Computational investigation of pLGICs interacting with general anesthetics is surprisingly tricky. This article/chapter provides guidelines for reproducing the approach that we’ve refined over a decade. Sruthi gives some warnings for avoiding docking pitfalls and tips on running unbiased (traditional) molecular dynamics simulation. For more advanced users, she provides steps for rigorously calculating binding affinities and testing convergence.
Alchemical free energy perturbation is a rigorous technique the lab uses frequently for measuring ligand binding affinities. This new paper has an updated and simplified approach that we’ve developed over many years – motivated by challenges in measuring and interpreting binding affinities for membrane proteins. This approach even works for non-dilute reference state or a complex, phase-separated bulk! We’ve also included calculation of cholesterol affinities for 3 different GPCRs as a sample application.
Our new book chapter (in a great volume edited by Irena Levitan at the University of Illinois at Chicago) reviews our simulations of cholesterol and other sterols interacting with pLGICs. It also includes a brief teaser of Liam’s new coarse-grained simulations involving nAChRs in phase-separated quasi-neuronal membranes, and offers some simulation-inspired ideas for experiments with straightforward interpretations.
It’s official. Much appreciation to all who helped along the way – students, postdocs, collaborators, colleagues, referees, program officers, friends, mentors, family.
Kristen Woods, a Masters student in Computational and Integrative Biology has joined the group! Kristen was also here at Rutgers-Camden for her undergraduate degree and decided to stay at our unique campus for graduate school. She will add to the group’s growing ‘coarse-grained’ arm, which simulates complex neuronal membranes over longer length and time scales.
New article on interactions of general anesthetics with GABA(A) receptors in Journal of Biological Chemistry
Research on the mechanism of general anesthesia from our collaboration with Dr. Roderic Eckenhoff’s group at University of Pennsylvania, is now in press at J Biol Chem:
“A Novel Bifunctional Alkylphenol Anesthetic Allows Characterization of GABAA Receptor Subunit Binding Selectivity in Synaptosomes” by Kellie A. Woll, Sruthi Murlidaran, Benika J. Pinch, Jérôme Hénin, Xiaoshi Wang, Reza Salari, Manuel Covarrubias, William P. Dailey, Grace Brannigan, Benjamin A. Garcia, and Roderic G. Eckenhoff.
The experimental side of this work, carried out at Penn and Thomas Jefferson University, involved using click chemistry and photoaffinity labeling to detect differences in binding of the general anesthetic propofol* to subunits forming the GABA(A) receptor. The experiments were done in neurons, where general anesthesia actually takes place.
On the computational side, we used a sophisticated MD technique called Alchemical Free Energy Perturbation to calculate affinities of propofol for sites found in each interface between subunits, and we determined how small changes in the amino acids forming the sites can result in large differences in how strongly the anesthetic binds.
This was challenging because the differences are subtle, but important because GABA(A) receptors across the human central nervous system have many subtle differences with dramatic effects.
*in experiments, actually a propofol analog with modifications necessary for the experimental technique.
Dr Thomas Joseph MD PhD just started a postdoc at Penn in the Anesthesiology department with our collaborators in the Eckenhoff group. Tom is a computational researcher and he’ll be a very active visitor in the Brannigan group, carrying out simulations investigating membrane protein (esp GPCR) pharmacology!