124 research outputs found
Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy (FCS): Theory and applications
In the current AFM experiments the distribution of unfolding times, P(t), is
measured by applying a constant stretching force f_s from which the apparent
unfolding rate is obtained. To describe the complexity of the underlying energy
landscape requires additional probes that can incorporate the dynamics of
tension propagation and relaxation of the polypeptide chain upon force quench.
We introduce a theory of force correlation spectroscopy (FCS) to map the
parameters of the energy landscape of proteins. In the FCS the joint
distribution, P(T,t) of folding and unfolding times is constructed by repeated
application of cycles of stretching at constant fs, separated by release
periods T during which the force is quenched to f_q<f_s. During the release
period, the protein can collapse to a manifold of compact states or refold. We
show that P(T,t) can be used to resolve the kinetics of unfolding as well as
formation of native contacts and to extract the parameters of the energy
landscape using chain extension as the reaction coordinate and P(T,t). We
illustrate the utility of the proposed formalism by analyzing simulations of
unfolding-refolding trajectories of a coarse-grained protein S1 with beta-sheet
architecture for several values of f_s, T and f_q=0. The simulations of
stretch-relax trajectories are used to map many of the parameters that
characterize the energy landscape of S1.Comment: 23 pages, 9 figures; accepted to Biophysical Journa
Probing protein-protein interactions by dynamic force correlated spectroscopy (FCS)
We develop a formalism for single molecule dynamic force spectroscopy to map
the energy landscape of protein-protein complex (). The joint
distribution of unbinding lifetimes and
measurable in a compression-tension cycle, which accounts for the internal
relaxation dynamics of the proteins under tension, shows that the histogram of
is not Poissonian. The theory is applied to the forced unbinding of
protein , modeled as a wormlike chain, from . We propose a new
class of experiments which can resolve the effect of internal protein dynamics
on the unbinding lifetimes.Comment: 12 pages, 3 figures, accepted to Phys. Rev. Let
Role of internal chain dynamics on the rupture kinetic of adhesive contacts
We study the forced rupture of adhesive contacts between monomers that are not covalently linked in a
Rouse chain. When the applied force (f) to the chain end is less than the critical force for rupture (fc), the
reversible rupture process is coupled to the internal Rouse modes. If f=fc > 1 the rupture is irreversible.
In both limits, the nonexponential distribution of contact lifetimes, which depends sensitively on the
location of the contact, follows the double-exponential (Gumbel) distribution. When two contacts are well
separated along the chain, the rate limiting step in the sequential rupture kinetics is the disruption of the
contact that is in the chain interior. If the two contacts are close to each other, they cooperate to sustain the
stress, which results in an ‘‘all-or-none’’ transition
Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles
We present a new theory for modeling forced indentation spectral lineshapes
of biological particles, which considers non-linear Hertzian deformation due to
an indenter-particle physical contact and bending deformations of curved beams
modeling the particle structure. The bending of beams beyond the critical point
triggers the particle dynamic transition to the collapsed state, an extreme
event leading to the catastrophic force drop as observed in the force
(F)-deformation (X) spectra. The theory interprets fine features of the
spectra: the slope of the FX curves and the position of force-peak signal, in
terms of mechanical characteristics --- the Young's moduli for Hertzian and
bending deformations E_H and E_b, and the probability distribution of the
maximum strength with the strength of the strongest beam F_b^* and the beams'
failure rate m. The theory is applied to successfully characterize the
curves for spherical virus particles --- CCMV, TrV, and AdV
Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico
Microtubules, the primary components of the chromosome segregation machinery,
are stabilized by longitudinal and lateral non-covalent bonds between the
tubulin subunits. However, the thermodynamics of these bonds and the
microtubule physico-chemical properties are poorly understood. Here, we explore
the biomechanics of microtubule polymers using multiscale computational
modeling and nanoindentations in silico of a contiguous microtubule fragment. A
close match between the simulated and experimental force-deformation spectra
enabled us to correlate the microtubule biomechanics with dynamic structural
transitions at the nanoscale. Our mechanical testing revealed that the
compressed MT behaves as a system of rigid elements interconnected through a
network of lateral and longitudinal elastic bonds. The initial regime of
continuous elastic deformation of the microtubule is followed by the transition
regime, during which the microtubule lattice undergoes discrete structural
changes, which include first the reversible dissociation of lateral bonds
followed by irreversible dissociation of the longitudinal bonds. We have
determined the free energies of dissociation of the lateral (6.9+/-0.4
kcal/mol) and longitudinal (14.9+/-1.5 kcal/mol) tubulin-tubulin bonds. These
values in conjunction with the large flexural rigidity of tubulin
protofilaments obtained (18,000-26,000 pN*nm^2), support the idea that the
disassembling microtubule is capable of generating a large mechanical force to
move chromosomes during cell division. Our computational modeling offers a
comprehensive quantitative platform to link molecular tubulin characteristics
with the physiological behavior of microtubules. The developed in silico
nanoindentation method provides a powerful tool for the exploration of
biomechanical properties of other cytoskeletal and multiprotein assemblie
- …