Molecular simulation of protein dynamics and function
We use molecular simulations to study functional protein dynamics over a broad range of time scales. Quantum-mechanics/molecular mechanics (QM/MM) descriptions allow us to follow fast, photoexcitation-driven protein motions on the picosecond scale . The resulting simulation trajectories are compared directly to femtosecond time-resolved protein crystallography experiments at X-ray free electron lasers. To study the functional dynamics in molecular motors and pumps  on the nano- to millisecond time scales, we have used classical and QM/MM simulations [3-6]. In nonequilibrium simulations, we drive these biomolecular machines by applying mechanical bias and inducing redox transitions that mimic their operation in a biological setting. The simulations help elucidate the molecular mechanisms underlying the efficient energy transduction processes in FoF1-ATP synthase [3-4] and the proton pump complex I [5-6].
T.R.M. Barends et al., “Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation,” Science, in press (2015). [https://www.sciencemag.org/content/early/2015/09/09/science.aac5492.short]
M. Wikström, V. Sharma, V.R.I. Kaila, J. Hosler, G. Hummer, “New perspectives on proton pumping in cellular respiration,” Chemical Reviews 115, 2196-2221 (2015). [http://dx.doi.org/10.1021/cr500448t]
K.-I. Okazaki, G. Hummer, “Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase,” Proc. Natl. Acad. Sci. U.S.A. 112, 10720-10725 (2015). [http://dx.doi.org/10.1073/pnas.1500691112]
K.-I. Okazaki, G. Hummer, “Phosphate release coupled to rotary motion of F1-ATPase,” Proc. Natl. Acad. Sci. USA 110, 16468-73 (2013).
V. Sharma, G. Belevich, A.P. Gamiz-Hernandez, T. Róga, I. Vattulainen, M. Verkhovskaya, M. Wikström, G. Hummer, V.R.I. Kaila, “Redox-induced activation of the proton pump in the respiratory complex I”, Proc. Natl. Acad. Sci. U.S.A. 112, 11571-11576 (2015). [http://dx.doi.org/10.1073/pnas.1503761112]
V. R. I. Kaila, M. Wikström, G. Hummer, “Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I,” Proc. Natl. Acad. Sci. USA 111, 6988–6993 (2014).
Speaker: Dr. Gerhard Hummer, Max Planck Institute of Biophysics, Franktfurt, Germany
Host: Prof. Dr. Ulrich Kleinekathöfer, Professor of Theoretical Physics, Focus Area: Health - Physics & Earth Sciences, Email: u.kleinekathoefer [at] jacobs-university.de, Tel: +49 421 200-3523, Link to Homepage: http://www.jacobs-university.de/ses/ukleinekathoefer