(376ah) Molecular Dynamics Modeling Based Investigation of Cryoconcentration of Solutes during Freezing and Its Impact on Protein Stability
- Conference: AIChE Annual Meeting
- Year: 2019
- Proceeding: 2019 AIChE Annual Meeting
- Group: Computational Molecular Science and Engineering Forum
- Time: Tuesday, November 12, 2019 - 3:30pm-5:00pm
Methods: The initial conditions applied into the MD simulations were selected based on previous cryoconcentration experiments in which 1 L bottles containing 600 mL of a protein solution of 0.5 mg/mL lactate dehydrogenase (LDH) in 10 mM phosphate buffer at pH 7.0 with or without 2.5% (w/v) sucrose were frozen at -30°C. Therefore, LDH, phosphate salts and sucrose molecules were added into the simulation box. The MD simulation trajectories and their analyses were carried out using GROMACS/VMD software. We applied both MARTINI and CHARMM force-field for all-atom as well as coarse-grained simulations, respectively. The initial coordinates for LDH were taken from the protein data bank entries (pdb: 5NQB). The protein was initially modeled using the psfgen tool in VMD, and then further solvated in a simulation box and charge-neutralized with NaPO4. The box volume was optimized in the NPT ensemble by initially applying 500 cycles of a conjugate-gradient minimization scheme followed by a short 40-ps MD run in NPT assemble. The temperature was controlled using the Langevin thermostat, and the pressure was controlled by the Nose-Hoover barostat. The simulations were carried out using periodic boundary conditions. These briefly equilibrated systems of LDH protein were further subjected to MD simulation sets in the NVT ensemble. Computations were performed on HPC, a supercomputer cluster at the University of Connecticut.
Results and Discussion: The cryoconcentration effect was evaluated applying a model protein solvated in a simulation box of aqueous solvent in which different ions and stabilizers were added for case studies. Analyses of the resulted trajectories reveal the effect of temperature, ionic strength, and solutes concentration on the protein unfolding state, biomolecular interactions, and protein aggregation.