Biology subjects

Anden, O.

Publications and source records attributed to Anden, O..

3 recordsLinked to original sources

bioRxiv2025

Structure and dynamics of a multidomain ligand-gated ion channel revealed under acidic conditions

Pentameric ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution, including key targets of biophysical studies and therapeutic development. However, the intrinsically allosteric, polymodal, modular nature of gating in this protein family presents persistent challenges to biophysical characterization. The bacterial channel DeCLIC constitutes a provocative model system for structure, function, and dynamics in this family, including a modulatory N-terminal domain (NTD). Previous closed structures of DeCLIC support a rationale for its inhibition by calcium via a site of conserved relevance in other family members; however, mechanisms of gating in DeCLIC and properties of its open state have remained unclear. Here we integrated structure-function methods including cryogenic electron microscopy (cryo-EM), molecular dynamics simulations and small-angle neutron scattering under acidic conditions to characterize a previously unreported conformation of DeCLIC with a fully hydrated pore. In contrast to previous structures, the low-pH open conformation captured by cryo-EM was stable and permeable in simulations, and consistent with solution-phase behavior as measured by small-angle scattering. We further captured an alternative closed state of the channel, evidently promoted by depletion of modulatory calcium at low pH, exhibiting dynamic rearrangements in the N-terninal domain. The expanded-pore structure evidently corresponds to a functional open state of DeCLIC, while calcium-site and NTD dynamics drive channel closure, providing a detailed template for biophysical characterization of modulatory mechanisms in ligand-gated ion channels and related systems. Significance StatementThe bacterial protein DeCLIC is a provocative representative of the pentameric ligand-gated ion-channel family. Like its eukaryotic relatives, DeCLIC is sensitive to external calcium, and incorporates a possibly disordered modulatory domain. But as for many ion channels, the details of DeCLIC activation have remained unclear, as no stable open state has been characterized. Combining biophysical methods, including cryogenic electron microscopy, molecular dynamics simulations, and small-angle neutron scattering, allows us to capture, validate, and characterize an evidently open state of DeCLIC, as well as a closed state with a disordered modulatory region. Details of these structures, their function, and their dynamics allow us to propose a mechanism for DeCLIC gating, as well as a generalized scheme for the larger protein family.

biophysics↗

bioRxiv2024

Engineering cardiolipin binding to an artificial membrane protein

Integral membrane proteins carry out essential functions in the cell, and their activities are often modulated by specific protein-lipid interactions in the membrane. Here, we elucidate the intricate role of cardiolipin (CDL), a regulatory lipid, as a stabilizer of membrane proteins and their complexes. Using the in silico-designed model protein TMHC4_R (ROCKET) as a scaffold, we employ a combination of molecular dynamics simulations and native mass spectrometry to explore the protein features that facilitate preferential lipid interactions and mediate stabilization. We find that the spatial arrangement of positively charged residues as well as local conformational flexibility are factors that distinguish stabilizing from non-stabilizing CDL interactions. However, we also find that even in this controlled, artificial system, a clear-cut distinction between binding and stabilization is difficult to attain, revealing that overlapping lipid contacts can partially compensate for the effects of binding site mutations. Extending our insights to naturally occurring proteins, we identify a stabilizing CDL site within the E. coli rhomboid intramembrane protease GlpG and uncover its regulatory influence on enzyme substrate preference. In this work, we establish a framework for engineering functional lipid interactions, paving the way for the design of proteins with membrane-specific properties or functions.

biochemistry↗

bioRxiv2024

Vestibular modulation by stimulant derivatives in a pentameric ligand-gated ion channel

Allosteric modulation of pentameric ligand-gated ion channels (pLGICs) is critical to the action of neurotransmitters and many psychoactive drugs. However, details of their modulatory mechanisms remain unclear, especially beyond the orthosteric neurotransmitter-binding sites. The recently reported prokaryotic channel sTeLIC, a pH-gated homolog of eukaryotic receptors in the pLGIC family, is thought to be modulated by aromatic compounds via a relatively uncharacterized modulatory site in the extracellular vestibule. Here, we show that sTeLIC is sensitive to potentiation by psychostimulant derivatives. By determining new cryo-EM and X-ray structures in closed and open states, and testing the impact of targeted mutations on electrophysiological behavior, we show that several amphiphilic compounds preferentially bind a vestibular pocket in the contracted open-state extracellular domain. This work provides a detailed structure-function mechanism for allosteric potentiation via a noncanonical lig- and site, with potential conservation in eukaryotic pentameric ligand-gated ion channels.

biophysics↗