Investigation of the pH-dependent aggregation mechanisms of GCSF using low resolution protein characterization techniques and advanced molecular dynamics simulations
Research output: Contribution to journal › Journal article › Research › peer-review
Documents
- Fulltext
Final published version, 5.41 MB, PDF document
Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions.
Original language | English |
---|---|
Journal | Computational and Structural Biotechnology Journal |
Volume | 20 |
Pages (from-to) | 1439-1455 |
Number of pages | 17 |
ISSN | 2001-0370 |
DOIs | |
Publication status | Published - 2022 |
Bibliographical note
Funding Information:
We thank the European Synchrotron Radiation Facility for providing beam time for performing the SAXS experiments and Beamline Operator Manager Michael Sztucki for the measurements at beamline ID02. We thank Sergio Pantano for providing the SIRAH parameters for the protonated histidine. The simulations were carried at the High-Performance Computing (HPC) cluster at DTU. SKK received a Ph.D. scholarship funded through the DTU Alliance program. MS was supported by the TUM International Graduate School of Science and Engineering (IGSSE). In memory of Prof. Dr. Iris Antes who unfortunately passed away during the duration of this work on Aug. 4, 2021.
Publisher Copyright:
© 2022
- Aggregation, Coarse grained simulations, Granulocyte stimulating factor, Molecular dynamics, Small angle X-ray scattering
Research areas
ID: 339267185