The Florence EMBIO group: people and scientific activity Lapo Casetti Dipartimento di Fisica and CSD

1
The Florence EMBIO grouppeople 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
experiment Atomic Force Microscopy How it
works Pulling proteins Modeling Simple
statistical models Reconstructing the (free)
energy landscape
theory Simple models of proteins BPN
models Dynamical simulations Energy
landscape Geometric and topological
properties Dynamics on the connectivity
graph Dr. Lorenzo Bongini
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
Experimental protocol
10
Sawtooth pattern
Oberhauser et al., PNAS 98, p.468-472 (2001)
11
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
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
z
z
0
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