Principles of RNA compaction : insights from equilibrium folding pathway of p...
2015BPSposterQL
1. Capturing the Mechanical unfolding pathway
of a Large Protein with Coiled-coil Probes
Qing Lia
, Zack Schollb,c
, Piotr E. Marszaleka
Abstract
1.We report the development of novel mechanical
folding probes that are based on antiparallel coiled-coil
polypeptides. Such probes can be conveniently inserted,
at the DNA level, at different positions within the protein
of interest where they minimally disturb the host protein
structure.
2.During single-molecule force spectroscopy
measurements, the forced unfolding of the probes
captures the progress of the unfolding front through the
host protein structure, which allows unfolding pathways
of large proteins to be directly identified
NI6C Sequential Unfolding
1. Marszalek, P. E., Lu, H., Li, H., Carrion-Vazquez, M., Oberhauser, A. F.,Schulten, K., and Fernandez, J. M. (1999). Mechanical unfolding intermediates in
titin modules. Nature 402, 100–103
2. Lee, W., X. Zeng, ., P. E. Marszalek. (2010). Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics
simulations. J. Biol. Chem. 285:38167–38172.
3. Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ, Li H. (2003). Structure and function of archaeal box C/D sRNP core proteins. Nature Structural
Biology 10(4):256–263
Lee W. et al (2010) J. Biol. Chem
Single Molecule Force
Spectroscopy by AFM
CG Simulation
Conclusions
Unfolding Pathway of
NI10C Probed by CC
1
2
3
4
5 7
6
100 nm
100pN
AFM Principle AFM Unfolding Pattern
of poly-Titin I27 Domains[1]
1.NI10C follows a sequential, vectorial unfolding C→N
process.
2.More generally, anti-parallel coiled coil peptides could be
very useful for examining unfolding pathways of large
multidomain proteins.
We thank Jane Clarke for for providing the plasmids with poly I27 domains. This
work was supported by NSF grant MCB-1052208 to PEM. P.E.M. also acknowledges
kind support from the Kimberly–Clark Corporation.
AFM experimental
Unfolding of NI6C[2]
Acknowledgements
a
Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708
b
Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708
c
Program in Structural Biology and Biophysics, Duke University, Durham, North Carolina, 27708
1
3
6
4
5
7
2
Coarse-grained pulling
simulation of NI6C[2]
CC Unfolding Profile
References
1NT2[3]
CC Superimposed results
Fractional extension
comparison
![Capturing the Mechanical unfolding pathway
of a Large Protein with Coiled-coil Probes
Qing Lia
, Zack Schollb,c
, Piotr E. Marszaleka
Abstract
1.We report the development of novel mechanical
folding probes that are based on antiparallel coiled-coil
polypeptides. Such probes can be conveniently inserted,
at the DNA level, at different positions within the protein
of interest where they minimally disturb the host protein
structure.
2.During single-molecule force spectroscopy
measurements, the forced unfolding of the probes
captures the progress of the unfolding front through the
host protein structure, which allows unfolding pathways
of large proteins to be directly identified
NI6C Sequential Unfolding
1. Marszalek, P. E., Lu, H., Li, H., Carrion-Vazquez, M., Oberhauser, A. F.,Schulten, K., and Fernandez, J. M. (1999). Mechanical unfolding intermediates in
titin modules. Nature 402, 100–103
2. Lee, W., X. Zeng, ., P. E. Marszalek. (2010). Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics
simulations. J. Biol. Chem. 285:38167–38172.
3. Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ, Li H. (2003). Structure and function of archaeal box C/D sRNP core proteins. Nature Structural
Biology 10(4):256–263
Lee W. et al (2010) J. Biol. Chem
Single Molecule Force
Spectroscopy by AFM
CG Simulation
Conclusions
Unfolding Pathway of
NI10C Probed by CC
1
2
3
4
5 7
6
100 nm
100pN
AFM Principle AFM Unfolding Pattern
of poly-Titin I27 Domains[1]
1.NI10C follows a sequential, vectorial unfolding C→N
process.
2.More generally, anti-parallel coiled coil peptides could be
very useful for examining unfolding pathways of large
multidomain proteins.
We thank Jane Clarke for for providing the plasmids with poly I27 domains. This
work was supported by NSF grant MCB-1052208 to PEM. P.E.M. also acknowledges
kind support from the Kimberly–Clark Corporation.
AFM experimental
Unfolding of NI6C[2]
Acknowledgements
a
Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708
b
Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708
c
Program in Structural Biology and Biophysics, Duke University, Durham, North Carolina, 27708
1
3
6
4
5
7
2
Coarse-grained pulling
simulation of NI6C[2]
CC Unfolding Profile
References
1NT2[3]
CC Superimposed results
Fractional extension
comparison](https://image.slidesharecdn.com/417ebb94-5895-4172-81c5-69af3e47eb9f-160105195648/85/2015BPSposterQL-1-320.jpg)
