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Gulsevin, A.

Publications and source records attributed to Gulsevin, A..

2 recordsLinked to original sources
bioRxiv2021

The allosteric activation of α7 nAChR by α-conotoxin MrIC is modified by mutations at the vestibular site

-conotoxins are 13-19 amino acid toxin peptides that bind various nicotinic acetylcholine receptor (nAChR) subtypes. -conotoxin Mr1.7c (MrIC) is a 17 amino acid peptide that targets 7 nAChR. Although MrIC has no activating effect on 7 nAChR when applied by itself, it evokes a large response when co-applied with the type II positive allosteric modulator PNU-120596, which potentiates 7 nAChR response by recovering it from a desensitized state. Lack of standalone activity despite activation upon co-application with a positive allosteric modulator was previously observed for molecules that bind to an extracellular domain allosteric activation (AA) site at the vestibule of the receptor. We hypothesized that MrIC may activate 7 nAChR allosterically through this site. We ran voltage-clamp electrophysiology experiments and in silico peptide docking calculations to gather evidence in support of 7 nAChR activation by MrIC through the AA site. The experiments with the wild-type 7 nAChR supported an allosteric mode of action, which was confirmed by the increased MrIC + PNU-120596 responses of three 7 nAChR AA site mutants that were designed in silico to improve MrIC binding. Overall, our results shed light on allosteric activation of 7 nAChR by MrIC and suggest involvement of the AA site. Significance Statement-conotoxin MrIC (MrIC) is an allosteric agonist of the 7 nicotinic acetylcholine receptor (nAChR). This mode of action is unique among -conotoxins since these peptides typically act as orthosteric antagonists of nAChR. However, the mechanism of 7 nAChR activation by MrIC has been elusive so far. This work demonstrates that activation by MrIC is independent of the 7 nAChR orthosteric site and is related to a vestibular allosteric activation site at the extracellular domain of the receptor. Our experimental and computational studies identified the residues that play a role in allosteric activation and confirmed the utility of ensemble docking methods in understanding peptide - nAChR interactions, thus providing a basis for the design of peptides for allosteric modulation of nAChR.

biophysics↗
bioRxiv2020

Prediction of amphipathic helix - membrane interactions with Rosetta

Amphipathic helices have hydrophobic and hydrophilic/charged residues situated on opposite faces of the helix. They can anchor peripheral membrane proteins to the membrane, be attached to integral membrane proteins, or exist as independent peptides. Despite the widespread presence of membrane-interacting amphipathic helices, there is no computational tool within Rosetta to model their interactions with membranes. In order to address this need, we developed the AmphiScan protocol with PyRosetta, which runs a grid search to find the most favorable position of an amphipathic helix with respect to the membrane. The performance of the algorithm was tested in benchmarks with the RosettaMembrane, ref2015_memb, and franklin2019 score functions on six engineered and 44 naturally-occurring amphipathic helices using membrane coordinates from the OPM and PDBTM databases, OREMPRO server, and MD simulations for comparison. The AmphiScan protocol predicted the coordinates of amphipathic helices within less than 3[A] of the reference structures and identified membrane-embedded residues with a Matthews Correlation Constant (MCC) of up to 0.57. Overall, AmphiScan stands as fast, accurate, and highly-customizable protocol that can be pipelined with other Rosetta and Python applications.

biophysics↗