calque

Workshops

Interactions and Transport of Charged Species in Bulk and at Interfaces

July 4, 2016 to July 7, 2016
Location : CECAM-AT

Charge Transport at Biological Interfaces: Insights from Molecular Dynamics Simulations

Vania Calandrini


Coauthor(s) : Chao Zhang [1,2], Denis G. Knyazev [3], Yana A. Vereshaga [1], Jens Dreyer [1,2], Emiliano Ippoliti [1,2], Trung Hai Nguyen [1], Justin Finnerty [1], P. Strodel [1], Bob Eisenberg [4], Paolo Carloni [1,2], and Peter Pohl [3]
[1] German Research School for Simulation Sciences, Forschungszentrum Jülich, Germany [2] IAS5/INM9 Forschungszentrum Jülich, Germany [3] Institute of Biophysics, Johannes Kepler University, Linz, Austria [4] Rush University Medical Center, Chicago, USA

Abstract

Monovalent ions (Na+, K+, Cl-, H+) are ubiquitously present in biological systems. Among them, Na+, K+ and Cl- are the most abundant; they regulate metabolism and signaling transduction through transmembrane concentration gradients [1] and stabilize proteins, lipids, and nucleic acids through both specific and non-specific interactions [2,3]. Lateral H+ migration along membranes [4] is of vital importance for cellular energy homeostasis and various proton-coupled transport processes [1]. For instance, the synthesis of adenosine triphosphate (ATP), the free energy carrier in living systems, would cease if specific membrane-bound enzymes (proton pumps and ATP synthase as the proton source and the proton sink, respectively) would stop creating and consuming a transmembrane proton gradient [5].
Most of what we know today about the biophysical properties of monovalent ions has been discovered by experiments, but an increasingly important role - complementary to experiment - is played by molecular simulations. Here, I will provide with an overview of the HPC-based contributions from our group on the transport properties of monovalent ions at water-hydrophobic interfaces [6,7], and the energetics of ion permeation through membrane channels [8-10].



References

[1] J. J. R. Frausto da Silva and R. J. P. Williams, ‘The biological chemistry of the elements: the inorganic chemistry of life’, Oxford University Press (2001).
[2] A Ke, F Ding, J Batchelor, and J Doudna. Structure, 15, 281, (2007).
[3] J Vieregg, W Cheng, C Bustamante, and I Tinoco Jr. J Am Chem Soc, 129, 14966, (2005)
[4] A Springer, V Hagen, D A Cherepanov, Y N Antonenko, and P Pohl, Proc Nat Acad Sci USA, 108, 14461, (2011)
[5] N Agmon and M Gutman, Nat Chem, 3, 840, (2011)
[6] C. Zhang and Paolo Carloni, J. Phys.: Condens. Matter 24 (2012) 124109
[7] C. Zhang, Denis G. Knyazev, Yana A. Vereshagaa, Emiliano Ippoliti, Trung Hai Nguyen, Paolo Carloni, and Peter Pohl, J Am Chem Soc, 109, 9744, 2012
[8] J Dreyer, C. Zhang, E. Ippoliti, and P. Carloni, J. Chem. Theory Comput., 9, 3826, 2013
[9] J Dreyer, P. Strodel, E. Ippoliti, J. Finnerty, B. Eisenberg, and P. Carloni, J. Phys. Chem. B, 117, 13534, 2013
[10] V. Calandrini, J. Dreyer, E. Ippoliti and P. Carloni, J Chem Phys 141, 22D521 (2014)