Past Initiatives and Seeds

Seeds 2008-2010

Structural and biophysical characterization of flagellar bend formation
Daniela Nicastro


Eukaryotic cilia and flagella are a marvel of evolutionary engineering. In this highly conserved organelle, thousands of motor proteins coordinate to generate a large scale, high frequency (~50Hz) beating motion that enables cells to move or propel fluid. Our goal is to characterize how constraints built into the structure of the flagella, such as an elastic nexin link that binds neighboring microtubules, effect its function. Using genetics we will systematically remove individual building blocks (proteins) of the flagella, identify these components using electron microscopy, and relate this data to the overall material properties of the flagella. Our systematic deconstruction of this complex hierarchical biological nanomachine will provide valuable lessons  for the design of novel biomimetic materials.


Dynamics of Transcription Factor Release from DNA 
Jeff Gelles

Transcription factors are proteins that control the development and environmental responses of all cells. Transcription factors function by recognizing and forming stable interactions with a nucleotide sequence located at a defined, single location on a long duplex DNA polymer. In this project, we will investigate the underlying physics that govern the dynamic interactions of transcription factor proteins with DNA, processes which are fundamental to the regulation of gene expression in all organisms. Using singlemolecule fluorescence microscopy techniques developed in the lab, we will make precise quantitative measurements of the lifetime distributions for complexes between individual transcription factor molecules and single linear DNA molecules that are immobilized by attachment of one end to a surface.

Intracellular hydrogelation resulting from self-assembly of small molecules 
Bing Xu

Recent studies reveal that the self-assembly of nanofibers within gels, like the formation of cellular nanostructures (e.g., actin filaments, microtubules, and viral capsids), follows a nucleation and growth mechanism. intrahydroThis common feature leads to an intriguing and poorly explored question: How does a cell respond to the intracellular hydrogelation resulting from the self-assembly of small organic molecules? To answer this question, we will form a hydrogel of small molecules inside cells. The conventional routes (e.g., a change of temperature, pH, or ionic strength) for making a supramolecular hydrogel, however, disrupt cellular processes and prevent precise evaluation of intracellular selfassembly. The goal of this seed project is to develop a new method in which an enzyme catalytically converts a precursor to a hydrogelator and triggers molecular self-assembly and hydrogelation

Seeds 2010 - 2012

Design of Electrocatalysts for Renewable Energy Applications
Christine Thomas


Homogeneous catalysts for renewable energy applications such as the conversion of CO2 (industrial byproduct) into CO (industrially viable carbon feedstock) using solar energy (in the form of converted electrical energy) have been developed using a combination of an early transition metal (Zr) and a late transition metal (Co). The ongoing challenge that this  project, using seed funding provided by MRSEC and led by Christine Thomas, addresses is how to improve the efficiency of electron transfer from an electrode surface to a catalyst in solution. The ultimate goal is to develop methods to tether heterobimetallic catalysts or precatalysts to conducting surfaces to both improve the efficiency of electron transfer and design catalyst systems that would be useful on an industrial scale. Catalysts with functionalities amenable to “click” chemistry are under development.


Engineering lipid membrane conformations using proteins involved in transport within cells
Avital Rodal


Biological membranes are pinched, bent, and deformed into highly specialized shapes that are tailored for compartmentalizing biochemical processes within cells. In a project with seed funding from the MRSEC, Avi Rodal, in collaboration with Jane Kondev and Mike Hagan, is exploring the physical basis for how a cohort of curved membrane-deforming proteins called F-BAR proteins act to sculpt membranes. The Rodal group has devised biochemical and cellular assays to generate membrane tubules of specific shape, lipid composition, and stiffness. These assays allow the use of a combination of experiments and theory to explore how tweaking the membrane deformation machinery modulates membrane organization and structure. They have found that apparently structurally similar membrane deforming proteins produce tubules with very different properties, and are exploring whether the basis for these differences is in properties of protein interaction with the membrane, local changes in membrane composition, or the effects of protein assembly into higher order structures.

Seeds 2012 - 2014

DNA template the self-assembly of small nucleopeptides to generate monodispersed multifunctional nanostructures
Bing Xu


Xu group has extensive expertise in design and synthesis of small molecular weight compounds that are capable of assembling into 1D filamentous structure in response to various environmental cues.  However, these assembly techniques produce filaments that inherently have a large length polydispersity which is difficult if not impossible to control. In contrast, Nature is capable of assembling structures of exquisite precision and reproducibility. The ultimate goal of this seed proposal is to develop synthetic filaments whose monodispersity approaches those found in biological viruses. We plan to use DNA as the template to interact with small molecules developed in Xu group (i.e., nucleopeptides or the conjugates of nucleobase, amino acids, and glycoside) for chiral self-assembly, with the goal to mimic the self-assembly of virus and generate nanostructures with diverse shapes but finite dimensions.  If successful, the resulting filamentous structures would provide unique materials from both the fundamental and applied perspective. Such virus-like particles could be used as agents for delivery of drug or DNA to cells. From a fundamental perspective synthetic monodisperse filaments would provide unique and highly controllable building blocks for studies of self-assembly, a central research focus of the Brandeis MRSEC. 

Bing Xu and Zvonimir Dogic will work collaboratively on this project, with Xu focusing on the synthesis of the nanofilaments and Dogic studying the pathways of self-assembly.

Active Control of Filamentous Actin Networks
Bruce Goode

Proposed research: This seed proposal merges physical theory and experimental biochemistry to address the fundamental problem of how nanometer scale interactions lead to micron scale structures. Perhaps nowhere is this question of ‘disparate scales’ more evident than in the observation that the length, dynamics, and architecture of micron-sized actin and microtubule polymer systems are controlled by nanometer sized cytoskeletal regulatory proteins (e.g. formins and molecular motors); Figure 1A. Remarkably, modulation of a few key molecular control points can lead to formation of strikingly different polymer networks (from the same
building blocks), with special ized geometries and polymer organization, tailored to different functions.


Figure 1: The formin damper Smy1. (A) TIRF microscopy images of fluorescently labeled actin filaments in the presence and absence of the formin Bnr1 and its damper Smy1, which leads to fewer and shorter filaments. (B) Smy1 reduces the rate of Bnr1-mediated elongation of actin filaments measured by TIRF, reflected by the slopes of the lines. (C) Concentration-dependent inhibitory effects of wild type and mutant Smy1 proteins on Bnr1-mediated actin assembly.

The focus of our investigation will be the formation of actin cables and the question: how is their unique size and shape specified? Since the same protein machinery used for cable formation (e.g. formins, profilin, tropomyosin, fimbrin, and cofilin) is found in virtual ly a l l eukaryotic cells [5,6,7,8], and is used (in combination with other proteins) to build diverse actin polymer networks, the principles we establ ish should have far-reaching application to understanding the control of actin network length and shape. The goal of this proposal is to test, using theory and experiment, the hypothesis that this myriad of proteins assert their control of actin cable length and shape through only a handful of coarse-grained parameters, the key ones being cable assembly and disassembly rates, and
cable stiffness.

Studies of a dynamic eukaryotic supramolecular assembly and its bio-inspired engineering of functional nanoparticles

Single yeast cells before (no stress) and following(stressed)
nutrient depletion. In these images above a single yeast
protein is fused with a green fluorescent protein to
visualize by confocal microscopy the assembly dynamics
of stress granules. (click image to enlarge)

Daniel A. Pomeranz Krummel
A eukaryotic cell possesses nuclear and cytoplasmic non-membranous subcellular organelles critical to processing and synthesis of ribonucleic acid (RNA). One of the most fascinating of these aggregates is the stress granule. A eukaryotic cell undergoes substantial biochemical and structural changes induced by stress, including formation in the cytoplasm of dynamic 100-200 nm diameter stress granules that appear to contribute to translational inhibition by sequestering messenger-RNA molecules. We are investigating how this sub-cellular aggregate is formed, disassembled, and what is integral to its activity. Central to the Brandeis MRSEC is the theme of assembly of biological materials. We propose to explore the assembly of this fascinating human aggregate in collaboration with MRSEC members Fraden and Hagan. Their long-standing interests in macromolecular assembly mechanisms and methods development to elucidate such phenomena will be significant to advance an understanding of the assembly of stress granules.