Scientists measure cellular membrane thickness inside cells for the first time

LA JOLLA, CA—Scientists have long known that cellular membranes vary in thickness, but measuring those differences inside actual cells has been out of reach. Until now, scientists could only measure membrane thickness in simplified, artificial systems: lipids in a test tube, stripped of the proteins and complexity found in real cells. Now, scientists at Scripps Research have developed a method that measures membrane thickness directly inside cells for the first time, revealing variations that were previously invisible.

The findings, published in the Journal of Cell Biology on December 26, 2025, build upon an existing computational method called Surface Morphometrics developed in the laboratory of Danielle Grotjahn, associate professor at Scripps Research and senior author of the study. Using advanced imaging techniques and computational analysis, this method unveils how membrane composition changes across various cell states and in response to disease. Grotjahn and her team used an innovative approach that also allows researchers to view cellular structures in a near-native context—providing greater understanding of how cells behave in their natural state. These results could help unlock new insights into cell biology and improve drug development.

“Membranes don’t exist in isolation—they’re shaped by the proteins and structures around them,” says Grotjahn. “By measuring thickness inside intact cells, we can start to understand how all of these components work together.”

Cell membranes are fundamental to life. They define the boundaries of cells and their internal components, called organelles, which include the mitochondria and endoplasmic reticulum, among others. The thickness of these membranes influences how proteins embed within them, how molecules pass through and how organelles carry out their specialized tasks.

“The Surface Morphometrics pipeline allows for an unprecedented look at cellular organization,” says Michaela Medina, a postdoctoral researcher in the Grotjahn lab and co-first author. “Even the smallest changes in membrane thickness can have an outsized impact on biological function.”

Applying their method to animal and yeast cells, the team discovered striking variations. In the mitochondria—the compartments that generate energy for the cell—the outer membrane was significantly thinner than the inner membrane in both cell types, a difference that likely reflects how the quantity of lipids and proteins drives its distinct composition. In mammalian cells, even specialized folds within the inner membrane, called cristae, had thicker membranes than regions pressed against the outer membrane. The researchers also found that membrane thickness correlates with curvature, suggesting that proteins embedded in curved regions may be shaping membrane structure.

The Surface Morphometrics pipeline also includes a component called “patch-based” analysis, which pinpoints membrane characteristics at specific protein locations. Developed by Ya-Ting “Atty” Chang, a graduate student at the Skaggs Graduate School of Chemical and Biological Sciences and co-first author of the study, the analysis works like a molecular “cookie cutter,” isolating small circular sections of membrane where the protein of interest resides. Researchers can then measure the characteristics of that tiny “patch” and compare it to other membrane areas without that protein, revealing how proteins and membranes influence each other.

“There are likely many proteins on membrane surfaces that we haven’t discovered yet,” says Chang. “Patch-based analysis gives us a way to find them—by scanning for patterns that hint at a protein’s presence before we even know to look for it.”

Grotjahn and her team applied patch-based analysis to examine ATP synthase, a protein that generates cellular energy. They found this protein tends to cluster in regions where membranes are both curved and unusually thick—a pattern that would have been impossible to detect without the ability to zoom in on precise locations.

With these tools in hand, the team is poised to investigate questions that were previously out of reach—mapping how proteins move over time, how they reshape the membranes around them and what new biology might be hiding in plain sight.

In addition to Grotjahn, Medina, and Chang, authors of the study, “Surface morphometrics reveals local membrane thickness variation in organellar subcompartments,” include Hamidreza Rahmani and Daniel Fuentes of Scripps Research; Benjamin A. Barad of Scripps Research and Oregon Health & Science University School of Medicine; Mark Frank of Oregon Health & Science University School of Medicine; Zidan Khan and Frederick A. Heberle of the University of Tennessee, Knoxville; and M. Neal Waxham of University of Texas Medical School at Houston.

This work is supported by the ARCS (Achievement rewards for college scientists) foundation, National Institute of Allergy and Infectious Disease (NIAID) grant 5T32AI170496-03 NIH grant R01GM138887, the William Wheless III endowment, the Collins Medical Trust, The Pew Scholars Program, Nadia’s Gift Foundation Innovator Award of the Damon Runyon Cancer Foundation (DRR-65-21) and the National Institutes of Health (NIH) grant RF1NS125674. This work used equipment supported by NIH grant S10OD032467.

About Scripps Research

Scripps Research is an independent, nonprofit biomedical research institute ranked one of the most influential in the world for its impact on innovation by Nature Index. We are advancing human health through profound discoveries that address pressing medical concerns around the globe. Our drug discovery and development division, Calibr-Skaggs, works hand-in-hand with scientists across disciplines to bring new medicines to patients as quickly and efficiently as possible, while teams at Scripps Research Translational Institute harness genomics, digital medicine and cutting-edge informatics to understand individual health and render more effective healthcare. Scripps Research also trains the next generation of leading scientists at our Skaggs Graduate School, consistently named among the top 10 US programs for chemistry and biological sciences. Learn more at www.scripps.edu.

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