author = DJBrockwell #" and "# EPaci #" and "# RCZinober #" and "#
GSBeddard #" and "# PDOlmsted #" and "# DASmith #" and "# RNPerham #"
and "# SERadford,
- title = "Pulling geometry defines the mechanical resistance of a beta-sheet
+ title = "Pulling geometry defines the mechanical resistance of a $\beta$-sheet
protein",
year = 2003,
month = sep,
are still unclear, although the orientation of secondary structural
elements relative to the applied force vector is thought to have an
important function. Here, by using a method of protein immobilization
- that allows force to be applied to the same all-beta protein, E2lip3,
+ that allows force to be applied to the same all-$\beta$ protein, E2lip3,
in two different directions, we show that the energy landscape for
mechanical unfolding is markedly anisotropic. These results, in
combination with molecular dynamics (MD) simulations, reveal that the
force spectroscopy. Force-extension and force-clamp curves obtained
from Lethocerus projectin and Drosophila recombinant projectin or
kettin fragments revealed that fibronectin type III domains in
- projectin are mechanically weaker (unfolding force, Fu {approx} 50-150
- pN) than Ig-domains (Fu {approx} 150-250 pN). Among Ig domains in
+ projectin are mechanically weaker (unfolding force, Fu $\approx$ 50-150
+ pN) than Ig-domains (Fu $\approx$ 150-250 pN). Among Ig domains in
Sls/kettin, the domains near the N terminus are less stable than those
- near the C terminus. Projectin domains refolded very fast [85% at 15
- s-1 (25{degrees}C)] and even under high forces (15-30 pN). Temperature
+ near the C terminus. Projectin domains refolded very fast [85\% at 15
+ s-1 (25$\degrees$C)] and even under high forces (15-30 pN). Temperature
affected the unfolding forces with a Q10 of 1.3, whereas the refolding
speed had a Q10 of 2-3, probably reflecting the cooperative nature of
the folding mechanism. High bending rigidities of projectin and kettin
pages = "63--91",
doi = "10.1016/S0079-6107(00)00017-1",
issn = "0079-6107",
- eprint = "http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1302160&blo
- btype=pdf",
+ eprint = "http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1302160&blobtype=pdf",
url = "http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302160",
keywords = "Elasticity;Hydrogen Bonding;Microscopy, Atomic Force;Protein
Denaturation;Protein Engineering;Protein Folding;Recombinant
the dynamic measurement of these processes at the single-molecule
level. Protein engineering techniques allow the construction of
homomeric polyproteins for the precise analysis of the mechanical
- unfolding of single domains. alpha-Helical domains are mechanically
- compliant, whereas beta-sandwich domains, particularly those that
+ unfolding of single domains. $\alpha$-Helical domains are mechanically
+ compliant, whereas $\beta$-sandwich domains, particularly those that
resist unfolding with backbone hydrogen bonds between strands
perpendicular to the applied force, are more stable and appear
frequently in proteins subject to mechanical forces. The mechanical
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
+ as 22 $k_BT$. 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,
pattern recognition, GFP",
abstract = "Single molecule force spectroscopy has given experimental
access to the mechanical properties of protein molecules. Typically,
- less than 1% of the experimental recordings reflect true single
+ less than 1\% of the experimental recordings reflect true single
molecule events due to abundant surface and multiple-molecule
interactions. A key issue in single molecule force spectroscopy is thus
to identify the characteristic mechanical `fingerprint' of a specific
the first crystal form and biotin bound in only two subunits in a
second. The major change associated with binding of biotin is the
closure of the surface loop incorporating residues 45 to 52. Residues
- 49 to 52 display a 3(10) helical conformation in unbound subunits of
+ 49 to 52 display a $3_{10}$ helical conformation in unbound subunits of
our structures as opposed to the disordered loops observed in other
structure determinations of streptavidin. In addition, the open
- conformation is stabilized by a beta-sheet hydrogen bond between
+ conformation is stabilized by a $\beta$-sheet hydrogen bond between
residues 45 and 52, which cannot occur in the closed conformation. The
- 3(10) helix is observed in nearly all unbound subunits of both the co-
+ $3_{10}$ helix is observed in nearly all unbound subunits of both the co-
crystallized and ligand-free structures. An analysis of the temperature
factors of the binding loop regions suggests that the mobility of the
closed loops in the complexed structures is lower than in the open
segment that could be stretched entropically depending on the tip
attachment site. The data presented here provide direct information
about the forces required to extract an individual monomer from the
- core of the PrP90-231 amyloid, and indicate that the beta-sheet core of
- this amyloid starts at residue approximately 164-169. The latter
+ core of the PrP90-231 amyloid, and indicate that the $\beta$-sheet core of
+ this amyloid starts at residue $\approx$164-169. The latter
finding has important implications for the ongoing debate regarding the
structure of PrP amyloid."
}
contain such cryptic sites that promote the assembly of extracellular
matrix FN fibrils. We have combined NMR and steered molecular dynamics
simulations to study the structure and mechanical unfolding pathway of
- FN-III1. This study finds that FN-III1 consists of a {beta}-sandwich
+ FN-III1. This study finds that FN-III1 consists of a $\beta$-sandwich
structure that unfolds to a mechanically stable intermediate about four
times the length of the native folded state. Considering previous
experimental findings, our studies provide a structural model by which
elasticity. Its physiological extension is largely derived from the
PEVK segment, rich in proline (P), glutamate (E), valine (V), and
lysine (K) residues. We studied recombinant PEVK molecules containing
- the two conserved elements: {approx}28-residue PEVK repeats and E-rich
+ the two conserved elements: $\approx$28-residue PEVK repeats and E-rich
motifs. Single molecule experiments revealed that calcium-induced
conformational changes reduce the bending rigidity of the PEVK
fragments, and site-directed mutagenesis identified four glutamate
distance, occurs in distinct multiple stages. To clarify the molecular
nature of folding starting from stretched conformations, we have probed
the folding dynamics, upon force quench, for the single I27 domain from
- the muscle protein titin by using a C{alpha}-Go model. Upon temperature
+ the muscle protein titin by using a C$\alpha$-Go model. Upon temperature
quench, collapse and folding of I27 are synchronous. In contrast,
refolding from stretched initial structures not only increases the
folding and collapse time scales but also decouples the two kinetic
with the stretched state to compact random coil transition.
Surprisingly, force quench does not alter the nature of the refolding
kinetics, but merely increases the height of the free-energy folding
- barrier. Force quench refolding times scale as f1.gif, where {Delta}xf
- {approx} 0.6 nm is the location of the average transition state along
+ barrier. Force quench refolding times scale as f1.gif, where $\Delta x_f$
+ $\approx$ 0.6 nm is the location of the average transition state along
the reaction coordinate given by end-to-end distance. We predict that
- {tau}F and the folding mechanism can be dramatically altered by the
+ $\tau_F$ and the folding mechanism can be dramatically altered by the
initial and/or final values of force. The implications of our results
for design and analysis of experiments are discussed."
}
loading rates and time scales that closely match those used in atomic
force microscopy experiments. By using the combined approach, we show
that forced unfolding of GFP involves a bifurcation in the pathways to
- the stretched state. After detachment of an N-terminal {alpha}-helix,
+ the stretched state. After detachment of an N-terminal $\alpha$-helix,
unfolding proceeds along two distinct pathways. In the dominant
pathway, unfolding starts from the detachment of the primary N-terminal
-strand, while in the minor pathway rupture of the last, C-terminal
extensive substitution, FNoTNc retains both the three-dimensional
structure and the cell adhesion activity of FNfn10. Atomic force
microscopy experiments reveal that the unfolding forces of the
- engineered protein FNoTNc increase by {approx}20% to match those of
+ engineered protein FNoTNc increase by $\approx$20\% to match those of
TNfn3. Thus, we have specifically designed a protein with increased
mechanical stability. Our results demonstrate that core engineering can
be used to change the mechanical strength of proteins while retaining
number of critical hydrogen bonds in the peripheral
strands. Interestingly, the simulations predict that lowering
the pH from 7 to ∼4.7 will increase the mechanical stability
- of FNfn10 significantly (by ∼33 %) due to the protonation of a
+ of FNfn10 significantly (by ∼33 \%) due to the protonation of a
few key acidic residues in the A and B strands. To test this
simulation prediction, we used single-molecule atomic force
microscopy (AFM) to investigate the mechanical stability of
eprint = "http://www.pnas.org/cgi/reprint/104/22/9278.pdf",
url = "http://www.pnas.org/cgi/content/abstract/104/22/9278",
abstract = "It is recognized that shear topology of two directly connected
- force-bearing terminal [beta]-strands is a common feature among the
+ force-bearing terminal $\beta$-strands is a common feature among the
vast majority of mechanically stable proteins known so far. However,
these proteins belong to only two distinct protein folds, Ig-like
- [beta] sandwich fold and [beta]-grasp fold, significantly hindering
+ $\beta$ sandwich fold and $\beta$-grasp fold, significantly hindering
delineating molecular determinants of mechanical stability and rational
tuning of mechanical properties. Here we combine single-molecule atomic
force microscopy and steered molecular dynamics simulation to reveal
that the de novo designed Top7 fold [Kuhlman B, Dantas G, Ireton GC,
Varani G, Stoddard BL, Baker D (2003) Science 302:13641368] represents
- a mechanically stable protein fold that is distinct from Ig-like [beta]
- sandwich and [beta]-grasp folds. Although the two force-bearing [beta]
+ a mechanically stable protein fold that is distinct from Ig-like $\beta$
+ sandwich and $\beta$-grasp folds. Although the two force-bearing $\beta$
strands of Top7 are not directly connected, Top7 displays significant
mechanical stability, demonstrating that the direct connectivity of
- force-bearing [beta] strands in shear topology is not mandatory for
+ force-bearing $\beta$ strands in shear topology is not mandatory for
mechanical stability. This finding broadens our understanding of the
design of mechanically stable proteins and expands the protein fold
space where mechanically stable proteins can be screened. Moreover, our
with different height of energy barrier. Such insights enabled us to
rationally tune the mechanical stability of Top7 by redesigning its
mechanical unfolding pathway. Our study demonstrates that computational
- biology methods (including de novo design) offer great potential for
+ biology methods (including \emph{de novo} design) offer great potential for
designing proteins of defined topology to achieve significant and
tunable mechanical properties in a rational and systematic fashion."
}
photoactive yellow protein (PYP), a prototype of the PAS domain family.
Mechanical unfolding of Cys-linked PYP multimers in the presence and
absence of illumination reveals that, in contrast to previous studies,
- the PAS domain itself is extended by {approx}3 nm (at the 10-pN
- detection limit of the measurement) and destabilized by {approx}30% in
+ the PAS domain itself is extended by $\approx$3 nm (at the 10-pN
+ detection limit of the measurement) and destabilized by $\approx$30\% in
the light-activated state of PYP. Comparative measurements and steered
molecular dynamics simulations of two double-Cys PYP mutants that probe
different regions of the PAS domain quantify the anisotropy in
resolution of multidimensional spectroscopy with the chirality-specific
sensitivity of amide vibrations to structure. We demonstrate how the
structural sensitivity of cross-peaks in two-dimensional correlation
- plots of chiral signals of an {alpha} helix and a [beta] hairpin may be
+ plots of chiral signals of an $\alpha$ helix and a $\beta$ hairpin may be
used to clearly resolve structural and dynamical details undetectable
by one-dimensional techniques (e.g. circular dichroism) and identify
structures indistinguishable by NMR."
projects / thesis.git / commitdiff