Simulation of ion transport and substrate translocation through nanopores
Final Report Abstract
In this project the transport of ions and substrates through biological nanopores was investigated mainly using classical molecular dynamics (MD) simulations. Based on earlier successes when comparing similar simulation data with experimental electrophysiology findings using KCl as salt, more bulky salts were used. Again excellent agreement with experiment was achieved for the pore conduction leading to interesting insight into the interaction pattern of the ionic particles and the channel walls. For transport through the outer membrane protein F (OmpF) from Escherichia coli it could be shown that more bulky ions need to obtain the proper orientation before they can pass the narrowest part of the pore. The full-atomistic MD simulations were also able to explain the weak anion selectivity of the N-acetylneuraminic acid-inducible (NanC) channel. Furthermore, this pore shows a conductance asymmetry with respect to the direction of the applied voltage. This feature based could be explained on a molecular level. A mutation was proposed which possibly makes a reasonable molecular diode based from this channel. The studies on OmpF and NanC employed applied field simulations. For channels with low conductivities this is still unfeasible for routine calculations. One of these channels, OprO, was studied in detail using free energy calculations. OprP is an outer membrane protein of Pseudomonas aeruginosa and is involved in high-affinity uptake of phosphate under phosphate starvation conditions. To understand the selectivity for the transport of specific ions, the free energy profiles for the OprP porin was studied to define the energetics of phosphate, sulfate, chloride, and potassium ion transport. Atomic-level analysis revealed that the overall electrostatic environment of the channel was responsible for the anion selectivity of the pore, while the particular balance of interactions between the permeating ions and water as well as channel residues drove the selectivity between different anions. A detailed investigation of the structurefunction relationship of OprP was inevitable to decipher the anion and phosphate selectivity of this porin in particular and to broaden the present understanding of the ion selectivity of different channels. To this end we investigated the role of the central arginine of OprP, R133, using mutations in terms of its effects in selectivity and ion transport properties of the pore. Moreover, mutations of the single negatively charged residue (D94) among several positively charged residues in the two central binding sites for phosphate were performed in silico. The presence of this negatively charged residue in a binding site for negatively charged phosphate ions is highly surprising due to the potentially reduced binding affinity. Detailed analysis indicated that this anionic residue in the phosphate binding site, despite its negative charge, maintained energetically favorable phosphate binding sites in the central region of the channel. At the same time it decreased the residence time thus preventing excessively strong binding of phosphate that would oppose phosphate flux through the channel. Two-dimensional free-energy calculations have been determined for the transport of some antibiotics through the outer membrane pores OmpC and OprP. This is a first step in a detailed understanding of molecular interactions during the translocation process. Studies in this direction will be continued. Moreover, a new coarse-grained Brownian dynamics code is being developed and tested for the transport of ions and substrate molecules. This code allows for an explicit full-atom description of parts of the channel and the substrates as well. This development tries to fill the gap between standard Brownian dynamics simulation with static pores and fully flexible all-atom MD simulations.
Publications
- Probing the Transport of Ionic Liquids in Aqueous Solution Through Nanopores, J. Phys. Chem. Lett. 2, 2331–2336 (2011)
N. Modi, P. R. Singh, K. R. Mahendran, R. Schulz, M. Winterhalter and U. Kleinekathöfer
- Feature article: Computational modeling of ion transport through nanopores, Nanoscale 4, 6166–6180 (2012)
N. Modi, M. Winterhalter and U. Kleinekathöfer
(See online at https://doi.org/10.1039/c2nr31024d) - Modeling the Ion Selectivity of the Phosphate Specific Channel OprP, J. Phys. Chem. Lett. 3, 3639–3645 (2012)
N. Modi, R. Benz, R. E. W. Hancock and U. Kleinekathöfer
(See online at https://doi.org/10.1021/jz301637d) - Role of the central arginine R133 towards the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation, Biochemistry 52, 5522–5532 (2013)
N. Modi, I. Bárcena-Uribarri, M. Bains, R. Benz, R. E. Hancock and U. Kleinekathöfer
(See online at https://doi.org/10.1021/bi400522b) - Simulation of Ion Transport through an N-Acetylneuraminic Acid-Inducible Membrane Channel: From Understanding to Engineering, J. Phys. Chem. B 117, 15 966–15 975 (2013)
J. Lu, N. Modi and U. Kleinekathöfer
(See online at https://doi.org/10.1021/jp408495v) - Tuning the affinity of anion binding sites in porin channels with negatively charged residues: Molecular details for OprP, ACS Chem. Biol.
N. Modi, I. Bárcena-Uribarri, M. Bains, R. Benz, R. E. Hancock and U. Kleinekathöfer
(See online at https://doi.org/10.1021/cb500399j)
