Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Session I Abstracts

Distinguishing between Allosteric Mechanisms Using Structural Mass-Spectrometry Is Demonstrated for the Chaperonin GroEL Amnon Horovitz . Weizmann Institute of Science, Rehovot, Israel. Allosteric regulation is often described by the concerted Monod–Wyman–Changeux or sequential Koshland–Némethy–Filmer models of cooperativity. In general, however, it has been impossible to distinguish between these allosteric models using ensemble measurements of ligand binding in bulk protein solutions. In this talk, a new structural mass-spectrometry approach will be described that breaks this impasse by providing the full distribution of ligand- bound states of a protein complex. Given this distribution, it is possible to determine all the binding constants of a ligand to a highly multimeric cooperative system and, thus, infer its allosteric mechanism. The approach will be demonstrated for the chaperonin GroEL that consists of two back-to-back stacked heptameric rings with a cavity at each end where protein folding can take place. GroEL displays intra-ring positive cooperativity and inter-ring negative cooperativity in ATP binding, with respect to ATP, that are crucial for its function. It will be shown that this new approach provides evidence for a concerted mechanism of allosteric switching and information on the ATP-loading pathway. The impact of the concerted nature of the intra-ring allosteric transitions of GroEL on its folding function will be discussed.

Ras: a Structural Biologist View and Questions Ruth Nussinov . NCI, Frederick, MD, USA.

Ras proteins are small GTPases that act as signal transducers between cell surface receptors and several intracellular signaling cascades. KRas4B is among the frequently mutated oncogenes in human tumors. Ras proteins consist of highly homologous catalytic domains, and flexible C- terminal hypervariable regions (HVRs) that differ significantly across Ras isoforms. We have been focusing on key mechanistic questions in Ras biology from the structural standpoint. These include whether Ras forms dimers, and if so what is their structural landscape; how do Ras dimers activate Raf, a key Ras effector in a major signaling pathway; how calmodulin inhibit Raf signaling, and the potential role of the hypervariable region and its membrane anchoring regulation. We believe that structural biology, computations and experiment, are uniquely able to tackle these fascinating questions.

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