Architecture of Bacterial Cell Division Protein FtsZ Polymers

BPJ_113_8.c1.inddFtsZ is a self-assembling protein that forms the contractile ring guiding the cell division machinery in most bacteria. FtsZ is structurally homologous to tubulin, the subunit of eukaryotic microtubules. FtsZ monomers associate head-to-tail forming  single-stranded filaments that hydrolyze GTP, in a partially understood process. However, how FtsZ filaments organize in the dynamic division ring is still a challenging problem. Rather than forming a well-defined structure, such as band or tubule, FtsZ filaments laterally associate among them in a relatively disordered fashion.  FtsZ filaments bind partner and regulatory proteins, including those tethering them to the inner face of the plasma membrane.

The cover image for the October 17 issue of Biophysical Journal is an artistic representation of the organization that we propose for FtsZ assemblies.  FtsZ filaments made of FtsZ monomers laterally associate through the disordered C-terminal tails, forming loose bundles. Small-angle X-ray solution scattering results (exemplified by the graph on the left) indicated a characteristic 7 nm center-to-center lateral spacing between FtsZ filaments. By modeling comprehensive building and scattering calculations we saw that multiple associated filaments of variable curvature and length were required to reproduce the X-ray scattering features. These calculations also showed a 2-nm gap was left between core filament structures. We hypothesized that the gap would be bridged by the FtsZ intrinsically disordered C-terminal linker region, as in the model bundle in the center of the image. Cryo-electron microscopy provided views of unstained individual assemblies in vitrified solutions (blue background in the bottom half). Analyzing polymers assembled from FtsZ protein constructs with diverse C-termini supported the model.

Combining several biophysical approaches has provided insight into the self-organizing properties of FtsZ that we think underlie the assembly of the bacterial division ring. It should be noted that bacterial division is still a clinically unexplored target for the discovery of new antibacterials needed to counter the spread of antibiotic resistant pathogens.

-Sonia Huecas, Erney Ramirez-Aportela, Albert Vergoñós, Rafael Nuñez-Ramirez, Oscar Llorca, David Juan-Rodriguez, María A. Oliva, Patricia Castellen, and José M. Andreu


Importance of Biophysics in Breast Cancer Progression

October is Breast Cancer Awareness Month in the US. We spoke with University of California, San Diego graduate student Pranjali Beri and her PI, BPS member Adam J. Engler, about their research on breast cancer and other epithelial-based cancers. 

What is the connection between your research and cancer?

Cancer is the second leading cause of death in the US, resulting in approximately 600,000 deaths in 2016. The negative prognosis associated with cancer is due in large part to metastasis of a primary tumor. Cancer metastasis is the process by which tumor cells leave the primary tumor, enter the blood stream (intravasation), exit the blood stream at a different site in the body (extravasation), and establish a secondary tumor. However, tumors are exceedingly heterogeneous and only a small fraction of cancer cells from the primary tumor are capable of establishing secondary tumors. The metastatic potential of identical solid tumor types also varies from patient-to-patient due to expression differences of critical markers, making it nearly impossible to identify a universal biomarker that can predict metastatic potential of all solid tumors.

fig 1 A

Cancer cell migration away from the primary tumor is driven, in part, by physical interactions between cells and the surrounding extracellular matrix. Protein clusters known as focal adhesions allow cells to attach to the matrix proteins, and stability and strength of these attachments plays a role in regulating cancer cell migration. Our research is attempting to understand the link between adhesion strength via focal adhesions and cancer cell dissemination. In our recently publication, we quantify population adhesion strength of various epithelial cancer cell lines by utilizing a spinning-disk shear assay (Figure 1a). The shear stress required to detach 75% of the cell population serves as a metric to describe the adhesion strength of that population. In the presence of conditions that mimic the tissue adjacent to tumors, e.g. low divalent cations, we found that heterogeneous adhesion strength for the most aggressive cells indicate that subpopulations within aggressive cell lines were capable of metastatic behavior. This is similar to the small fraction of the primary tumor previously thought to contain stem cell-like properties of self-renewal, differentiation, and migration.

fig 1 B

Currently, our research further seeks to sort, capture, and analyze cells with more labile focal adhesions in response to stromal cation concentrations. We have developed a parallel plate flow chamber assay to isolate weakly adherent cells (Figure 1b) and characterize their migratory propensity in relation to strongly adherent as well as unselected cell populations. By demonstrating that there is a link between adhesion strength and migratory propensity of the cancer cells, we can use it as a biophysical marker for metastatic potential.

Why is your research important to those concerned about cancer?

Epithelial tumors, or carcinomas, are the most common type of cancer. There is no universal biomarker that acts as an indicator for metastatic potential. However, most epithelial cancers undergo metastasis. Having a physical indicator of metastasis can be beneficial in identifying the aggressiveness of a tumor and its likelihood of forming secondary metastases, independent of the type of epithelial tumor that it is.

How did you get into this research?

Throughout my undergraduate career, I have been interested in microfluidic devices and their applications as diagnostic devices. In graduate school, I joined the Engler lab in order to apply my microfluidics background towards cancer metastasis research.

How long have you been working on it?

I began working with microfluidic devices during my undergraduate studies. However, it was in graduate school that I used it to study cancer cell dissemination.

Do you receive public funding for this work? If so, from what agency?

I am currently funded by the National Science Foundation through their Graduate Research Fellowship Program. This research is also funded by the National Institute of Health and the Department of Defense Congressionally Directed Medical Research Program.

Have you had any surprising findings thus far?

Tissue adjacent to tumors has dramatically lower ion concentrations than in the tumor. In our previous publication, heterogeneity is most pronounced in highly metastatic cancer cell lines, but only when exposed to low ion conditions that mimic adjacent tissue; in the presence of high cation concentration, akin to the tumor microenvironment, metastatic cells are mechanically indistinguishable from their non-metastatic counterparts. This shift in adhesion strength was not present in non-metastatic cancer cell lines but was present in epithelial cancer cell lines from other tumors as well, including prostate and lung. While these previous studies could isolate the strongly adherent fraction remaining attached, recent experiments using flow chamber assays indicate that weakly adherent cells from the same cell lines display increased migration speed and are more processive in comparison to unsorted or strongly adherent populations. These results indicate that adhesion strength can potentially act as a biophysical marker of metastatic potential, and that the weakly adherent cells are likely to have the highest metastatic potential.

What is particularly interesting about this work from the perspective of other researchers?

Our fluidic-based separation method could allow us to isolate cancer cells by their metastatic potential. The adhesion strength-based separation method can serve as a potential prognostic device that exposes patient biopsies to shear stress, correlates weakly adherent cell isolation with metastatic potential, and makes a prognostic determination about the likelihood to metastatic disease in the future.

What is particularly interesting about this work from the perspective of the public?

By establishing the link between adhesion strength of the cells in the tumor and the metastatic potential of the tumor, we can ascertain the aggressiveness of patient tumors and tailor treatments accordingly.

An Optically Induced Electrokinetics Microfluidics Chip

BPJ_113_7.c1.inddUsing florescence molecules for bio-marking of cells is a widely accepted technology. However, the auto-fluorescence on the surface of living cells strongly influences the fluorescence-based detection of labeled molecules and is also harmful to cells. Then again, cell dielectric information can be obtained through non-invasive and label-free techniques, which have been shown as a possible bio-marking method.  For instance, the structure-based microfluidics method is a prevalent technique that can obtain cell membrane capacitance/conductance through use of custom-designed microfluidics structures. However, the measurement efficiency and performance of this scheme depend strongly on the use of microstructures with specific and sophisticated designs tailored to the cell size. The microstructures also cannot be altered after they are fabricated by the conventional micro-matching technique. In our paper, we report a new method to determine cell dielectric properties by using a coupled optical-electrical based microfluidics technique.

The cover image for the October 3 issue of the Biophysical Journal is an illustration of the optically induced electrokinetics approach developed by our team to acquire the cellular electrical conductance and capacitance using a specialized microfluidics chip. In the foreground of the cover is an exploded view of the optically induced electrokinetics (OEK) microfluidics chip which is able to generate localized force to trap each individual cell. The nine red and yellow pillars are the simulation results of the optically projected virtual electrodes showing the electric field distribution in the OEK microfluidic chip. In the back of the illustration is a light projector and a microscope. They are used to direct and shrink the light patterns projected onto the OEK microfluidics chip to trap the cells.

This image was inspired by combing the theoretical simulation and experimental approach we performed in this study. It presents how the incident light can trap individual cells using the optically induced electrokinetics forces exerted on the cells.  Depending on how each cell reacts to the exerted electrokinetics forces, we can determine the dielectric parameters of individual cells using the specialized microfluidics chip shown in the cover image.

—Yuliang Zhao, Lianqing Liu, Yuechao Wang, Wen Jung Li, Gwo-Bin Lee, Wenfeng Liang

Rallying for Medical Research so that Young Scientists Can Have Research Careers

Rally med research 2017

The Rally for Medical Research is a truly inspiring event that was established in 2013. Held every September, this event organized on Capitol Hill continues to grow, bringing together national organizations and people in support of Medical Research. The purpose of the rally is to call on the nation’s policy makers to make research funding for the National Institutes of Health (NIH) a national priority and raise awareness about the importance of research funding.

This year, I had the opportunity to attend the Rally and share my own story with top IL policy makers on behalf of the Biophysical Society. The Rally brought together medical doctors, scientists, patients, and organizations to lobby for robust, sustained, and predictable funding for the NIH by increasing the current budget by 2 billion dollars for fiscal year 2018 and to ask Congress to increase the budget caps on non-defense discretionary spending that were imposed by the Budget Control Act of 2011.

I went to the rally as a former research scientist in order to speak out for the early career scientist that are and will be affected by sequestration. I, myself, was a scientist affected by this – having studied and worked in multiple labs that struggled to maintain their funding. As a result, I had to make a difficult decision for myself: to continue on in a field that does not seem to value me or to move on to something that will. I chose the latter. While meeting with the Senate and Congress Houses for my state, I was able to relay to key policy makers how sequestration and cutting the NIH budget affect scientists, like myself, and how many of us have already responded: scientists may leave, many of us already have; whether that be moving to the private sector moving to countries that have sustained funding.  This also dissuades students from ever entering the field.

Through this experience, myself, a former medical research scientist, I’ve learned a lot, not only about lobbying but also about how politics in general works, and how as a constituent we can instill change. So last week, with my own personal story of the struggles of being a scientists in today’s market, I was able to convey my story along with the story of others (many of us from IL met with policy makers at the offices of congressman to the Senate Offices) with the hopes of reframing how these politicians see current policies involving medical research and helping to convert that idea into the language of government policy.  I hope I was able to make a difference and hopefully give a face to the affected scientist.


–Vidhya Sivakumaran, BPS member

Understanding Alzheimer’s Disease through Biophysics Research

September 21 is World Alzheimer’s Day. Alzheimer’s disease is the leading cause of dementia, from which 47 million people worldwide suffer. It affects memory, thinking, orientation, comprehension, calculation, learning capacity, language, and judgement. 

In recognition of World Alzheimer’s Day, we spoke with two Biophysical Society members whose research aims to improve understanding of the mechanisms behind Alzheimer’s and other neurodegenerative diseases.

Liz Rhoades, University of Pennsylvania


What is the connection between your research and Alzheimer’s disease?

We study the protein tau, which is a microtubule associated protein.  In Alzheimer’s and other neurodegenerative disorders, tau forms fibrillar aggregates that are deposited in brain tissue.  There are six isoforms of tau found in adult humans and alteration in the amounts of the isoforms are linked to disease development. Interactions of tau with microtubules are normally regulated by phosphorylation and tau aggregates derived from patient tissues are hyperphosphorylated, providing a link between loss of native tau function and disease as well.

Why is your research important to those concerned about Alzheimer’s?

We are working to understand basic aspects of tau function because we of the insight it provides to loss of function in disease.  Despite rather intensive study, molecular details of tau function are still lacking.  This is at least in part due to the fact that tau is large intrinsically disordered protein and thus it is challenging to characterize its structural features, particularly when associated with tubulin (the soluble building blocks of microtubules) and microtubules. For example, a few years ago, we observed that tau binds to soluble tubulin, a feature that had not previously received much attention. Our results suggests that it binds with similar affinity to tubulin as it does to microtubules which suggests that understanding how mutation impacts its interactions with tubulin is as important as characterizing how It interacts with microtubules. This is important because therapeutic strategies may very well involve targeting interactions between tau and its functional binding partners – we need to know who those partners are and the relevant features of the interaction!


The image here is from a paper that was published in PNAS last fall. It shows tau binding to two soluble tubulin dimers, and is based on our single molecule FRET measurements. It highlights how tau retains a primarily disordered state while binding and initiating tubulin polymerization. 

How did you get into this area of research?

We had been looking at tau aggregation in the lab for a couple of years, and then I had a few students – two graduate students and an undergraduate –  who were very interested in working with tubulin.  They were they ones who really pushed to get things up and running.  Anyone who has ever done a tubulin purification in their lab knows that this is not a trivial undertaking!

How long have you been working on it?

6 or 7 years

Do you receive public funding for this work? If so, from what agency?

In the past we received funding from NSF (MCB)  and currently we receive funding from NIH (NIA).

Have you had any surprise findings thus far?

I think most findings I get excited about are surprises, but there are three that I can think of as particularly surprising.  The first was that tau binding to soluble tubulin had been largely overlooked in previous studies. We started working with soluble tubulin because it was easier for us to use in single molecule experiments (one of our primary tools) and only as we began to get interested results, do we recognize that there really was not a deep literature on tau-tubulin. The second was the tau point mutants linked to different neurodegenerative disorders bound more tightly to tubulin than the wild-type tau.  Our expectation based on the tau-microtubule literature was the mutation should decrease the binding affinity.  We are still working to understand the impact of this on tau function.  The third is that a region which flank the microtubule binding region has a high affinity for tubulin and allows for tau to bind to multiple tubulin dimers simultaneous to form a ‘fuzzy complex’.  This work was published in Biophysical Journal this summer.

What is particularly interesting about the work from the perspective of other researchers?

I think some of it is probably methodology – we are using single molecule FRET and FCS to investigate tau-tubulin and working to make useful measurements in relatively complex, heterogeneous systems.

What is particularly interesting about the work from the perspective of the public?

Understanding tau’s interactions with native binding partners may provide new targets for therapeutics.  I think anyone who has a family member or loved one who suffers from Alzheimer’s or another neurodegenerative disorder would find that interesting.

Dieter Willbold, Heinrich-Heine-Universität Düsseldorf and Forschungszentrum Jülich

image description

What is the connection between your research and Alzheimer’s disease?

My interest is focused on three-dimensional structures and dynamics of medically relevant proteins at atomic resolution and their interactions with native and artificial ligands. Autophagy and neurodegenerative diseases, which by the way do have a clear connection with each other, fall within my main interest areas. I want to understand protein aggregation in time and space at high resolution. And, I want to develop strategies and compounds that allow intervention and prevention. And the protein I am working on now for a very long time as a researcher is the Alzheimer’s disease (AD) related amyloid-beta protein (Aβ).

Why is your research important to those concerned about Alzheimer’s?

We do a lot of in-depth basic science on aggregation of Aβ, tau, alpha-synuclein, and many other proteins. We also design compounds for novel disease intervention strategies, and develop novel biomarkers and assays to measure them appropriately and most sensitively. All three, basic science, drug design and biomarker development, are based on biophysical principles and physico-chemical “thinking” and heavily rely on respective methods, such as NMR, x-ray crystallography, cryo-electron microscopy, ultracentrifugation, surface plasmon resonance, micro-calorimetry, TIRF microscopy, AFM, micro-thermophoresis, biolayer interference, and all kinds of spectroscopies.


Figure 1: Cross section through the Aβ fibril illustrating the stepwise overlapping arrangement of the Aβ proteins. (Copyright: Forschungszentrum Jülich / HHU Düsseldorf / Gunnar Schröder). See also: .

How did you get into this area of research?

Already during my PhD project, which was mainly on the 3D structure determination of the transactivator protein (Tat) of the equine homologue of the HIV virus, I was engaged in structural studies of the amyloid-beta protein (Aβ) by NMR spectroscopy with some of the results published in 1995 with Paul Rösch being my supervisor and mentor. Ever since then, I was thinking of potential therapeutic intervention strategies. Since 1999, when I was heading my own junior research group in Jena, I had the necessary resources to at least start research on intervention strategies.

Soon after, I became involved in projects on prion diseases and prion protein (PrP) aggregation, when I accepted my first professorship at the Heinrich Heine University Düsseldorf in very close collaboration with Detlev Riesner. The common themes in these protein misfolding or protein aggregation diseases became quite clear. In my view, any intervention strategy – rather than a prevention strategy – needed to target toxic aggregates and get rid of them, rather than to reduce the formation of the monomeric species. As a biophysicist, I thought it would be a good idea to shift equilibria between monomers and aggregates away from the toxic aggregates (or oligomers as they are called today). To do this, we looked for compounds that bind to Aβ monomers with the free binding energy being used to lower the free energy level of monomers thus shifting the thermodynamic equilibrium towards Aβ monomers. The wording we use nowadays is that such a compound stabilizes Aβ in an aggregation-incompetent conformation. Because this is also happening with Aβ monomer units within Aβ oligomers, such a compound is also able to damage and destroy already pre-formed Aβ oligomers leading ultimately to their elimination. To identify a useful lead compound, we used mirror image phage display selection, a tool that allows selection of a compound from huge peptide libraries, but yielding a fully D-enantiomeric peptide, that does not have the disadvantages of normal L-peptides, which are very easily degraded and immunogenic. Our lead compound with the name “D3” (D-peptide from the third selection trial) showed really nice properties in vitro and in vivo. When we then wanted to elucidate the mechanism of action, it was essential to establish a whole zoo of methods and assays, which brought me even deeper into the field of protein aggregation in general and Alzheimer’s in particular. I just wanted to elucidate and pinpoint the mechanism of action and to reveal structural details of any interaction of Aβ with itself and with ligands.

Do you receive public funding for this work? If so, from what agency?

Yes, now we do. In the beginning, I was not successful at securing additional money from funding agencies, e.g., the DFG. The project received great review reports about the underlying idea, but the panels ultimately decided that the project was too risky. Therefore, I used most of the institutional resources (which was not much in those years) for the project. Only in 2007, the Volkswagen-Stiftung funded a side project. Since 2013, I did and still do receive significant funding from the Helmholtz-Gemeinschaft, the federal ministry BMBF, the EU, and also from the Michael J Fox Foundation, the Weston Brain Institute, Alzheimer’s Research UK, as well as the Alzheimer’s Association. We have also been part of a JPND network.

Have you had any surprise findings thus far?

Yes indeed — many! Just to describe some: our lead compound D3 worked effectively not only in vitro, but also in several animal models. This has been a successful long-term collaboration with my dear colleagues Thomas van Groen, Inga Kadish and Antje Willuweit. D3 improved cognition in several models and decelerated neurodegeneration in an additional animal model that we have received from my dear collaborator Uli Demuth. We established an assay called QIAD that allows us to quantify Aβ oligomer elimination efficiency ( We found that D3 efficiently eliminates Aβ oligomers, but many compounds that have already been in the clinics and failed are not able to do this. By following aggregation of N-terminally truncated and pyro-glutamate-modified Aβ (pEAβ) by NMR and CD spectroscopy, we found intermediates with helical secondary structure during aggregation.

When we tried to follow Aβ aggregation by SANS and analytical ultracentrifugation (AUC), we did not find any intermediates between monomers and penta- or hexamers ( Thus, Aβ seed formation may be a reaction of very high order. In our recent research, (7th Sep 2017, we published a high resolution cryo-EM structure of Aβ fibrils. This structure provided many surprising findings in one hit including: all 42 residues of Aβ(1-42) are part of the fibril structure, there is no C2 symmetry between the two proto-filaments of the fibril, both ends of the fibril are different, each Aβ monomer subunit contacts many other subunits and six Aβ monomers form the minimal fibril unit. See also the respective report in .

What is particularly interesting about the work from the perspective of the public?

I think that from the perspective of the public, two questions are relevant and interesting: Can we visualize highly complex things? Especially as structural biologists, we indeed can. Just look at the beautiful picture of the Aβ fibril at atomic resolution below. The second question is, of course: Can we contribute to efforts for improving the quality of life, for example by developing therapeutic strategies and drug candidates? Yes, we can also do (or at least try to do) this. It is, however, a huge undertaking that needs substantial funding and teamwork with many experts and specialists that you would not contact for basic science.

Just today (18th Sep 2017), we founded a company named Priavoid that will take an optimized derivative of D3 into clinical studies and hopefully to the market someday. In parallel, because Aβ oligomer elimination is our most favored mechanism of action, we have developed a technology called sFIDA (surface-based fluorescence intensity distribution analysis), which is able to quantify Aβ oligomers in body liquids like CSF and blood at single particle sensitivity ( The development of this technology was and is important to ultimately show target engagement of our Aβ oligomer eliminating compounds. sFIDA will also be useful for early diagnosis of any protein misfolding disease, to recruit the “right” patients for clinical studies and to follow treatment success, if there is one. Thus, all in all, I think we have developed interesting results for the public domain.

Is there anything else you would like to add?

During the initial stages of the above described project to develop a novel therapeutic strategy for AD and to identify suitable compounds, there was only myself and my PhD student, Katja Wiesehan. Currently, there are many colleagues and coworkers that are the most experienced experts in their fields. It is such a beautiful experience to work and think with all of them and all the junior researchers, and to finally get things done. Please, have look at them and their groups in Düsseldorf ( and Jülich ( with outstations in Grenoble and Hamburg. Finally, I shall not forget the many, many collaborators, of which I named only a few above.

Temperature-Adapted Zebrafish Membranes Show Their Stripes

BPJ_113_6.c1.inddOrganisms that do not maintain a constant body temperature must have some mechanism to adapt their physiological functions in order to survive at a range of temperatures.  For individual cells within the organism, the cellular membrane serves as a platform for cellular signaling and cell-cell interaction. The organization and physical properties of plasma membrane lipids are sensitive to changes in temperature. When giant plasma membrane vesicles (GPMVs)— derived from cells grown in culture— are cooled slightly below growth temperature, they separate into distinct ordered and disordered liquid phases. These phases can be observed through fluorescence imaging of a phase-selective dye. ZF4 cells, derived from zebrafish, can be adapted to grow at a range of temperatures and GPMVs derived from these cells were used in our study to examine how these cells change the makeup of their plasma membranes to adapt to changes in temperature.

The cover image of the September 19th issue of Biophysical Journal focuses on an imagined “zebrafish,” which was composed of a fluorescence image of a ZF4-derived GPMV with stripe-like phase separated domains, combined with photographs of a zebrafish and a zebra.  These three images were blended together in Photoshop to create our chimeric zebrafish. In this cover image, we wanted to highlight the idea that lipid organization of the plasma membrane could be central to the physiology and function of the organism as a whole. For this reason, we used the fluorescence image of the phase-separated GPMV as the focal point of our “zebrafish,” and used the common visual motif of stripes to draw a comparison between the organization at the sub-cellular level of plasma membrane lipids to the organization at the level of the whole organism. This zebrafish swims through a sea of phase-separated GPMVs, shown in the background, again highlighting the theme of lipid organization.

Projects exploring how the physical properties of the plasma membrane impact membrane organization and function are ongoing in the Veatch Laboratory. This interest applies to a variety of biological processes, from immunoreceptor function to general anesthesia.

– Margaret Burns, Kathleen C. Wisser, Jing Wu, Ilya Levental, Sarah Veatch

Become a BPS Student Leader: Set Up One of the Inaugural Biophysical Society Student Chapters

Student Chapters blog

The Biophysical Society is excited to launch the BPS Student Chapter program this fall, with the first Chapters to be recognized starting in the Spring semester. This program aims to build active student chapters around the globe, increase student membership and participation within the Society, and promote biophysics as a discipline across college campuses through activities organized by the chapters. Students who become officers or participate in the chapters will have an opportunity to take an active leadership role within their institutions and the Biophysical Society, with special opportunities to participate in activities at future Society meetings.

Chapters may be formed within a single institution, or regional chapters may be developed among multiple, neighboring institutions. Recognized chapters will be reimbursed up to $200 by the Society to assist with getting started.

Chapters wishing to be recognized starting in the spring semester of 2018 must submit the Endorsement and Petition Form, Chapter Bylaws, and the Chapter Information Sheet to the Society Office via email to by November 1, 2017, for consideration. Applicants will be notified in mid-December regarding the status of their recognition.

For more information and a complete list of instructions on forming an official BPS Student Chapter visit