Goode, Gelles and Kondev labs synergize in discovery of a new synergistic actin depolymerization mechanism

Shashank Shekhar, Jane Kondev, Jeff Gelles and Bruce Goode

Shashank Shekhar, Jane Kondev, Jeff Gelles and Bruce Goode

All animal and plant cells contain a highly elaborate system of filamentous protein polymers called the actin cytoskeleton, a scaffold that can be rapidly transformed to alter a cell’s shape and function. A critical step in reconfiguring this scaffold is the rapid disassembly (or turnover) of the actin filaments. But how is this achieved? It has long been known that the protein Cofilin plays a central role in this process, but it has been unclear how Cofilin achieves this feat. Cofilin can sever actin filaments into smaller fragments to promote their disassembly, but whether it also catalyzes subunit dissociation from filament ends has remained uncertain and controversial. Until now, this problem has been difficult to address because of limitations in directly observing Cofilin’s biochemical effects at filament ends. However, a new study published in Nature Communications led by postdoctoral associate Dr. Shashank Shekhar, jointly mentored by Bruce Goode, Jeff Gelles and Jane Kondev, uses microfluidics-assisted single molecule TIRF imaging to tackle the problem.

The new study shows that Cofilin and one other protein (Srv2/CAP) intimately collaborate at one end of the actin filament to accelerate subunit dissociation by over 300-fold! These are the fastest rates of actin depolymerization ever observed. Further, these results establish a new paradigm in which a protein that decorates filament sides (Cofilin) works in concert with a protein that binds to filament ends (Srv2/CAP) to produce an activity that is orders of magnitude stronger than the that of either protein alone.

Video of cofilin and Srv2/CAP collaborating

The work was funded by National Institutes of Health, National Science Foundation MRSEC and Simons Foundation grant.

 Basketball, Dancing Proteins, and Life-saving Drugs

Dorothee Kern, Brandeis Magazine article

Dorothee Kern (center) with students in her Brandeis lab. (Image: Mike Lovett)

The Fall 2019 issue of Brandeis Magazine features a cover story on Professor of Biochemistry and HHMI Investigator Dorothee Kern.  The article describes Kern’s trajectory from her youth and education in the former East Germany to her current research and teaching at Brandeis to her co-founding of Relay Therapeutics, a Cambridge company pioneering new approaches to anti-cancer drug discovery.

 

Jeff Gelles elected to American Academy of Arts and Sciences

Jeff Gelles, 2019 AAAS recipient

credit: Heratch Ekmekjian

Jeff Gelles, the Aron and Imre Tauber Professor of Biochemistry and Molecular Pharmacology, has been elected to the American Academy of Arts and Sciences. He was among the  more than 200 outstanding individuals that were elected to the Academy in 2019 and announced on April 17.

The Gelles lab studies “little engines” or the nanometer-sized machines made of protein, RNA, and DNA molecules that carry out the essential processes in living cells.  The lab uses single-molecule light microscopy methods to study the functional mechanisms of these macromolecular complexes in cytoskeletal function, transcription and transcription regulation, and RNA processing.

Founded in 17890, the Academy recognizes the outstanding achievements of individuals in academia, the arts, business, government, and public affairs.

Read more: Amacad.org, BrandeisNow

 

 

 

 

Student Research Results in Recent JIB Paper

Images from research paper from Pochapsky and Lovett labsBy Thomas Pochapsky, Professor of Chemistry & Biochemistry

We don’t usually consider PineSol, Vick’s VapoRub and Lemon Pledge as food, but it is a good thing that some bacteria can.  The active components of those products are terpenes, small organic molecules that are produced by evergreens to repel insects, promote wound healing and prevent infection.  The bacteria that can use terpenes as food are a critical part of the forest ecosystem:  Without them, the soil would rapidly become saturated with toxic terpenes.  Members of the Pochapsky and Lovett laboratories in Chemistry and Biology are curious about what enzymes are involved in terpene metabolism.  In particular, why would one bacterial strain feast on a particular terpene (camphor, for example) while ignoring others?

The first step in terpene breakdown by bacteria is often the addition of an oxygen atom at a particular place in the terpene molecule, providing a “handle” for subsequent enzymes in the breakdown pathway.  The enzymes that catalyze these oxygenation reactions are called cytochromes P450.  P450 enzymes perform important reactions in humans, including steroid hormone biosynthesis and drug metabolism and activation.  Human P450s are targets for cancer chemotherapy and treatment of fungal infections.  A specific inhibitor of P450 is a component of the AIDS “cocktail” treatment, slowing the breakdown of the other cocktail components so the drugs do not have to be taken as often.

Despite the importance and wide scope of the P450 enzyme family, we don’t know much about how a particular P450 goes about choosing a molecule to work on (the substrate) or where it will put the oxygen (the product).  This is what the Brandeis labs are interested in finding out.  What particular sequence of amino acids gives rise to the substrate/product combination of a given P450? Answers to this question will aid in drug design and bio-engineering projects.

The project employs multiple scientific techniques in order to get at the answers to these questions, including bacterial genome sequencing, messenger RNA transcription, enzyme isolation, activity assays, mass spectrometry and enzyme structure determination.  As complicated as it sounds, though, the project lends itself nicely to undergraduate research:  Three of the authors on this paper are undergraduates, Phillix Esquea ‘18, Hannah Lloyd ’20 and Yihao Zhuang ’18.  Phillix was a Brandeis Science Posse recruit, and is now working with a Wall Street investment bank in NYC.  Yihao is enrolled in graduate school at the University of Michigan School of Pharmacy, and Hannah Lloyd is still at Brandeis, continuing her work on the project.  Even high school students got in on the act:  Teddy Pochapsky and Jeffrey Matthews are both seniors at Malden Catholic High School, and collected soil samples used for isolation of terpene-eating bacterial strains.  (One of the newly isolated bacterial strains is named in their honor, Pseudomonas strain TPJM).

“A new approach to understanding structure-function relationships in cytochromes P450 by targeting terpene metabolism in the wild.” Nathan R.Wong, Xinyue Liu, Hannah Lloyd, Allison M. Colthart, Alexander E. Ferrazzoli, Deani L. Cooper, Yihao Zhuang, Phillix Esquea, Jeffrey Futcher, Theodore M. Pochapsky, Jeffrey M. Matthews, Thomas C. Pochapsky.  Journal of Inorganic Biochemistry. Volume 188, November 2018, Pages 96-101.  https://doi.org/10.1016/j.jinorgbio.2018.08.006.

Encoding taste and place in the hippocampus

The ambience of a good meal can sometimes be as memorable as the taste of the food itself. A new study from Shantanu Jadhav and Donald Katz’s labs, published in the February 18 edition of The Journal of Neuroscience, may help explain why. This research identified a subset of neurons in the hippocampus of rats that respond to both places and tastes.

The hippocampus is a brain region that has long been implicated in learning and memory, especially in the spatial domain. Neurons in this area called “place cells” respond to specific locations as animals explore their environments. The hippocampus is also connected to the taste system and active during taste learning. However, little is known about taste processing in the hippocampus. Can place cells help demarcate the locations of food?

To test this hypothesis, Neuroscience PhD student Linnea Herzog, together with staff member Leila May Pascual and Brandeis undergraduates Seneca Scott and Elon Mathieson, recorded from neurons in the hippocampus of rats as the rats explored a chamber. At the same time, different tastes were delivered directly onto the rats’ tongues.

Analyzing how place cells responded to tastes delivered inside or outside of their place field

The researchers found that about 20% of hippocampal neurons responded to tastes, and could discriminate between tastes based on palatability. Of these taste-responsive neurons, place cells only responded to tastes that were consumed within that cell’s preferred location. These results suggest that taste responses are overlaid onto existing mental maps. These place- and taste-responsive cells form a cognitive “taste map” that may help animals remember the locations of food.

Read more:  So close, rats can almost taste it

Leading Science: Magnifying the Mind

Brandeis Magnify the Mind

Written by Zosia Busé, B.A. ’20

Joshua Trachtenberg, graduated from Brandeis in 1990 and is a leader in studying the living brain in action using advanced imaging technology. After establishing his research laboratory at UCLA, he founded a company – Neurolabware – in order to build the sophisticated custom research microscopes that are needed to perform groundbreaking work in understanding how the brain develops and how diseases and injuries interrupt its normal functioning. His company is created by scientists and for scientists, and is unique in creating high quality microscopes that are easy to use but also have the flexibility to be used in creative ways in innovative experiments, and in combination with a variety of other devices.

Brandeis University is now seeking to acquire one of these advanced microscopes that can observe fundamental processes inside the living brains of animals engaged in advanced behaviors. The resonant scanning two-photon microscope from Neurolabware allows researchers to understand and image large networks of neurons in order to visualize which cells and networks are involved with specific memories or how these processes go awry in disease. “This approach is unparalleled. There is no other technique around that could possibly touch this,” Trachtenberg says.

Previous two-photon technologies permitted only very slow imaging, allowing scientists to take a picture about every two seconds, but the resonant two-photon technology is a major breakthrough that allows scientists to take pictures at about 30 frames per second. This speed increase is a major game changer. Not only can one observe activity in the brain at a higher speed, but it is possible to take pictures at a speed that is faster than the movement artifacts that must be accounted for, such as breathing or heart beats. Because one can see the movement, it can be corrected, allowing high resolution functional imaging of structures as small as single synaptic spines in the living brain. Further, advances in laser technology and fluorescent labels now allow scientists to see deeper into the brain than ever before, compounding the recent advantages of increased speed.

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