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

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PhosphoHero is in Charge of Neurofilaments’ Order

BPJ_112_5.c1.inddGels are neither solids nor liquids but rather a network of deformable and crosslinked polymers. Therefore, it is not surprising that the mechanical properties of synthetic gels are controlled by the degree of cross-linking, achieved, for example, by photopolymerization or the addition of chemical agents. One of the best examples of mechanically supporting bio-gels is the cytoskeleton, where crosslinked polymers (actin, microtubules and intermediate filaments) form a viscoelastic network. For microtubules and actin networks, analogues biological cross-linkers (associated proteins) have been identified. Nonetheless, in some important cases, the biophysical crosslinking mechanism or the existence of associated crosslinking proteins have not been identified.

Neurofilaments (NF) are neuronal specific intermediate filaments that form spaced filamentous networks in the long axon projections. Each neurofilament resembles a bottlebrush: a semi-flexible filament decorated with protruding floppy (intrinsically disordered) long carboxyl terminal tails. The tails engage in extensive crosslinking interactions, which have been the focus of many studies.

In addition to their lack of secondary rigid structure, NF tails contain many “phosphorylation sites”. These sites are specific amino-acid sequences recognized by enzymes that can add or remove charged phosphate groups, known as phosphorylation and dephosphorylation, respectively.

Our cover image for the March 14 issue of the Biophysical Journal illustrates an NF gel made of well aligned bottlebrushes at the front, and un-oriented ones at the back. The superhero (PhosphoHero) artistically illustrates the roles of NF phosphorylation. On the one hand, PhosphoHero increases the cross-linking between the filaments via the generation of ionic bridging between opposite charged residues. This in turn aligns the red filaments in nematic liquid crystalline order, as depicted by the crossed polarized NF hydrogel microscopy in the background. On the other hand, phosphorylation also increases the tails’ net negative charge, and consequently its compression response. Thus, phosphorylation acts as a regulatory knob to control the structure, orientation and mechanical properties of the cellular scaffold, the cytoskeleton.

Future studies into the role of intrinsically disordered proteins, and in particular their tunable phosphorylation states and their role in long-range alignment should be full of further surprises. Intrinsically disordered proteins were evolutionally selected to hold functional, although sometimes atypical properties, characteristic to superheroes.

The cover was hand-drawn and then digitally colored in Photoshop by Eliran Malka.

– Eti Malka-Gibor, Micha Kornreich, Adi Laser-Azogui, Ofer Doron, Irena Zingerman-Koladko, Jan Harapin, Ohad Medalia, Roy Beck

Disulfide Bridge: More Than Just a Simple Bond

BPJ_110_8.c1.inddDisulfide bridges, a common type of covalent bond in protein structures, are usually believed to maintain structural stability of proteins, especially small peptides that lack hydrophobic cores.  Our study, in this April 26 issue of Biophysical Journal, revealed that disulfide bridges are also critical, at least in the case of the MCoTI-II peptide, for holding together a native structure that is frustrated.

The cover image shows the native structure (left) as well as snapshots from folding/unfolding molecular dynamics simulations of the cyclic peptide named MCoTI-II, which acts as a trypsin inhibitor in plants and has three disulfide bonds in its native state (red, green, and blue). In the context of its folding funnel, our simulations showed that the peptide is frustrated near the bottom of the funnel (native structure, middle), but not as frustrated higher up in the funnel (unfolded states, right). The formation of two of the three disulfide bridges was found to be anti-correlated when the peptide approaches the native state, yet both are critical for snapping the frustrated native structure into place. The protein structures in the cover image are visualized through VMD (http://www.ks.uiuc.edu/Research/vmd/).

When the sequence of protein isn’t perfect for folding, perhaps as a result of evolution for function, disulfide bridges can play a role holding together a frustrated structure that cannot form otherwise. Furthermore, due to the extreme stability and interesting biological activities of cyclotides such as MCoTI-II, our studies may also shed light on engineering cyclotides as novel pharmaceuticals in the future.

-Yi Zhang, Paramjit S. Bansal, David Wilson, Klaus Schulten, Martin Gruebele, Norelle L. Daly

Expanding the Biophysics Network in Kentucky

Organized by Trevor Creamer, University of Kentucky, the 4th Bluegrass Molecular Biophysics Symposium, held on Monday, May 18, at the University of Kentucky, brought together nearly one hundred people. Registrants came from KentucKYky, Ohio, Tennessee, Indiana, and North Carolina.

The symposium covered the broad field of molecular biophysics with talks and posters on subjects ranging from lipids to proteins and describing work done with a wide variety of techniques. The breadth of subjects covered demonstrates that molecular biophysics is alive and well in this region of the country. Creamer notes that the quality of molecular biophysics-based research being done in the region is outstanding. This was apparent from both the talks and the more than 40 posters presented.

Creamer was surprised at the number of people who have attended this symposium more than once. He found it extremely gratifying because of the distance people are willing to travel for a one day event like this. Each year, symposium attracts new people from the surrounding areas; a pair of biophysicists traveled from Western Carolina University, over 280 miles away!
Creamer hopes to host another event next year.

Were you at the Kentucky Networking Event? Share some of you experiences in the comments below!

Bringing Together Biophysicists in the Hoosier State

The Biophysical Society recently sponsored a networking event for biophysicists in Indiana. The event, titled “The Hitchhiker’s Guide to the Protein Galaxy: A Mini-symposium on Integrating Structure, Function, and Interactions of the Protein Universe,” was held at Purdue University on May 13-14, 2015, and was organized by Satchal K. Erramilli, Duy P. Hua, Adriano Mendes, Phillip Rushton, Brendan Sullivan, Sakshi Tomar, all of Purdue University. Satchal Erramilli reports on the event – and explains its interesting title.

poster

Attendees mingle during the poster session.

You many wonder why we chose the “Hitchhiker’s Guide to the Galaxy” as the theme for a symposium on protein science and biophysical research. The classic novel by Douglas Adams, which we often wax nostalgic about, is an excellent work of fiction, but is also filled with concepts that can readily be applied to scientific inquiry. The book contains a long tangent on the validity of mice models, includes an excellent digression on “Somebody Else’s Problems”, and is peppered with discussions on evolution. Most significantly, the book’s most famous story – the meaning of life – is an allegory for asking the right questions, as important an exercise as any for a scientist.

And so we drew on themes from the book for our symposium, “The Hitchhiker’s Guide to the Protein Galaxy”. We were charmed to find many attendees and sponsors shared our enthusiasm for the novel, and some of the credit for the event’s success has to be ascribed to the theme. Indeed, we found many attendees were as excited to discuss the book as they were to discuss science.

The symposium was held at Purdue University on May 13th and 14th, 2015, with the goal of bringing together protein scientists and biophysical researchers from all across campus. Thanks to the generosity of our sponsors, we were able to expand the scope of the event to include attendees and presenters from nearby institutions and, in some cases, beyond. We had over 130 attendees, with nearly two dozen coming from nearby institutions in Indiana and Illinois, and some even as far off as Cornell, the N.I.H., and Texas Tech. This can only be described as apropos for a Hitchhiker-themed symposium.

We felt the event should reflect the depth and breadth of structural biology research here at Purdue, and thus it included aspects of protein science ranging from basic to applied, from individual proteins to whole cell studies. The presenters had backgrounds as diverse as their topics, and included several young faculty members, postdoctoral scholars, and senior graduate students. Topics ranged from protein structure and function to biophysical methods and high-resolution electron microscopy, and much more. Attendees clearly enjoyed being able to hitchhike around the Protein Galaxy during the two days of the symposium.

organizers

The Hitchhiker’s Guide to the Protein Galaxy organizers pose for a photo.

The presence and participation of our external attendees enriched the experience for all at this event, and their interactions with local researchers offered the potential for fruitful collaborations. In particular, we recognize our keynote speaker, Dr. Tony Kossiakoff, who was an excellent guest of honor for the event and drew an audience exceeding the venue’s capacity. As an unexpected addition, and entirely a product of the enthusiasm of several of our visitors, we were able to organize an impromptu career workshop, which our graduate students found tremendously useful. We hope to have even more external presenters next time.

We definitely plan to have this event again next year. We can only hope to again receive such tremendous support from our sponsors, who far exceeded our expectations with their willingness to sponsor the symposium, the awards, and contribute in many other ways. We were thrilled to get this networking grant from the Biophysical Society, which, besides providing us with money, also provided visibility for the event beyond what we could have hoped for. A big shout out goes to April Murphy, who made time not just to assist us and help market the symposium but also to visit us and take part in our event. It was a pleasure to work with her and everyone else who helped make this a success, and we hope to see her and many others at the next iteration of this symposium. See you again next year, fellow hitchhikers!

Biophysical Tools Key to Understanding How Ebola Spreads

On most days, biophysicists go about their work with little public interest.  The things they work on are complex, very specific, and impossible to see with the naked eye. Every once in a while though, biophysicists find their work in the spotlight due to public events such as a disease outbreak. With the ebola outbreak in west Africa in the news, the research of Biophysical Society members Michelle Digman, University of California Irvine, and Robert Stahelin, University of Notre Dame has attracted increased attention. Digman was kind enough to answer some questions about her work for us.

Actin cytoskeleton (red) and Ebola VP40 virus budding (green).

Actin cytoskeleton (red) and Ebola VP40 virus budding (green).

What is the connection between your research and Ebola?

My research aims are to develop enabling technologies in optical microscopy to be able to measure protein dynamics in living cells. These fluorescent fluctuation measurements measure spatial-temporal interaction at the molecular scale in real time. My colleague, Professor Robert Stahelin at the Indiana University School of Medicine and the University of Notre Dame, who is studying protein-lipid interactions in the life cycle of the Ebola virus, wanted us to use these biophysical approaches to measure the membrane binding behavior of the Ebola virus matrix protein, VP40. Given that we both are interested in understanding protein regulation and function we teamed up to understand how VP40 from the Ebola virus assembles into virus like particles (VLPs) in live cells.

Why is your research important to those concerned about finding a cure/stopping the spread of Ebola?

Our research involves studying the egress of the virus particles and understanding the mechanism of spreading. There is not a large body of literature that addresses how the ebola virus assembles and how it interacts with endogenous proteins, lipid membranes, or cytoskeletal structures in living cells. I think this information can be useful in developing small molecule targets for therapy.

How did you get into this area of research?

This collaboration, with Stahelin, started mutual interests to learn more about virus protein interactions in living cells. Our microscopic tools allowed us to measure protein assembly, aggregation and interactions. We realized once the VP40 protein was expressed in live cells with a fluorescent tag that the best way to follow protein assembly was to use dual color particle tracking.

How long have you been working on it?

We have been collaborating for 3 years.

Do you receive federal funding for this work? 

Yes, I am the Co-PI of the Laboratory for Fluorescence Dynamics (LFD) which is a P41 Biomedical Technology Resource Center (BTRC) funded by NIGMS at NIH. We have 5 core technological research projects, over 10 driving biological problems, collaborative research projects as well as training and dissemination of the technologies developed at the LFD. As such, our work with Stahelin also included training one of his graduate students, Emmanuel Adu Gyamfi, who spearheaded this project for his Ph.D. thesis.

Have you had any surprise findings thus far? 

Everything we learned with the Ebola VP40 protein was a surprise. It was never studied before in living cells and in real time. Using the number and molecular brightness (N&B) and with the 3D particle tracking methods, we were able to calculate the aggregation process on the actin filaments.

What is particularly interesting about your work on the Ebola VP40 protein from the perspective of other researchers?

The Ebola VP40 protein is sufficient to make virus like particles from human cells.  Thus, we study the assembly of one single virus particle at a time directly inside the cell to understand the spatial and temporal distribution of VP40 within the plasma membrane before a new virus particle leaves the cell membrane.

What is particularly interesting about your research from the perspective of the public?

With the recently identified structural information on VP40 that came available from Dr. Saphire’s lab at The Scripps Research Institute, we are starting to unravel the mechanism of how new virus particles are formed to sustain and spread Ebola infections.

With Ebola a top story in the news, are you receiving more inquiries about your work?  Does the attention to the disease affect you in other ways?

Yes, mostly from family and friends. Stahelin, on the other hand, has appeared on a local news broadcast, been interviewed on a radio show, and interviewed by the local newspaper.   has received the most inquiries.

 

Building a Social Network in Milwaukee

wisconsin1 wisconsin4BPS sponsored the second biophysics networking event in Wisconsin on March 29 at the Milwaukee School of Engineering (MSOE). BPS student member, Michelle Hasse, and other students at MSOE, organized the event, bringing together over 55 scientists from MSOE, University of Wisconsin, Milwaukee, Concordia University, Indiana University-Purdue University Indianapolis (IUPUI), and Rosalind Franklin University. The attendees included undergraduate students, graduate students, and professors.

The topic of the day was the structural determination of proteins. Speakers included Jason Kowalski, MSOE; Sheeri Biendarra, MSOE; Marious Schmidt, University Milwaukee, Wisconsin; and Daniel Sem, Concordia University. The event also featured three graduate student posters presentations from IUPUI and Rosalind Franklin University. Because of the intimate atmosphere of the event, attendees were able to have in depth conversations with the speakers and poster presenters about their research and make connections with those at other institutions.

Through the talks and poster presentations, the organizer hoped biophysicists from the area would be able to build relationships by sharing their research. With the jump in attendance and increase in popularity of this year’s event, students at MSEO plan on hosting another event next spring!

We’re you at the Wisconsin networking event? Let us know your favorite part of the event in the comments below.