Browsing by Author "Noskov, Sergei Yu."

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    Novel Electrostatic Mechanisms Controlling the Conformational Switching of L-plastin
    (2018-06-12) Fanning, John Keenan; Noskov, Sergei Yu.; Vogel, Hans J.; Maccallum, Justin L.; Prenner, Elmar J.; Ng, Kenneth Kai Sing
    L-plastin is an actin-bundling protein that promotes the motility of both hematopoietic and metastatic cancer cells. The high definition structure of the calcium-binding regulatory domain of human L-plastin was recently determined, allowing computational research on this portion of the protein. The Drude polarizable force field was used to provide accurate computational simulations of the calcium-binding domain in conjunction with experimental validation to shown that L-plastin can regulate calcium-binding, and thus actin-bundling, through internal electrostatic interactions. Through this work the Drude force field was also benchmarked, to show that it provides comparable results to classical force fields with the added ability to simulate polarizability. Overall, a novel mechanism which allows L-plastin to self-regulate its calcium-binding affinity was developed.
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    Uncovering Molecular Mechanisms in Control of Cardiac Ion Channels’ Function by Combined Computer Simulations and Experiments
    (2021-08-17) Miranda-Delgado, Williams Ernesto; Noskov, Sergei Yu.; Tieleman, Peter D.; Duff, Henry; Prenner, Elmar
    A myriad of cellular responses is dependent on selective membrane-permeation of charged species through membrane proteins known as ion channels. Among them, the ryanodine receptor (RyR2) and the human ether-a-go-go related gene (hERG1) channels are directly involved in the onset of cardiac arrhythmias via unknown mechanisms. Not surprisingly, the functions of these channels are tightly regulated by endogenous and exogenous ligands (e.g. membrane-lipids and drugs). Deciphering the thermodynamics and kinetics of these processes is key to better understand the pathophysiology of diseases and the design of new therapeutics. This thesis sheds light on the molecular mechanisms underpinning selective cation permeation and the lipophilic regulation of cardiac ion channels by combining computational and experimental electrophysiology/mutagenesis approaches. My studies on RyR2 firmly establish that the large cation-selective conductance achieved by this channel results from a narrow and short pore containing a wide selectivity filter and flanked by rings of negatively-charged residues. These features determine fast permeation of partially-dehydrated cations through reduction of desolvation penalties and the accumulation of coulombic repulsion. Furthermore, my work pointed to a structurally unstable SF as a critical element in the process of fast inactivation in hERG1 channels. These rapid conformational transitions control K+ permeation via spontaneous dehydration/re-hydration dynamics at the selectivity filter. Conversely, the pro-arrhythmic gain-of-function mutation hERG1-N629D significantly stabilized the filter in a state permeable to both K+ and Na+, constituting a first-of-its-kind approach for linking genomic information to a phenotype using structurally realistic models of hERG1 channel. Lastly, my research focused on the lipophilic regulation of hERG1 by ceramide-based probes. At the molecular level, the amphipathic nature of ceramides drives their accumulation at a unique crevice created by the non-swapped topology of hERG1, exhibiting preferential binding to the closed-state of the channel. I showed that ceramides are non-conventional tonic blockers that target the channel through the lipophilic route via a conformational selection mechanism. Overall, the new knowledge resulting from my doctoral thesis may help the future development of antiarrhythmic and anticancer therapies and for designing bio-inspired synthetic nanopores with potential industrial applications for water desalination and electricity generation.