinationR 2 = 0.9 and a good predictability for an external test set withR 2 = 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.