Separating proteins and manipulating live cells using magnetic nanoparticles

Brandeis grad students Yue Pan (Chemistry) and Marcus Long (Biochemistry), together with Professors Lizbeth Hedstrom and Bing Xu, have synthesized novel 6 nm diameter magnetic nanobeads (comparable in size to a globular protein) and used them to separate specific proteins from a cell lysate and manipulate live cells. This work has just appeared online in the journal Chemical Science.

Selectively binding glutathione-S-transferase fusion proteins using
glutathione-decorated iron oxide nanoparticles and down-stream applications

These small, magnetic beads have numerous advantages over larger traditional glutathione-modified beads, including rapid purification, and ultra low non-specific binding. Importantly, both the purified GST and the protein of interest (POI) preserve their innate properties. They also demonstrate that functionalized iron oxide nanoparticles can be used to manipulate live cells. This work  establishes design principles for decorating magnetic nanoparticles that will ultimately should lead to a general and comprehensive platform for studying biological interactions and biological systems using a magnetic force.

Getting a Leg Up on Movement Disorders

Over 40 million people worldwide suffer from movement disorders, which are clinically defined as any type of affliction that affects the speed, fluency, ease, or quality of motion. The symptoms of these disorders can manifest in many different ways (the most common being tics, tremors, dystonia, and chorea), and treatment is still elusive for a large number of these often debilitating diseases.  The past several decades, however, have seen enormous advances in our understanding of the genes and proteins underlying these conditions, and what remains to be determined is the way in which these molecules interact with each other to produce either normal or pathological locomotor patterns.

Scaffolding proteins have recently become a point of interest in the field of movement disorders.  As their name implies, these proteins act as “scaffolds” to tether other proteins together, thus facilitating protein-protein interactions.  It has long been thought that scaffolding protein dysfunction could disrupt the formation of protein complexes critical for the production normal locomotion, but evidence for such conjectures has remained elusive.

in a recent article in the journal GENETICS, Dr. Leslie Griffith’s lab at Brandeis University published work implicating one such scaffolding protein of the MAGUK family, known as CASK-b, in locomotor pathology. Using the fruit fly Drosophila melanogaster as a model system, researchers in the lab combined recently-developed genetic tools with cutting-edge computer behavior analysis software to demonstrate that knocking out this protein produces a complex motor deficit (see figure below).  Furthermore, this deficit appears to stem from a loss of CASK-b in the central nervous system, suggesting it plays a role in higher-order regulation of motor output.  Interestingly, both the major locomotor control center of the insect brain (known as the ellipsoid body), as well as the motor neurons which the locomotor control center regulates, do not appear to require this protein to produce normal locomotor patterns.  This finding implies that a novel region or regions of the fly brain may be contributing to central locomotor control.  Understanding both the specific mechanism through which this protein acts, as well as the underlying circuitry responsible for this deficit, could contribute largely to the field of movement disorders as a whole.

Another surprising finding to come out of this study was the discovery of an additional mRNA transcript that arises from an alternative promoter in the CASK locus.  Although similar to CASK-b in many ways, this alternative protein is actually most homologous to another member of the same family in vertebrates, known as MPP1.  MPP1, like most of its MAGUK cousins, is also a scaffolding protein that plays a vital role in bringing various proteins together into signaling complexes, thus providing more opportunities for complex interactions to take place.  The Drosophila genome has many fewer MAGUK proteins than most mammalian genomes.  This finding implies that through utilization of alternative start sites that generate multiple proteins, the fly can still end up with a wide array of subcellular interactions.  It is this underlying diversity of molecular interactions that is thought to allow the fly to produce to a variety of unusually complex behaviors, such as courtship, aggression, flight, and in this case motor control.

Inaugural Neuro + MCB Graduate Student Social a Success

On Friday January 14th the first of an anticipated quarterly series of social events for Biology graduate students took place.  The concept for this entirely student-funded gathering was developed by myself (Scott Neal, MCB) and co-organizer Sean O’Toole (Neuro) with two goals in mind.  First, it would represent an opportunity to introduce first year students to their more senior classmates, many of whom they have not yet had occasion to interact with.  Additionally, it would generate a greater sense of community amongst all students in the Neuroscience and MCB graduate programs.  We strongly believe that social interaction is an integral part of graduate student life.  Too often students become isolated within their own labs and we wished to provide a means to change this.  By encouraging our colleagues to engage each other outside of the academic forum their graduate student experiences, and by extension their scientific productivity, might be improved.  This interaction may also foster inter-lab collaborations and promote mentorship opportunities.

Nearly half of all enrolled graduate students in the MCB and Neuroscience programs were welcomed to this event where they enjoyed snacks, beverages and conversation.  It provided an opportunity for graduate students to breach the normal social barriers (e.g. working in different buildings) and to learn about the interests of and approaches taken by our classmates as they develop their young careers. One attendee commented “We really need to do this more often; this was a great idea!”  Based on the success of this event we hope to expand future gatherings to include post-doctoral fellows and other life science graduate students.  These inclusions might create additional mentorship opportunities and will broaden the perspectives of all participants.

We all stand to benefit from camaraderie within the Brandeis Life Sciences community, whether it be from the ease at which we can walk down the hall to borrow a reagent or by the simple pleasure of recognizing each other and exchanging a brief “hello” as we rush to our next experiment.  Thank you to all of the students who participated and otherwise contributed to the success of this inaugural event.

Neurons branch out: a role for Rem2

The development of the central nervous system involves a series of complex yet tightly-regulated processes, including the formation of synapses, the sites of communication between neurons, and the morphogenesis of the dendritic arbor, where the majority of synaptic contacts occur. Importantly, the misregulation of these processes is a hallmark of many neurodevelopmental disorders, including autism and mental retardation. However, the molecular mechanisms that underlie these structural and functional changes remain largely obscure.

The lab of Prof. Suzanne Paradis at Brandeis is working to identify and characterize molecules that regulate neural development in the rodent hippocampus. A recently accepted manuscript at Developmental Neurobiology by Brandeis Neurocience Ph.D. student Amy Ghiretti and Dr. Paradis uses RNAi in primary hippocampal cultures to identify novel roles for the GTPase Rem2 in several neurodevelopmental processes. The RNAi-mediated decrease of Rem2 leads to the formation of fewer excitatory synapses, and also results in increased dendritic complexity, suggesting that Rem2 functions normally to promote synapse formation and to inhibit dendritic branching. Additionally, the binding of Rem2 to the calcium-binding protein calmodulin was identified as a key interaction that distinguishes the signaling pathways through which Rem2 mediates synapse development and dendritic branching. Overall, this study identifies Rem2 as a novel regulator of several neurodevelopmental processes, and importantly, suggests that Rem2 regulates excitatory synapse development and dendritic morphology via separable and distinct signaling pathways.

Figure: Neurons in which Rem2 protein expression has been decreased by RNAi (top) show increased dendritic branching compared to control neurons (bottom), suggesting Rem2 acts to inhibit branching

Chiral Equivariant Cohomology

Prof. Bong Lian from Math writes:

In the 1950’s, French mathematicians Henri Cartan and Armand Borel defined a new topological invariant that was capable of distinguishing symmetries of certain geometric spaces known as G-manifolds. Cartan and Borel called their invariant the Equivariant Cohomology of a G-manifold. It was new in that it was able to capture essential aspects of geometric operations, called Lie group actions (after Sophus Lie), on manifolds that ordinary cohomology theory was unable to detect. Hence it provides a new conceptual framework for studying symmetries of spaces on the one hand, and offers a powerful tool for computing ordinary cohomology of these spaces, on the other.

In the late 80’s, physicists invented String Theory in their attempt to construct a grand unified field theory. They found that certain solutions to String Theory are essentially governed by an algebraic structure called a Chiral Algebra. This turns out to be a new structure that generalizes many fundamental algebraic constructs in mathematics, including commutative algebras and Lie algebras. A question was then raised as to whether there exists a natural theory that integrates both the Cartan-Borel invariant and Vertex Algebras. This hypothetical theory, which I learned about as a graduate student at Yale University, was dubbed the stringy analogue of the Equivariant Cohomology theory.

In 2004, Andrew Linshaw, a Brandeis PhD student (now Research Fellow, U. Darmstadt), and I constructed such a theory, which we coined the Chiral Equivariant Cohomology (CEC) of a G-manifold. In our latest paper, joint with another Brandeis PhD student, Bailin Song (now Assoc. Prof., Univ. of Science and Technology of China), we showed that not only does the CEC subsumes the Cartan-Borel theory, it goes well beyond that. For example, we have found an infinite family of Lie group actions on spheres that the Cartan-Borel theory is too weak to distinguish, but have non-isomorphic CEC. This proves that the CEC theory is strictly stronger as a topological invariant than the Cartan-Borel invariant. The paper appears in the December 2010 issue of the American Journal of Mathematics (Volume 132, Number 6).

Spring-loading the active site of cytochrome P450

Enzymes differ from other catalysts in the exceptional substrate selectivity they exhibit.  However, the active sites of related enzymes are often very similar, even though different substrates are acted upon (for example in the superfamily of cytochrome P450s).  How does a given enzyme preferentially bind a particular substrate?  In a new paper appearing in the jounal Metallomics, Chemistry grad student Marina Dang and Profs. Susan Sondej Pochapsky and Thomas Pochapsky use nuclear magnetic resonance (NMR) to identify a helical structure remote from the active site of the enzyme cytochrome P450cam that is responsive to changes in substrate.  They propose that this helix can adjust the position of residues that contact substrate in the enzyme active site, much like the spring that holds batteries in place against electrical contacts in a flashlight.

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