Lipids hit a “sweet spot” to direct cellular membrane remodeling.

Lipid membrane reshaping is critical to many common cellular processes, including cargo trafficking, cell motility, and organelle biogenesis. The Rodal lab studies how dynamic membrane remodeling is achieved by the active interplay between lipids and proteins. Recent results, published in Cell Reports, demonstrate that for the membrane remodeling protein Nervous Wreck (Nwk), intramolecular autoregulation and membrane charge work together in surprising ways to restrict remodeling to a limited range of lipid compositions.

F-BAR (Fes/Cip4 homology Bin/Amphiphysin/Rvs) domain family proteins are important mediators of membrane remodeling events. The F-BAR domain forms a crescent-shaped α-helical dimer that interacts with and deforms negatively charged membrane phospholipids by assembling into higher-order scaffolds. In this paper, Kelley et al. have shown that the neuronal F-BAR protein Nwk is autoregulated by its C-terminal SH3 domains, which interact directly with the F-BAR domain to inhibit membrane binding. Until now, the dogma in the field has been that increasing concentrations of negatively charged lipids would increase Nwk membrane binding, and thus would induce membrane deformation.

Surprisingly, Kelley et al. found that autoregulation does not mediate this kind of simple “on-off” switch for membrane remodeling. Instead, increasing the concentration of negatively charged lipids increases membrane binding, but inhibits F-BAR membrane deforming activities (see below). Using a combination of in vitro assays and single particle electron microscopy, they found that the Nwk F-BAR domain efficiently assembles into higher-order structures and deforms membranes only within “sweet spot” of negative membrane charge, and that autoregulation elevates this range. The implication of this work is that autoregulation could either reduce membrane binding or promote higher-order assembly, depending on local cellular membrane composition. This study suggests a significant role for the regulation of membrane composition in remodeling.

Brandeis authors on the study included Molecular and Cell Biology graduate students Charlotte Kelley and Shiyu Wang, staff member Tania Eskin, and undergraduate Emily Messelaar ’13 from the Rodal lab; postdoctoral fellow Kangkang Song, Associate Professor of Biology Daniela Nicastro (currently at UT Southwestern), and Associate Professor of Physics Michael Hagan.

Kelley CF, Messelaar EM, Eskin TL, Wang S, Song K, Vishnia K, Becalska AN, Shupliakov O, Hagan MF, Danino D, Sokolova OS, Nicastro D, Rodal AA. Membrane Charge Directs the Outcome of F-BAR Domain Lipid Binding and Autoregulation. Cell reports. 2015;13(11):2597-609.

JBS Offers “Bio-Inspired Design” Course

Maria de Boef Miara, Lecturer in Biology at Brandeis University, will be leading a course titled Bio-Inspired Design this summer (June 1 thru August 7, 2015). Bio-Inspired Design is part of the Justice Brandeis Semester (JBS). JBS combines courses and experiential learning to provide complete, immersive experiences so students can deeply examine a specific area of study.

Bio-Inspired Design is designed for students from a wide spectrum of disciplines, but may be particularly appealing to students in Biology, Biological Physics, Environmental Studies or HSSP areas. This is a 10-week course providing 12 credits.

Students in Bio-Inspired Design will spend the summer working with biologists, engineers and artists in a variety of settings. They will explore intriguing life forms and develop the quantitative tools needed to work at the intersection of form and function.

Genetics Training Grant Retreat to be held Friday, 9/26/14

The annual Genetics Training Grant seminar is being held on Friday, September 26th at the Shapiro Campus Center Auditorium at Brandeis University. Four cutting-edge synthetic biologists: Timothy Lu, Ron Weiss, William Shih and Ahmad Khalil will share their research for the Synthetic Biology: Insights and Applications” symposium.
 
Brandeis graduate students and post-docs will have the opportunity to meet the speakers and present their work in a poster session after the talks. We encourage researchers from all departments to contribute. If you are currently, or previously were on the Genetics Training Grant, presentation of a poster is expected. 

Schedule for GTG Retreat

9:30-10:30 Ron Weiss (MIT, Dept. of Biological Engineering)
“Synthetic biology: from parts to modules to therapeutic systems.”
10:30-11:00 Coffee Break
11:00-12:00 Timothy Lu (MIT, Dept. of Biology Engineering)
“Synthetic biology for human health applications.”
12:00-1:30 Break/Lunch
1:30-2:30 William Shih (Wyss Institute)
“DNA nanostructures as building blocks for molecular biophysics and future therapeutics.”
2:30-3:30 Ahmad Khalil (Boston University, Biomedical Engineering)
“Building molecular assemblies to control the flow of biological information.”
3:30-5:00 Poster session
Shapiro Science Center 2nd floor.
All life sciences students are invited to present.

John Wardle Named Division of Science Head

John Wardle, Division of ScienceSusan Birren, Dean of Arts and Sciences, has announced that John Wardle, Professor of Physics, will be the new Head of the Division of Science.

The following is Susan’s email:

“I am pleased to announce that John Wardle will be the new Head of the Division of Science.  John is an astrophysicist and Professor of Physics and is a former chair of the Physics department.  In his new role he will oversee science-wide programs and initiatives, including the summer undergraduate research program and will work with Division of Science faculty and staff to identify new directions for the division.  I am delighted that he has agreed to take on this role and I hope that you will join with me in welcoming him.

We all owe a debt of gratitude to Eve Marder who, as the first Head of the Division, created and steered many of the priorities of the Division.  During her time as Head, Eve ably represented the Sciences at Brandeis and beyond, worked to make the Summer Undergraduate Science Program a flourishing success, changed the way we trained students and postdocs in the ethical conduct of research, and worked tirelessly to secure funding and recognition for the Sciences.  Thank you Eve!”

Tenure-track faculty position in Biochemistry

The Department of Biochemistry at Brandeis University invites applications for a tenure-track faculty position, to begin Fall 2014. We are searching for a creative scientist who will establish an independent research program and who in addition will maintain a strong interest in teaching Biochemistry at the undergraduate and graduate levels. The research program should address fundamental questions of biological, biochemical, or biophysical mechanism. Brandeis University offers the rare combination of a vigorous research institution in a liberal-arts college setting. The suburban campus is located 20 minutes from Boston and Cambridge and is part of the vibrant community of academic and biotechnology centers in the Boston area. The application should include a cover letter, curriculum vitae, statement of research accomplishments and future plans, copies of relevant publications, and three letters of reference. Applications will be accepted only through AcademicJobsOnline at https://academicjobsonline.org/ajo/jobs/3366. Additional inquiries may be directed to Dan Oprian, Professor of Biochemistry (oprian@brandeis.edu). First consideration will be given to applications received by December 1, 2013.

Brandeis University is an Equal Opportunity Employer, committed to building a culturally diverse intellectual community. We particularly welcome applications from women and minority candidates.

Simulations Say Viral Genome Lengths are Optimal for Capsid Assembly

Viruses are infectious agents made up of proteins and a genome made of DNA or RNA. Upon infecting a host cell, viruses hijack the cell’s gene expression machinery and force it to produce copies of the viral genome and proteins, which then assemble into new viruses that can eventually infect other host cells. Because assembly is an essential step in the viral life cycle, understanding how this process occurs could significantly advance the fight against viral diseases.

In many viral families, a protein shell called a capsid forms around the viral genome during the assembly process. Capsids can also assemble around nucleic acids in solution, indicating that a host cell is not required for their formation. Since capsid proteins are positively charged, and nucleic acids are negatively charged, electrostatic interactions between the two are thought to be important in capsid assembly. Current questions of interest are how structural features of the viral genome affect assembly, and why the negative charge on viral genomes is actually far greater than the positive charge on capsids. These questions are difficult to address experimentally because most of the intermediates that form during virus assembly are too short-lived to be imaged.

hagan-capsid-sim

Snapshots from a computer simulation in which model capsid subunits (blue) assemble around a linear, negatively charged polymer (red). Positive charges on the capsid proteins are shown in yellow.

In a new paper in eLife, Brandeis postdoc Jason Perlmutter, Physics grad student Cong Qiao, and Associate Professor Michael Hagan have used state of the art computational methods and advances in graphical processing units (on our High Performance Computing cluster) to produce the most realistic model of capsid assembly to date. They showed that the stability of the complex formed between the nucleic acid and the capsid depends on the length of the viral genome. Yield was highest for genomes within a certain range of lengths, and capsids that assembled around longer or shorter genomes tended to be malformed.

Perlmutter et al. also explored how structural features of the virus — including base-pairing between viral nucleic acids, and the size and charge of the capsid — determine the optimal length of the viral genome. When they included structural data from real viruses in their simulations and predicted the optimal lengths for the viral genome, the results were very similar to those seen in existing viruses. This indicates that the structure of the viral genome has been optimized to promote packaging into capsids. Understanding this relationship between structure and packaging will make it easier to develop antiviral agents that thwart or misdirect virus assembly, and could aid the redesign of viruses for use in gene therapy and drug delivery.

Perlmutter JD, Qiao C, Hagan MF. Viral genome structures are optimal for capsid assembly. eLife 2013;2:e00632

A facilitated diffusion confusion dissolution

To udirectbindfd1tilize the information contained within a cell’s genes, the enzyme RNA polymerase must find the beginning of each gene (the promoter).  Finding the beginning is a prodigious task:  RNAP must start at a particular base pair of DNA, but the cell contains millions of base pairs to choose from.  It has been proposed that gene-finding challenge is aided by a process termed ‘facilitated diffusion (FD).  In FD, RNA polymerase first binds to a random position on DNA and then slides along the DNA like a bead on a string until it encounters the target DNA sequence.

single-mol-testIn a recently published study in PNAS (1), biophysicists Larry Friedman and Jeffrey Mumm worked with Prof. Jeff Gelles in the Brandeis Biochemistry department to test key predictions of the FD model.  They used a novel light microscope that Friedman and colleagues invented and built at Brandeis, a microscope that can directly observe the binding of an individual RNA polymerase to a single DNA.  The scientists studied the σ54 RNA polymerase holoenzyme, an RNA polymerase found in most species of bacteria.  Surprisingly, none of the three predictions of the FD model that the experiments tested were found to be valid, demonstrating that target finding by the polymerase is not accelerated by sliding along DNA.  Friedman and colleagues instead propose that RNA polymerases are present in such large numbers that they can diffuse through the cell and efficiently bind to their target sites directly.  The absence of FD may explain how other proteins can bind to positions on the DNA that flank gene start sites and yet not interfere with RNA polymerase finding the gene.

Is this the end of the story? Not likely, given previous publications suggesting FD plays a role for some other DNA binding proteins. Using single-molecule techniques like those developed in the Gelles lab, scientists in next few years should give us a better idea if FD is very rare or very common. [editor: as a chemical engineer, I’m sad to see FD not have a role — it seemed like such a nice theory…]

Friedman LJ, Mumm JP, Gelles J. RNA polymerase approaches its promoter without long-range sliding along DNA.  Proc Natl Acad Sci U S A. 2013 May 29. [Epub ahead of print]

 

 

Materials in Motion: Engineering Bio-Inspired Motile Matter

Life is on the move! Motion is ubiquitous in biology. From the gargantuan steps of an elephant to the tiniest single celled amoeba, movement in biology is a complex phenomenon that originates at the cellular level and involves the organization and regulation of thousands of proteins. These proteins do everything from mixing the cytoplasm to driving cell motility and cell division. Deciphering the origins of motion is no easy feat and scientists have been studying such complex behavior for quite some time. With biology as an inspiration, studying these complex behaviors provides insight into engineering principals which will allow researchers to develop an entirely new category of far-from-equilibrium materials that spontaneously move, flow or swim.

In a recent report in the journal Nature, a team of researchers from Brandeis University consisting of Tim Sanchez, Daniel T. N. Chen, Stephen J. DeCamp, Michael Heymann, and Zvonimir Dogic have constructed a minimal experimental system for studying far-from-equilibrium materials. This system demonstrates the assembly of a simple mixture of proteins that results in a hierarchy of phenomena. This hierarchy begins with extending bundles of bio-filaments, produces networks that mix themselves, and finally culminates in active liquid crystals that impart self-motility to large emulsion droplets.

Their system consists of three basic components: 1) microtubule filaments, 2) kinesin motor proteins which exert forces between microtubule filaments, and 3) a depletion agent which bundles microtubule filaments together. When put together under well-defined conditions, these components form bundled active networks (BANs) that exhibit large-scale spontaneous motion driven by internally generated active stresses. These motions, in turn, drive coherent fluid flows. These features bear a striking resemblance to a biological process called cytoplasmic streaming, in which the cellular cytoskeleton spontaneously mixes its content. Additionally, the system has great potential for testing active matter theories because the researchers can precisely tune the relevant system parameters, such as ATP and protein concentration.

 

The researchers also demonstrate the utility of this biologically-inspired synthetic system by studying materials science topics that have no direct biological analog. Under dense confinement to an oil-water interface, microtubule bundles undergo a spontaneous transition to an aligned state. Soft matter physics describes such materials as liquid crystals, which are the materials used to make liquid crystal displays (LCDs). These active liquid crystals show a rich variety of dynamical behavior that is totally inaccessible to their equilibrium analogs and opens an avenue for studying an entirely new class of materials with highly desirable properties.

Lastly, inspired by streaming flows that occur in cells, the researchers encapsulate the bundled active networks into spherical emulsion droplets. Within the droplet, microtubules again formed a self-organized nematic liquid crystal at the oil-water interface. When the droplets were partially squished between glass plates, the streaming flows generated by the dynamic liquid crystals lead to the emergence of spontaneous self-motility.

This research constitutes several important advances in the studies of the cytoskeleton, non-equilibrium statistical mechanics, soft-condensed matter, active matter, and the hydrodynamics of fluid mixing. The researchers have demonstrated the use of biological materials to produce biomimetic functions ranging from self-motility to spontaneous fluid flows using fundamentally new mechanisms. Additionally, the experimental system of bundled active microtubules is poised to be a model for exploring the physics of gels, liquid crystals, and emulsions under far-from-equilibrium conditions.

To see more videos from the Dogic lab at Brandeis University, check out their YouTube page.

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