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Force measurements on single molecules
Felix Rico
Institut Curie, Paris, France
AFM BioMed Summer School Marcoule 2011
3rd European Summer School on Theory and Practice of AFM in Life
Sciences and Medicine
August 29, 2011
Outline
1.! Introduction
2.! Theory
3.! Force spectroscopy methods
4.! Examples
5.! Other methods
Introduction: why mechanics of proteins?
•! Muscle: titin
Klaus Schulten lab http://www.ks.uiuc.edu
•! Muscle: titin •! Cytoskeletal elements: filamin, actin, talin, spectrin
Cooper GM. The Cell: A Molecular Approach. 2nd edition.
Schwaiger, I., et al. 2004 Nat Struct Mol Biol
Introduction: why mechanics of proteins?
•! Muscle: titin •! Cytoskeletal elements: filamin, actin, talin, spectrin
Cooper GM. The Cell: A Molecular Approach. 2nd edition.
del Rio, A., et al. 2009 Science
Introduction: why mechanics of proteins?
Cooper GM. The Cell: A Molecular Approach. 2nd edition.
•! Muscle: titin •! Cytoskeletal elements: filamin, actin, talin, spectrin
Johnson, C. P., et al. 2007 Science
Introduction: why mechanics of proteins?
Cooper GM. The Cell: A Molecular Approach. 2nd edition. Shimaoka 2003 Nature Reviews
Introduction: why mechanics of proteins?
•! Muscle: titin •! Cytoskeletal elements: filamin, actin, talin, spectrin
•! Extracellular matrix: fibronectin, collagen •! Membrane proteins: integrins, bacteriorhodopsin
•! Muscle: titin •! Cytoskeletal elements: filamin, actin, talin, spectrin
•! Extracellular matrix: fibronectin, collagen •! Membrane proteins: integrins, bacteriorhodopsin
pdb 2at9 Mitsuoka et al. 1999 J Mol Biol
p
cytosolic
extracellular
h!"
Introduction: why mechanics of proteins?
•! Muscle: titin •! Cytoskeletal elements: filamin, actin, talin, spectrin
•! Extracellular matrix: fibronectin, collagen •! Membrane proteins: integrins, bacteriorhodopsin
•! Antibodies
Cooper GM. The Cell: A Molecular Approach. 2nd edition.
Introduction: why mechanics of proteins?
Receptor/ligand (un)binding
Protein (un)folding
Ion channels activity
Vesicle fusion Free energy
Reaction coordinate
kº ~ exp(-#F0/kBT)
x!"
#F0
Biological processes described by an energy
landscape
Bell 1978 Science
-f#x
f
Bell-Evans theory
Force
ln(k
off)
-f#x
f
Bell-Evans theory
Force
ln(k
off)
Bell 1978 Science
Evans and Ritchie 1997 Biophys J
Bell 1978 Science
Evans and Ritchie 1997 Biophys J
-f#x
f(t)
ln(rf)
Bell-Evans theory
-f#x
f(t)
ln(rf)
Bell 1978 Science
Evans and Ritchie 1997 Biophys J
Bell-Evans theory
Dudko et al. 2006 Phys Rev Lett
Friddle 2008 Phys Rev Lett
More refined theories
Forc
e
distance
The foce-distance curve
loading
rate
force
contact
setpoint z
Foce-distance curves: calibration
invOLS: voltage to deflection spring constant: deflection to force
Hutter and Bechhoefer 1993, Rev Sci Instr
Spring constant calibration methods
Burnham 2003 Nanotechnol
5-20% uncertainty
Interference, viscous drag!
Huang 2006 Meas. Sci. Technol.
Interference, viscous drag!
Alcaraz et al. 2002 Langmuir Janovjak et al. 2005 Eur Biophys J
V-shaped
rectangular
AFM force measurements: dynamic force spectroscopy
Rel
ativ
e fre
quen
cy
Unbinding force (pN) Loading rate (pN/s)
Forc
e
Distance
37 µm/s
3.7 µm/s
0.37 µm/s
Force (pN)
200 nm 30 pN
ks
16012080400
fr
52±21 pN/s
427±73 pN/s
2.7±0.5 nN/s
Life
tune
(s)
0.01
0.1
1
10
12080400
Unb
indi
ng fo
rce
(pN
)
70
60
50
40
30
20
104 6
1022 4 6103 2 4 6
104
A B C D
Rico, F., et al. 2011 Life at the nanoscale
Bustamante, C., et al. 2000 Nat Rev Mol Cell Biol
Sandal, M., et al. 2006 Polymer
Worm-like chain model
AFM force measurements: dynamic force spectroscopy
Crampton, N. and D. J. Brockwell 2010 Curr. Opin. Struct. Biol.
AFM force measurements: force-clamp
Other techniques: locki-in, laser feedback controlled cantilever! (see refs.)
AFM force measurements: DFS vs. force-clamp
DFS Force-clamp
Time resolution 50-100 "s 3-10 ms
Force resolution 5-10 pN >20 pN (lifetime)
Limitations
Tedious data
processing, viscous drag
Complex setup,
feedback loop response
Advantages Simple setup elegant data
processing
AFM force measurements: experimental conditions
•! Indentation force: 500 pN
•! Contact time: 0-1s
•! Retraction speed: 1 nm/s to 100 "m/s
•! Cantilevers:
•! spring constant: 6 pN/nm-100 pN/nm (Biolevers, microlevers,
OTR4)
•! resonance frequency: >5kHz in liquid
•! tip: unsharpened, radius 10-20 nm
•! Force-clamp forces: 20-300 pN (depending on the unfolding lifetime)
•! Samples:
•! gold surface (to allow cysteines to bind)
•! high protein concentration: 0.1 mg/mL
Example: muscle protein titin
Klaus Schulten lab http://www.ks.uiuc.edu
Titin: first AFM measurements
Rief, M., et al. 1997 Science
Titin: force-clamp measurements
Oberhauser, et al. 2001 PNAS
Titin: deeper insight
Marszalek, P. E., et al. 1999 Nature
Titin: deeper insight
Marszalek, P. E., et al. 1999 Nature
Titin: deeper insight
Lu, H., et al. 1998 Biophys. J. Klaus Schulten lab http://www.ks.uiuc.edu
Titin: deeper insight
Lu, H., et al. 1998 Biophys. J. Klaus Schulten lab http://www.ks.uiuc.edu
References
Bell, G. I. (1978). "Models for Specific Adhesion of Cells to Cells." Science 200(4342): 618-627.
Bustamante, C., J. C. Macosko, et al. (2000). "Grabbing the cat by the tail: manipulating molecules one by one."
Nat Rev Mol Cell Biol 1(2): 130-136.
Butt, H. J. and M. Jaschke (1995). "Calculation of thermal noise in atomic force microscopy." Nanotechnology 6:
1-7.
Burnham, N. A., X. Chen, et al. (2003). "Comparison of calibration methods for atomic-force microscopy cantilevers." Nanotechnology 14(1): 1-6.
Crampton, N., K. Alzahrani, et al. (2011). "Mechanically Unfolding Protein L Using a Laser-Feedback-Controlled Cantilever." Biophysical Journal 100(7): 1800-1809.
Crampton, N. and D. J. Brockwell (2010). "Unravelling the design principles for single protein mechanical strength." Current Opinion in Structural Biology 20(4): 508-517.
del Rio, A., R. Perez-Jimenez, et al. (2009). "Stretching Single Talin Rod Molecules Activates Vinculin Binding."
Science 323(5914): 638-641.
Dudko, O. K., A. E. Filippov, et al. (2003). "Beyond the conventional description of dynamic force spectroscopy
of adhesion bonds." Proc Natl Acad Sci U S A 100(20): 11378-81.
Dudko, O. K., G. Hummer, et al. (2006). "Intrinsic rates and activation free energies from single-molecule pulling experiments." Physical Review Letters 96(10).
Dudko, O. K., G. Hummer, et al. (2008). "Theory, analysis, and interpretation of single-molecule force spectroscopy experiments." Proc Natl Acad Sci U S A 105(41): 15755-60.
Evans, E. and K. Ritchie (1997). "Dynamic strength of molecular adhesion bonds." Biophysical Journal 72(4): 1541-1555.
Friddle, R. W. (2008). "Unified model of dynamic forced barrier crossing in single molecules." Physical Review
Letters 100(13).
Friddle, R. W., P. Podsiadlo, et al. (2008). "Near-equilibrium chemical force microscopy." Journal of Physical
Chemistry C 112(13): 4986-4990.
Hutter, J. L. and J. Bechhoefer (1993). "Calibration of atomic-force microscope tips." Review of Scientific Instruments 64(7): 1868-1873.
References
Johnson, C. P., H.-Y. Tang, et al. (2007). "Forced Unfolding of Proteins Within Cells." Science 317(5838): 663-666.
Kellermayer, M. s. S. Z., S. B. Smith, et al. (1997). "Folding-Unfolding Transitions in Single Titin Molecules Characterized with Laser Tweezers." Science 276(5315): 1112-1116.
Lu, H., B. Isralewitz, et al. (1998). "Unfolding of Titin Immunoglobulin Domains by Steered Molecular Dynamics Simulation." Biophysical Journal 75(2): 662-671.
Marszalek, P. E., H. Lu, et al. (1999). "Mechanical unfolding intermediates in titin modules." Nature 402(6757):
100-103.
Oberhauser, A. F., P. K. Hansma, et al. (2001). "Stepwise unfolding of titin under force-clamp atomic force
microscopy." Proceedings of the National Academy of Sciences of the United States of America 98(2): 468-472.
Rico, F., C. Chu, et al. (2011). "Force-Clamp Measurements of Receptor-Ligand Interactions." Methods in Molecular Biology 736: 331-353.
Rief, M., M. Gautel, et al. (1997). "Reversible unfolding of individual titin immunoglobulin domains by AFM." Science 276(5315): 1109-12.
Sandal, M., F. Grandi, et al. (2006). "Single molecule force spectroscopy discovers mechanochemical switches in biology: The case of the disulfide bond." Polymer 47(7): 2571-2579.
Schlierf, M., F. Berkemeier, et al. (2007). "Direct Observation of Active Protein Folding Using Lock-in Force
Spectroscopy." Biophysical Journal 93(11): 3989-3998.
Schwaiger, I., A. Kardinal, et al. (2004). "A mechanical unfolding intermediate in an actin-crosslinking protein."
Nat Struct Mol Biol 11(1): 81-85.
Stark, R. W., T. Drobek, et al. (2001). "Thermomechanical noise of a free v-shaped cantilever for atomic-force microscopy." Ultramicroscopy 86(1-2): 207-215.
Williams, P. M., S. B. Fowler, et al. (2003). "Hidden complexity in the mechanical properties of titin." Nature 422(6930): 446-449