New first author publication for PhD student Nicolas Barbera!

Congrats to Nik for his first lead-author publication! Online Now at Biophysical Journal

Molecular Dynamics Simulations of Kir2.2 Interactions with an Ensemble of Cholesterol Molecules
Nicolas Barbera, Manuela A.A. Ayee, Belinda S. Akpa*, Irena Levitan* (*co-corresponding)

Cover pic for website


Abstract: Cholesterol is a major regulator of multiple types of ion channels, but the specific mechanisms and the dynamics of its interactions with the channels are not well understood. Kir2 channels were shown to be sensitive to cholesterol through direct interactions with “cholesterol-sensitive” regions on the channel protein. In this work, we used Martini coarse-grained simulations to analyze the long (μs) timescale dynamics of cholesterol with Kir2.2 channels embedded into a model membrane containing POPC phospholipid with 30 mol% cholesterol. This approach allows us to simulate the dynamic, unbiased migration of cholesterol molecules from the lipid membrane environment to the protein surface of Kir2.2 and explore the favorability of cholesterol interactions at both surface sites and recessed pockets of the channel. We found that the cholesterol environment surrounding Kir channels forms a complex milieu of different short- and long-term interactions, with multiple cholesterol molecules concurrently interacting with the channel. Furthermore, utilizing principles from network theory, we identified four discrete cholesterol binding sites within the previously identified cholesterol sensitive region, which exist depending on the conformational state of the channel – open or closed. We also discovered that a 2-fold decrease in the cholesterol level of the membrane, which we found earlier to increase Kir2 activity, results in a site-specific decrease of cholesterol occupancy at these sites in both the open and closed states: cholesterol molecules at the deepest of these discrete sites shows no change in occupancy at different cholesterol levels, while the remaining sites showed a marked decrease in occupancy.

EMRLab alumna Manuela Ayee joins the ranks of the professoriate!

M AyeeCongratulations to Dr Manuela Ayee for starting her faculty career as Assistant Professor of Chemical Engineering and Chemistry at Dordt College. After completing her PhD with us in Chemical Engineering, Manuela spent 3 years as a postdoc with Dr Irena Levitan at UIC’s College of Medicine. There she expanded on her computational interests in the structure and mechanics of lipid layers and acquired a skillset in complementary experimental methods in cell biology. Several publications later, she is now launching her independent, interdisciplinary research career at Dordt College just as it makes its transition to Dordt University. Congrats, Manuela!

EMRLab undergraduate researcher wins top award at NC State Spring Symposium

Congratulations to Animal Science Honors student Nicholas Biondo for delivering an outstanding presentation of his CALS Honors research project at the 2018 Undergraduate Research and Creativity Symposium!  Of 265 presentations, 24 were recognized by faculty and postdoc judges as outstanding.

Nick’s poster, entitled “What physicochemical properties are good predictors of drug sequestration? An investigation in support of lipid resuscitation“, detailed his use of molecular simulations to compare the partitioning behaviors of two tricyclic antidepressants across a lipid interface representative of a therapeutic emulsion.

Highlighting an HBCU student leader participating in AIChE-MAC’s Leadership Development Initiative

At the 2017 American Institute of Chemical Engineers Annual Meeting, Dr Akpa had a chance to sit down with one of the student leaders from the Minority Affairs Committee Student Leadership Development Initiative.  In this interview, Jakari Jackson, a senior undergraduate at Prairie View A&M, shared his thoughts on leadership in his student chapter and his passion for chemical engineering as a tool for navigating the world. Jakari was one of several students who received a Minority Serving Institutions’ Student Travel Grant to attend the annual meeting. Our thanks to the AICHE Annual Fund and Doing a World of Good campaign for supporting this initiative!

Dr Akpa was 2017 Chair of the Minority Affairs Committee (MAC) and remains engaged with mentoring and leadership development activities as 2018 Past Chair of MAC.

Welcoming the new year with a new publication in Biophysical Journal!

Ayee-biophysj2017Congrats to Manuela Ayee on her first author publication in Biophysical Journal! This collaborative effort with the Levitan group employs experimental biophysical and biochemical tools, along with molecular modeling, to explore the influence of oxidized lipid species on membrane structure and the apparent inverse relationship between the mechanics of the lipid bilayer and those of the endothelial cell.

Molecular-Scale Biophysical Modulation of an Endothelial Membrane by Oxidized Phospholipids

Highlighted in a New & Notable feature