13-19 June 2015
University of Alberta
America/Edmonton timezone
Welcome to the 2015 CAP Congress! / Bienvenue au congrès de l'ACP 2015!

Inferring compactness and asphericity of disordered protein ensembles by single molecule FRET spectroscopy and coarse grained simulations

18 Jun 2015, 10:15
15m
NINT Taylor room (University of Alberta)

NINT Taylor room

University of Alberta

Oral (Student, In Competition) / Orale (Étudiant(e), inscrit à la compétition) Medical and Biological Physics / Physique médicale et biologique (DMBP-DPMB) R1-2 Computational Biophysics (DMBP-DCMMP) / Biophysique numérique (DPMB-DPMCM)

Speaker

Mr Gregory Gomes (Department of Chemical and Physical Sciences, University of Toronto Mississauga and Department of Physics, University of Toronto)

Description

A large number of proteins, termed intrinsically disordered proteins (IDPs), fail to fold into well-defined three-dimensional structures. Many of these IDPs are associated with diseases, such as cancer or neurodegenerative disorders. In contrast to well-folded proteins, the polymer properties of IDPs are often crucial aspects of their functions. Correspondingly, to develop a better understanding of how disorder is used in function, we used a quantitative polymer-physics-based approach to analyze data from single-molecule FRET (smFRET) spectroscopy experiments. We infer the properties of the conformational ensemble by matching an experimental average transfer efficiency $ \rm \langle E \rangle_{exp}$ with one that is computed from a distribution $\rm P(R_{ee})$ of end-to-end distances $\rm R_{ee}$. In a refinement of the conventional approach, we use extensive sampling of coarse-grained protein chains with excluded volume to generate physically realistic $\rm P(R_{ee}|R_{g},A)$ conditioned on the radius of gyration $\rm R_{g}$ (a description of compactness) and asphericity A (a description of shape). This methodology is applied to residues 1-90 of the intrinsically disordered Cdk inhibitor Sic1, resulting in ensembles that are more compact than those deduced by conventional procedures which assume a Gaussian chain model without excluded volume. This result is in good agreement with SAXS measured Rg data and NMR measurements of the hydrodynamic radius. In future studies, this methodology will be applied to refine a polyelectrostatic model for phosphorylated Sic1’s ultrasensitive interaction with Cdc4 by providing information on the conformational shape and dimensions of bound and free phosphorylated Sic1, and to test whether possible adjustments to the polarizable charge distribution impact binding affinity.

Primary authors

Mr Gregory Gomes (Department of Chemical and Physical Sciences, University of Toronto Mississauga and Department of Physics, University of Toronto) Dr Jianhui Song (Department of Biochemistry and Department of Molecular Genetics and Department of Physics , University of Toronto)

Co-authors

Dr Claudiu C. Gradinaru (Department of Chemical and Physical Sciences, University of Toronto Mississauga and Department of Physics, University of Toronto) Dr Hue Sun Chan (Department of Biochemistry and Department of Molecular Genetics and Department of Physics, University of Toronto)

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