Chemistry Reference
In-Depth Information
importance [70], yet the details of the underlying distribution of conformations is
experimentally challenging.
Both X-ray crystallography and NMR structures bias the results towards the
average structure of the minimum energy conformations [71], such that the less-
visited metastable states are overlooked. The diversity in conformational energies of
the native state is further neglected by solution studies of protein folding/unfolding,
which use the two-state model to distinguish between the average pathways under
different experimental conditions using phi-value analysis [72].
On the other hand, the scale-free nature of the measured rate distribution, P(
a
),
characterized by the power law coef
cient, can be interpreted by a rough energy
landscape in which the energy states,
E
, are distributed with an exponential
), where the energy scale E
distribution
P
(
E
¼
6
:
7k
B
T. This result is based on the
assumption that the
Þ¼
t
:15
k
b
T
e
E= E
0
P
ð
E
ð
13
:
3
Þ
protein is hopping over a multitude of unfolding energy barriers via an Arrhenius
process [73]. This broad energy distribution reveals a wealth of conformational states
available to the protein which is not observed in the reaction coordinate of the end-to-
end length. Relatively small perturbations (below 1 nm) in the length of the protein
seem to have signi
cantly different free energies within this model. This interpreta-
tion, analogous to many other complex glassy systems [74], has previously been
encountered in the literature examining folded-protein dynamics at the single-
molecule level, including enzyme kinetics and activity [19
-
23, 75]. Structurally,
more detailed NMR relaxation experiments reveal deviations from the two-state
model for individual residues in a protein [76], and a separate work detects more
spatially diverse structures in the same protein ubiquitin than was previously
anticipated [18]. Using force-clampAFMwe have provided the
rst detailed signature
of such complex behavior encountered in the unfolding process [27]. In the next
sectionwe reveal the exciting newbreakthroughs in protein folding achieved through
force-clamp spectroscopy.
13.5
Protein Folding
A major goal of biomolecular science has been to understand the protein folding
problem. In the last few decades, signi
cant progress has been made, both from the
fundamental biochemical perspective [72, 77
79] and from the practical aspect of
predicting protein structure from sequence data [80], and even designing arti
-
cial
proteins [81]. From the physics perspective, there has also been a growing apprecia-
tion of the need to use appropriate statistical mechanical tools to characterize the free
energy landscape of a protein [25, 26, 82, 83].
Many theories have emerged as a result, largely supported by numerical simula-
tions of model protein systems [84
-
91]. However, what has been lacking is an
