Fishing for Knowledge: Physics Research Expands Understanding of Cell Biology
What do you know about cells, the fundamental structural unit of plant and animal life? All living cells have membranes that protect cellular integrity while controlling the flow of information and materials into and out of cells. A major component of cell membranes is lipid molecules, which form bilayered structures, while most of the work done inside cells is performed by proteins, linear molecules built from 20 different amino acids. Approximately 30 percent of the proteins in any given cell interact frequently with cell membranes or reside within the membranes to carry out their function.
This interaction between proteins and cell membranes is the focus of a new research paper from Associate Professor of Physics Gavin King and Professor of Physics Ioan Kosztin published in Scientific Reports. The study, “Multiple stochastic pathways in forced peptide–lipid membrane detachment,” was funded by a grant from the National Science Foundation and from the MU Research Board.
To study the interaction of proteins and cell membranes, King and Kosztin set up a conceptually simple experiment.
“Imagine you are going fishing, and you have a fishing rod, and in our case the fishing rod is an atomic force microscope,” King says. “We attach a lure, which is a short protein, to the end of the fishing rod and then very controllably and carefully we bring the lure down to the vicinity of a membrane. Sometimes the lure gets hooked or bitten by the fish or membrane, and when it does we can pull the lure back and ask, ‘How much force does it take to pull the lure out of the fish’s mouth?’”
(a) Experimental setup showing SecA2-11 interacting with a supported lipid bilayer. (b) Physical model. Peptide detachment involves the (c) last amino acid (AA) or (d) last and next-to-last AA, or occasionally the (e) last two AA from neighboring peptide chains.
Standard Model Needs an Upgrade
King says one curious result is that when the experiment was conducted repeatedly with the exact same variables, they got different results. He says there was no model available that could handle the complexity of the results, so he turned to theoretical physicist Kosztin to develop a new model.
“This fishing analogy is good but also imagine the air is very viscous and the lure is tiny, so any changes will lead to fluctuations, meaning the result will be by nature stochastic, or probabilistic,” Kosztin says. “There are very solid mathematical models that deal with stochastic quantities, but you will never be able to tell exactly in a given experiment what the actual force is to rupture or detach the protein from the membrane. The best you can do is to predict the probability distribution and the mean value of the detachment force for a large number of experiments. The existing models were not sufficient, so we had to take into account the complexity of the interaction.”
Kosztin came up with the theoretical framework, and King then tested that framework through experimentation, and both say their work has improved the predictive power of single molecule methodology.
“That’s an important driving force behind a lot of biophysics research,” King says. “We, as a community, are trying to improve the predictive power behind biological experiments.” Those experiments also showed there are numerous ways a protein can detach from a membrane, and that this separation can exhibit a “catch-bond” behavior.
“Imagine you are pulling on a rope—the general rule of thumb is if you pull on the rope harder it’s going to break faster, but a catch-bond is the opposite,” King says. “Much like a Chinese finger trap, the harder you pull on the trap the longer the trap lasts.”
He says an example of this catch-bond behavior could be a cell imbedded in an artery. “It has to be robust toward changes in blood flow around it—it doesn’t want to just pop off into the blood flow.”
Moving the Needle
Kosztin says the paper will provide the research community with a new and more accurate way to analyze their data when examining protein–membrane interactions.
King says it’s important to study these proteins if researchers want to better understand how the cell interacts with its cellular environment in order to create new drugs, for example.
“If you are a drug swimming around in extracellular space, and you want to influence the behavior of a cell, you have to go through a membrane in order to change the cell’s behavior,” King says. “Membrane proteins act as gatekeepers, so a drug tends to target these gatekeeper proteins and change their behavior if they can.”
King and Kosztin’s team also included Milica Utjesanovic and Tina Matin, both MU graduate students during the study, and Krishna Sigdel, a postdoctoral associate who is now an assistant professor of physics and astronomy at California State Polytechnic Institute.