folding and unfolding at the level of a single molecule, where the
distinction between the pathway model and funnel model is clearer.
They also provide a convenient benchmark for verifying molecular
-dynamics simulations, because it takes a quite a bit of computing
-power to simulate even one biopolymer with anything close to atomic
-resolution over experimental timescales. Even with significant
-computing resources, comparing molecular dynamics results with
-experimental data remains elusive. For example, experimental pulling
-speeds are on the order of \bareU{$\mu$m/s}, while simulation pulling
-speeds are on the order of
-\bareU{m/s}\citep{lu98,lu99,rief02,zhao06,berkemeier11}.
+dynamics simulations, because it takes lots of computing power to
+simulate even one biopolymer with anything close to atomic resolution
+over experimental time scales. Even with significant computing
+resources, comparing molecular dynamics results with experimental data
+remains elusive. For example, experimental pulling speeds are on the
+order of \bareU{$\mu$m/s}, while simulation pulling speeds are on the
+order of \bareU{m/s}\citep{lu98,lu99,rief02,zhao06,berkemeier11}.
% why AFM & what an AFM is
Single molecule techniques for manipulating biopolymers include
doi = "10.1073/pnas.0404549101",
eprint = "http://www.pnas.org/cgi/reprint/101/46/16192.pdf",
url = "http://www.pnas.org/cgi/content/abstract/101/46/16192",
- abstract = "We use single-molecule force spectroscopy to drive single GFP
- molecules from the native state through their complex energy landscape
- into the completely unfolded state. Unlike many smaller proteins,
- mechanical GFP unfolding proceeds by means of two subsequent
- intermediate states. The transition from the native state to the first
- intermediate state occurs near thermal equilibrium at {approx}35 pN and
+ abstract = "We use single-molecule force spectroscopy to drive
+ single GFP molecules from the native state through their
+ complex energy landscape into the completely unfolded
+ state. Unlike many smaller proteins, mechanical GFP unfolding
+ proceeds by means of two subsequent intermediate states. The
+ transition from the native state to the first intermediate
+ state occurs near thermal equilibrium at $\approx35\U{pN}$ and
is characterized by detachment of a seven-residue N-terminal
- {alpha}-helix from the beta barrel. We measure the equilibrium free
- energy cost associated with this transition as 22 kBT. Detachment of
- this small {alpha}-helix completely destabilizes GFP thermodynamically
- even though the {beta}-barrel is still intact and can bear load.
- Mechanical stability of the protein on the millisecond timescale,
- however, is determined by the activation barrier of unfolding the
- {beta}-barrel out of this thermodynamically unstable intermediate
- state. High bandwidth, time-resolved measurements of the cantilever
- relaxation phase upon unfolding of the {beta}-barrel revealed a second
- metastable mechanical intermediate with one complete {beta}-strand
- detached from the barrel. Quantitative analysis of force distributions
- and lifetimes lead to a detailed picture of the complex mechanical
+ $\alpha$-helix from the beta barrel. We measure the
+ equilibrium free energy cost associated with this transition
+ as 22 kBT. Detachment of this small $\alpha$-helix completely
+ destabilizes GFP thermodynamically even though the
+ $\beta$-barrel is still intact and can bear load. Mechanical
+ stability of the protein on the millisecond timescale,
+ however, is determined by the activation barrier of unfolding
+ the $\beta$-barrel out of this thermodynamically unstable
+ intermediate state. High bandwidth, time-resolved measurements
+ of the cantilever relaxation phase upon unfolding of the
+ $\beta$-barrel revealed a second metastable mechanical
+ intermediate with one complete $\beta$-strand detached from
+ the barrel. Quantitative analysis of force distributions and
+ lifetimes lead to a detailed picture of the complex mechanical
unfolding pathway through a rough energy landscape.",
note = "Nice energy-landscape-to-one-dimension compression graphic.
Unfolding Green Flourescent Protein (GFP) towards using it as an
pages = "105--128",
issn = "1056-8700",
doi = "10.1146/annurev.biophys.30.1.105",
- url = "http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.biophy
- s.30.1.105",
+ url = "http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.biophys.30.1.105",
keywords = "Biophysics;Kinetics;Microscopy, Atomic Force;Models,
Chemical;Protein Binding;Spectrum Analysis;Time Factors",
abstract = "On laboratory time scales, the energy landscape of a weak bond
protein) for all 20 structures deposited in the Protein Data Bank. Our
approach suggests a natural way to measure the phase diagram in the
(f,C) plane, where C is the concentration of denaturants.",
- note = "Simulated unfolding timescales for Ig27-like S1 and S2 domains"
+ note = {Simulated unfolding time scales for Ig27-like S1 and S2 domains.},
}
@article { klimov99,
including a characterization of the structures, albeit at a coarse-
grained level, of the three metastable intermediates.",
note = {Hiccup in unfolding leg corresponds to unfolding
- intermediate (\fref{figure}{2}). The unfolding timescale in GFP
- is about $6\U{ms}.}
+ intermediate (\fref{figure}{2}). The unfolding time scale in GFP
+ is about $6\U{ms}$.},
}
@article { nevo03,
projects / thesis.git / commitdiff