Faculty publish in respective discipline Annual Review journals
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Two Richard and Loan Hill Department of Biomedical Engineering faculty were recently highlighted in their fields Annual Review journals. BME Associate Professors Ao Ma’s work appeared in the Annual Review of Physical Chemistry while Zhangli Peng’s work appeared in the Annual Review of Fluid Mechanics.
Both are members of the UIC Center for Bioinformatics and Quantitative Biology.
Ao Ma
Ma’s featured research focuses on reaction coordinates, which are the few essential bonds of a protein that control its functional processes, including conformational change.
“Reaction coordinates are one of the most important concept in protein biophysics,” he said. “That’s because it is one of the central problem for protein studies.”
Despite recent advances in protein biophysics, including the AlphaFold, Google’s 2024 Nobel Prize-winning project, researchers’ understanding of how proteins function has not really changed.
“This is because we don’t really understand yet how structure determines function,” Ma said.
Protein conformational changes are an ensemble of functionally important shapes or structures, and the transitions between these conformations are critical for understanding protein function.
“The key idea to understanding protein conformational changes are so-called reaction coordinates,” Ma said. “Even though a protein has at least tens of thousands of coordinates, all of them are moving at any given time. But, for any given conformational change, this process is controlled by a very small number of highly connected coordinates, which we call reaction coordinates. So, if we can find the reaction coordinates of a specific conformational change then we can understand how it happens.”
One of Ma’s papers into this research, published in Nature Communications, in collaboration with his postdoctoral associate Huiyu Li, introduces a novel computational method that enables efficient predictive sampling of functionally important large-scale protein conformational changes, which solved a decades-long challenge.
The review article details both the history of the field of reaction coordinates and his teams’ own contribution with their recent breakthrough.
“The review connects the dots to the current status and how we got there and the collective effect of these individual contributions, how they push the field forward,” Ma said.
Zhangli Peng
Peng’s review focuses on the fluid mechanics of blood cells and vesicles squeezing through narrow constrictions, such as splenic slits, pulmonary capillaries, vascular endothelial gaps, and microfluidic channels.
Based on previous research, this article discusses the hydrodynamics of blood cells and vesicles through a narrow constriction, focusing on how cells deform to pass through tapered constrictions and affect their resistance as they squeeze through constrictions of various geometries.
More specifically, Peng’s research focused on the ways that red blood cells pass through the spleen and white blood cells pass through ports during immune responses, including the process of cancer cells passing throughout the body causing metastasis. It also focuses on understanding the behavior of a general process, such as cells passing through constrictions when subjected to forces or displacements, covering motion, energy, and force interaction.
Peng’s research can be applied to more artificial models, such as those using lipid particles, which are a very popular drug delivery option, and how they pass through different points in the microfluidics for your body.
“Cells or vesicle are typically eight microns, but the pore is 0.3 micron,” Peng said. “This is different than usual construction because the channel is larger than the cell or comparable to the cell, but here the channel actually is much smaller than a cell.”
Peng noted that it remains a challenge to understand how, through the intricate biological and mechanical processes, the microcirculation of blood through the smallest vessels—arterioles, capillaries, and venules—can function with exceptional efficiency and robustness.
This article comes from previous research with Peng’s collaborators Annie Viallat of the CNRS, Aix-Marseille University, France, and Yuan-Nan Young of the New Jersey Institute of Technology Department of Mathematical Sciences.
Ma and Peng also aim to collaborate on bridging length scales from molecules to cells to understand biophysics in physiology and pathology.
“By integrating our complementary expertise, we will investigate how mutations in cytoskeletal proteins induce conformational changes at the molecular level and how these alterations influence cellular mechanical properties and the ability of cells to traverse physical barriers, such as endothelial caps in the body,” Peng said.
They also plan to co-host the CBQB Journal Club in Biophysics together in fall 2026.