Biology subjects

Joseph, T. T.

Publications and source records attributed to Joseph, T. T..

4 recordsLinked to original sources

bioRxiv2024

The blobulator: a webtool for identification andvisual exploration of hydrophobic modularity inprotein sequences

While contiguous subsequences of hydrophobic residues are essential to protein structure and function, as in the hydrophobic core and transmembrane regions, there are no current bioinformatics tools for module identification focused on hydrophobicity. To fill this gap, we created the blobulator toolkit for detecting, visualizing, and characterizing hydrophobic modules in protein sequences. This toolkit uses our previously developed algorithm, blobulation, which was critical in both interpreting intra-protein contacts in a series of intrinsically disordered protein simulations [1] and defining the "local context" around disease-associated mutations across the human proteome [2]. The blobulator toolkit provides accessible, interactive, and scalable implementations of blobulation. These are available via a webtool, a VMD plugin, and a command line interface. We highlight use cases for visualization, interaction analysis, and modular annotation through three example applications: a globular protein, two orthologous membrane proteins, and an IDP. The blobulator webtool can be found at www.blobulator.branniganlab.org, and the source code with pip installable command line tool, as well as the VMD plugin with installation instructions, can be found on GitHub at www.GitHub.com/BranniganLab/blobulator.

bioinformatics↗

bioRxiv2024

Propofol directly binds and inhibits skeletal muscle ryanodine receptor 1 (RyR1)

As the primary Ca2+ release channel in skeletal muscle sarcoplasmic reticulum (SR), mutations in the type 1 ryanodine receptor (RyR1) or its binding partners underlie a constellation of muscle disorders, including malignant hyperthermia (MH). In patients with MH mutations, exposure to triggering drugs such as the halogenated volatile anesthetics biases RyR1 to an open state, resulting in uncontrolled Ca2+ release, sarcomere tension and heat production. Restoration of Ca2+ into the SR also consumes ATP, generating a further untenable metabolic load. When anesthetizing patients with known MH mutations, the non-triggering intravenous general anesthetic propofol is commonly substituted for triggering anesthetics. Evidence of direct binding of anesthetic agents to RyR1 or its binding partners is scant, and the atomic-level interactions of propofol with RyR1 are entirely unknown. Here, we show that propofol decreases RyR1 opening in heavy SR vesicles and planar lipid bilayers, and that it inhibits activator-induced Ca2+ release from SR in human skeletal muscle. In addition to confirming direct binding, photoaffinity labeling using m-azipropofol (AziPm) revealed several putative propofol binding sites on RyR1. Prediction of binding affinity by molecular dynamics simulation suggests that propofol binds at least one of these sites at clinical concentrations. These findings invite the hypothesis that in addition to propofol not triggering MH, it may also be protective against MH by inhibiting induced Ca2+ flux through RyR1.

pharmacology and toxicology↗

bioRxiv2022

Structural mechanism of leaflet-specific phospholipid modulation of a pentameric ligand-gated ion channel

Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To elucidate the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open conformation. The structure shows a bound phospholipid in an outer leaflet site, and conformational changes in the phospholipid binding site unique to the open state. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the open state of a pLGIC by specific, state-dependent binding to this site.

biophysics↗

bioRxiv2020

Mechanistic insights into volatile anesthetic modulation of K2P channels

K2P potassium channels are known to be modulated by volatile anesthetic (VA) drugs and play important roles in clinically relevant effects that accompany general anesthesia. Here, we utilize a photoaffinity analog of the VA isoflurane to identify a VA binding site in the TREK1 K2P channel. The functional importance of the identified site was validated by mutagenesis and biochemical modification. Molecular dynamic simulations of TREK1 in the presence of VA found multiple neighboring residues on TREK1 TM2, TM3 and TM4 that contribute to anesthetic binding. The identified VA binding region contains residues that play roles in the mechanisms by which heat, mechanical stretch, and pharmacological modulators alter TREK1 channel activity and overlaps with positions found to modulate TASK K2P channel VA sensitivity. Our findings define molecular contacts that mediate VA binding to TREK1 channels and suggest a mechanistic basis to explain how K2P channels are modulated by VAs.Competing Interest StatementThe authors have declared no competing interest.View Full Text

pharmacology and toxicology↗