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Computational study of the molecular details of ion permeation across the formate-nitrite transporters

dc.contributor.advisorHub, Jochen Dr.
dc.contributor.authorAtkovska, Kalina
dc.titleComputational study of the molecular details of ion permeation across the formate-nitrite transportersde
dc.contributor.refereeTittmann, Kai Prof. Dr.
dc.description.abstractengThe selective flux of molecules across biological membranes is essential for the normal function of any cell, and is governed by diverse membrane transport proteins. Historically, the focus in the membrane transport field was placed on cation channels of excitable tissues. Although this picture has changed in recent decades, there is still a world of non-mammalian membrane transport proteins, and proteins for transport of anions or neutral solutes, that is largely unexplored. The goal of this work is to quantitatively describe the molecular details of permeation across the formate-nitrite transporters (FNTs). FNTs transport a range of small monovalent anions across the membrane in bacteria, archaea, fungi, parasites, and green algae. Structurally, they share a fold with the aquaporin water channel, however, they have no sequence homology, and exhibit a different geometry of the permeation pore. Despite their almost ubiquitous nature, many aspects of their permeation mechanism are still unknown. It is not yet entirely clear whether they function as channels or transporters, or whether the family contains proteins of both types. A proton coupling to the permeation process has been strongly suggested, however, its exact nature has remained elusive. The role of a highly-conserved histidine residue in the center of the permeation pore has been debated. Finally, it is not certain whether all FNTs fit under the umbrella of one unifying fundamental mechanism of function. In this thesis, atomistic molecular dynamics (MD) simulations were employed to study the permeation mechanism across all FNT subfamilies with known structure: the nitrite channel NirC, the formate channel FocA, and the hydrosulfide channel HSC. The free energy profiles for permeation of multiple substrates across the FNTs were obtained by potential of mean force (PMF) calculations. The possibility of a "knock-on" permeation mechanism was studied using computational electrophysiology simulations. The role of the central histidine residue was thoroughly investigated by accounting for different protonation states, and by studying the details of its protonation using both, microscopic and macroscopic methods. Finally, the substrate protonation during permeation was studied using combined quantum mechanics/molecular mechanics (QM/MM) simulations. These calculations led to a general picture of the permeation across the FNTs, revealing that anions are not able to completely traverse the pore, and need to be therefore protonated in order to complete the permeation. This process was studied with most details in NirC. The permeation seems to occur in the following way: first, the central histidine protonation and anion binding in the pore occur in a coupled manner, after which the central histidine protonates the permeating anion, thereby weakening its binding and enabling its release from the pore. In FocA, an additional level of complexity is present in the permeation process, represented by flexible regions in the cytoplasmic portion of the protein. Such a general mechanism allows for high adaptability depending on the metabolic context and current needs of the cell, since in principle, it has the capacity for both, export and import of substrates, with or without proton
dc.contributor.coRefereeSteinem, Claudia Prof. Dr.
dc.subject.engformate-nitrite transportersde
dc.subject.engmolecular dynamicsde
dc.subject.engpotential of mean forcede
dc.subject.enganion channelde
dc.affiliation.instituteGöttinger Graduiertenschule für Neurowissenschaften, Biophysik und molekulare Biowissenschaften (GGNB)de
dc.subject.gokfullBiologie (PPN619462639)de

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