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Symposium on Chemical Biology

Schedule

13:30 Welcome from our directors
13:40-14:30 Anne-Claude Gavin
14:20-15:10 Akihiro Kusumi
15:10-15:40 Coffee Break
15:40-16:30 Yamuna Krishnan
16:30-17:20 Samie Jaffrey
Onwards : Apero & Networking

Presentations & Speakers

Lipid-protein complexes
Anne-Claude Gavin
EMBL –  Heidelberg – Germany

Plasma membrane domain mechanisms for signal transduction as revealed by single-molecule tracking
Akihiro Kusumi
Kyoto University – Kyoto – Japan

Molecular DNA devices in Living Systems
Yamuna Krishnan
The University of Chicago – Chicago- USA

Imaging RNA and RNA biology using RNA mimics of green fluorescent protein
Samie Jaffrey
Cornell University – Ithaca – USA

 Abstracts

Lipid-protein complexes
Anne-Claude Gavin, Group Leader & Senior Scientist, SCB Unit, EMBL-Heidelberg, Germany

Eukaryotic cells use membrane-bounded organelles with unique lipid and protein compositions to regulate and spatially organize cellular functions and signalling. As part of this tight control, many proteins are regulated by lipids. In humans, the importance of these regulatory circuits is evident from the variety of disorders arising from altered protein–lipid interactions, which constitute attractive targets for pharmaceutical drug development. However, the full repertoire of interactions remains poorly explored and exploited because their detection is still difficult to achieve on a large, systematic scale. I will describe a series of chemical biology approaches to characterize in vivo assembled, stable protein-lipid complexes(1) and to study lipid interactions with peripheral membrane proteins(2). Data from yeast and human cell lines reveal surprising insights, such as the discovery of a new family of oxysterol-binding protein, conserved in humans (where it has been linked to several diseases) with unexpected specificities for an important signaling lipid, phosphatidylserine. The assays are scalable to the proteome and/or lipidome levels and are easily adapted to the study of small-molecules that disrupt protein–lipid interactions.

 

Imaging RNA and RNA biology using RNA mimics of green fluorescent protein
Samie R. Jaffrey, Weill Medical College, Cornell University, New York, United States

Green fluorescent protein (GFP) and its derivatives have transformed the use and analysis of proteins for diverse applications. Like proteins, RNA has complex roles in cellular function and is increasingly used for various in vitro and in vivo applications, but a comparably robust and simple approach for fluorescently tagging RNA is lacking. We will describe the creation of RNA aptamers that bind fluorophores resembling the fluorophore in GFP. These fluorophores are nonfluorescent until they are bound by these RNAs.  These fluorescent RNA-fluorophore complexes RNAs activate the fluorescence of these fluorophores, resulting in a palette of RNA-fluorophore complexes that span the visible spectrum. An RNA-fluorophore complex resembling enhanced GFP (EGFP), termed Spinach, emits a green fluorescence comparable in brightness to fluorescent proteins. Spinach can be fused to RNAs and expressed in cells in order to image RNA localization and other RNA regulatory processes in cells. Spinach can be used to create sensors composed of RNA that enable the imaging of other biological molecules. We will discuss novel structure-guided and directed evolution approaches for generating novel optimized Spinach variants with improved photophysical properties.  We have used these approaches, as well as new fluorophore chemistries to create new RNA-fluorophore complexes suitable for imaging in yellow and red fluorescence channels.  These RNA mimics of GFP provide novel approaches to image RNA biology and other processes in cells.

 

Molecular DNA devices in Living Systems
Yamuna Krishnan, University of Chicago

Due to its nanoscale dimensions and ability to self-assemble via specific base pairing, DNA is rapidly taking on a new aspect where it is finding use as a construction element for architecture on the nanoscale.1 Structural DNA nanotechnology has yielded architectures of exquisite complexity and functionality in vitro. However, till 2009, the functionality of such synthetic DNA-based devices in living organisms remained elusive. Work from my group the last few years has bridged this gap where, we have chosen architecturally simple, DNA-based molecular devices and shown their functionality in complex living environments. Using two examples, from our lab, one of a rigid, DNA polyhedron2 and the other a molecular switch3 that functions as a pH sensor I will illustrate the potential of DNA based molecular devices as unique tools with which to interrogate living systems.

 

Plasma membrane domain mechanisms for signal transduction as revealed by single-molecule tracking
Akihiro Kusumi, Institute for Integrated Cell-Material Sciences (WPI-iCeMS) and Institute for Frontier Medical Sciences, Kyoto University, Japan

Single-molecule tracking techniques that are applicable to living cells are now providing researchers with the unprecedented ability to directly observe molecular behaviors in the plasma membranes (PMs) of living cells, and revolutionizing our understanding of the PM dynamics, structure, and signal transduction mechanisms (Kusumi et al. 2014; Kasai et al. 2014). The PM is considered the quasi-2D NON-ideal fluid that is associated with the actin-based membrane-skeleton meshwork, and its functions are likely enabled by the mechanisms based on such a unique dynamic structure, which I call membrane mechanisms. My group is largely responsible for advancing high-speed single molecule tracking with simultaneous multicolor recording. In this talk, I will propose, based on our observations made by this approach, that the cooperative action of the hierarchical three-tiered mesoscale (2–300 nm) domains—-actin-membrane-skeleton induced compartments (40–300 nm), raft domains (2–20 nm), and dynamic protein complex domains (3–10 nm)—-is critical for membrane function and distinguishes the plasma membrane from a classical Singer-Nicolson-type model (Kusumi et al. 2012a, b). In particular, I will pay special attention to the cell’s first steps for the formation of raft domains that involve GPI-anchored receptors (GPI-AR) and how the are converted to signaling raft domains ()Kusumi et al. 2012b). GPI-ARs continually form transient (~200 ms) homodimers (termed homodimer rafts) through ectodomain protein interactions, stabilized by raft-lipid interactions. Heterodimers do not form, suggesting a fundamental role for the specific ectodomain protein interaction. When CD59 was ligated, it formed stable oligomer rafts containing up to four CD59 molecules, which triggered intracellular Ca2+ responses that were dependent on GPI-anchorage and cholesterol, suggesting a key role played by transient homodimer rafts. Transient homodimer rafts are most likely one of the basic units for organization and function of raft domains containing GPI-ARs.