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CSDC Center for the Study of Complex Dynamics

The Florence EMBIO group: people and scientific activity Lapo Casetti Dipartimento di Fisica and CSDC, Università di Firenze. CSDC Center for the Study of Complex Dynamics. The CSDC is our “home”

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CSDC Center for the Study of Complex Dynamics

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  1. The Florence EMBIO group:people and scientific activityLapo CasettiDipartimento di Fisica and CSDC, Università di Firenze

  2. CSDCCenter for the Study of Complex Dynamics The CSDC is our “home” It is an inter-departmental structure of our University which hosts also researchers from the CNR (National Research Council) and from other research structures Graduate school on Nonlinear dynamics and complex systems: one graduate student funded by EMBIO starting January, 2006 All EMBIO researchers in Florence are part of CSDC

  3. People theory Physics Department Dr. Lorenzo Bongini Dr. Lapo Casetti Dr. Carlo Guardiani Prof. Roberto Livi Lorenzo Mazzoni EMBIO researcher Energetics Department Dr. Franco Bagnoli ISC - CNR Dr. Antonio Politi Dr. Alessandro Torcini INAF Dr. Marco Pettini experiment Physics Department Dr. Francesca Sbrana EMBIO graduate student EMBIO postdoc ISC - CNR Dr. Bruno Tiribilli Dr. Massimo Vassalli

  4. Call for applications! The call for applications for the EMBIO research position in the Florence group is being opened: look at www.unifi.it/bu The position is a research-only, fixed-term one (2 ½ years) starting April 1, 2006. Net salary is around 1500-1600 euros per month We are looking for a young but experienced researcher able to contribute with original ideas and to take a leading role in the theoretical side of the project We welcome applications from EMBIO partners The deadline is tight (August 20 or so) due to Italian rules, so hurry up!

  5. Outline theory Simple models of proteins BPN models Dynamical simulations Energy landscape Geometric and topological properties Dynamics on the “connectivity graph” Dr. Lorenzo Bongini experiment Atomic Force Microscopy How it works Pulling proteins Modeling Simple statistical models Reconstructing the (free) energy landscape

  6. Atomic Force Microscopy The probe is a micrometric cantilever, made by photo-litographic methods, with a sharp tip on the bottom. In the interaction potential with the sample, the cantilever behaves like an elastic spring with k ranging from 0.01 to 100 N/m An Atomic Force Microscope acts on the sample as a dynamometer able to probe the local interactions between tip and sample. If no specific interaction occurs between tip and sample, the system senses the geometry of the potential barrier defining the sample: the topography. By performing a scanning, the system spans the XY plane and the information collected can be imaged as a 2D map of the interaction. With standard cantilevers one obtains a topographic map of the surface (Microscopy) wherever using functionalised tips is possible to obtain specific maps such as magnetic, electric or affinity ones (Spectroscopy)

  7. Protein stretching

  8. Typical AFM stretching patterns Force Displacement Z

  9. Adsorption link The system studied behaves like a series of three springs. We have to choose the spring elastic constants accordingly to what we are interested in I30 T4 or T8 fragment I29 I28 Cys-Cys amino acids create a polar link with the gold substrate I27 Cys Cys Au Experimental protocol

  10. Sawtooth pattern Oberhauser et al., PNAS 98, p.468-472 (2001)

  11. The unfolding pattern is modeled like a polymer extension between two successive rupture events. The speed typically used allows to trait this region as in equilibrium. No information about folding is found by this approach; only mechanical parameters can be computed Modeling sawtooth patterns Force Displacement Z

  12. Polymer extension ERT Exponential rising of Tension FJC Freely-jointed chain WLC Worm-like chain

  13. WLC model Worm Like Chain Model Lp persistence length, LC contour length Z displacement, T temperature Li et al., Nature 418, p.998 (2002)

  14. Franco Bagnoli, Carlo Guardiani A unified approach Our aim is to find a simple model allowing a complete statistical description of the stretching experiment (not only polymer extension)

  15. The model: schematic view

  16. The model: basic features

  17. Energy: harmonic term

  18. Energy: interaction term

  19. A typical plot

  20. Beyond our toy model • Development of a more realistic protein model: • Three-dimensional model • Modelling of interactions between monomers • Study of the role of the mass of the cantilever and protein

  21. Free energy reconstruction N f r i 0 z z’ Reaction coordinate

  22. Free energy reconstruction: Jarzinski equality JE allows to reconstruct the free energy landscape by averaging over a set of non-equilibrium measurements

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