Soft Matter and Complex Systems Seminar
sala 1.40, ul. Pasteura 5
2023-05-26 (09:30) 
Paweł Krupa (IF PAN)
Molecular dynamics simulations to understand biological systems
Molecular modeling and simulations have become powerful tools for examining the structure, dynamics, and function of biological systems at atomic and molecular levels. As these methods continue to evolve, driven by advancements in software and hardware development, we can investigate larger and more complicated systems, extend simulation timescales, run more trajectories, and obtain more realistic results. Such capabilities allow us to reevaluate certain topics and uncover the limitations of oversimplified models used in both experimental and computational studies, which can produce physically correct outcomes that do not accurately represent much more complex physiological conditions.
In this talk, I will present examples demonstrating how we can construct reliable models of lipid bilayers and investigate their behavior, as well as the impact of other molecules, including ions, neurotransmitters, and proteins as by proper employment of molecular dynamics simulations, we can gain valuable insights into the intricate interactions and dynamics of complex biological systems, which often are not possible to be investigated experimentally [1–5]
References:
1. Rodziewicz-Motowidło, S., Krupa, P., Karska, N., Zhukov, I. & Lipińska, A. Why does the UL49.5 of herpes simplex 1 virus fail to inhibit the TAP-dependent antigen presentation? (2023) doi:10.26434/chemrxiv-2023-91b0s.
2. Graul, M. et al. The N-terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function. J. Mol. Biol. 435, 167964 (2023).
3. Gupta, A. et al. Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations. J. Phys. Chem. B 127, 1947–1955 (2023).
4. Huy Pham, D. Q., Krupa, P., Nguyen, H. L., La Penna, G. & Li, M. S. Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane. J. Phys. Chem. B 124, 3300–3314 (2020).
5. Krupa, P., Quoc Huy, P. D. & Li, M. S. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components. J. Chem. Phys. 151, 055101 (2019).
In this talk, I will present examples demonstrating how we can construct reliable models of lipid bilayers and investigate their behavior, as well as the impact of other molecules, including ions, neurotransmitters, and proteins as by proper employment of molecular dynamics simulations, we can gain valuable insights into the intricate interactions and dynamics of complex biological systems, which often are not possible to be investigated experimentally [1–5]
References:
1. Rodziewicz-Motowidło, S., Krupa, P., Karska, N., Zhukov, I. & Lipińska, A. Why does the UL49.5 of herpes simplex 1 virus fail to inhibit the TAP-dependent antigen presentation? (2023) doi:10.26434/chemrxiv-2023-91b0s.
2. Graul, M. et al. The N-terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function. J. Mol. Biol. 435, 167964 (2023).
3. Gupta, A. et al. Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations. J. Phys. Chem. B 127, 1947–1955 (2023).
4. Huy Pham, D. Q., Krupa, P., Nguyen, H. L., La Penna, G. & Li, M. S. Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane. J. Phys. Chem. B 124, 3300–3314 (2020).
5. Krupa, P., Quoc Huy, P. D. & Li, M. S. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components. J. Chem. Phys. 151, 055101 (2019).