24 research outputs found
Finite size effects on calorimetric cooperativity of two-state proteins
Finite size effects on the calorimetric cooperatity of the folding-unfolding
transition in two-state proteins are considered using the Go lattice models
with and without side chains. We show that for models without side chains a
dimensionless measure of calorimetric cooperativity kappa2 defined as the ratio
of the van't Hoff to calorimetric enthalpy does not depend on the number of
amino acids N. The average value of kappa2 is about 3/4 which is lower than the
experimental value kappa2=1. For models with side chains kappa2 approaches
unity as kappa2 \sim N^mu, where exponent mu=0.17. Above the critical chain
length Nc =135 these models can mimic the truly all-or-non folding-unfolding
transition.Comment: 3 eps figures. To appear in the special issue of Physica
Reversible stretching of homopolymers and random heteropolymers
We have analyzed the equilibrium response of chain molecules to stretching.
For a homogeneous sequence of monomers, the induced transition from compact
globule to extended coil below the -temperature is predicted to be
sharp. For random sequences, however, the transition may be smoothed by a
prevalence of necklace-like structures, in which globular regions and coil
regions coexist in a single chain. As we show in the context of a random
copolymer, preferential solvation of one monomer type lends stability to such
structures. The range of stretching forces over which necklaces are stable is
sensitive to chain length as well as sequence statistics.Comment: 14 pages, 4 figure
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
Hydrophobic and ionic-interactions in bulk and confined water with implications for collapse and folding of proteins
Water and water-mediated interactions determine thermodynamic and kinetics of
protein folding, protein aggregation and self-assembly in confined spaces. To
obtain insights into the role of water in the context of folding problems, we
describe computer simulations of a few related model systems. The dynamics of
collapse of eicosane shows that upon expulsion of water the linear hydrocarbon
chain adopts an ordered helical hairpin structure with 1.5 turns. The structure
of dimer of eicosane molecules has two well ordered helical hairpins that are
stacked perpendicular to each other. As a prelude to studying folding in
confined spaces we used simulations to understand changes in hydrophobic and
ionic interactions in nano droplets. Solvation of hydrophobic and charged
species change drastically in nano water droplets. Hydrophobic species are
localized at the boundary. The tendency of ions to be at the boundary where
water density is low increases as the charge density decreases. Interaction
between hydrophobic, polar, and charged residue are also profoundly altered in
confined spaces. Using the results of computer simulations and accounting for
loss of chain entropy upon confinement we argue and then demonstrate, using
simulations in explicit water, that ordered states of generic amphiphilic
peptide sequences should be stabilized in cylindrical nanopores
Parton rescattering and screening in Au+Au collisions at RHIC
We study the microscopic dynamics of quarks and gluons in relativistic heavy
ion collisions in the framework of the Parton Cascade Model. We use lowest
order perturbative QCD cross sections with fixed lower momentum cutoff p_0. We
calculate the time-evolution of the Debye-screening mass for Au+Au collisions
at sqrt(s)=200 GeV per nucleon pair. The screening mass is used to determine a
lower limit for the allowed range of p_0. We also determine the energy density
reached through hard and semi-hard processes at RHIC, obtain a lower bound for
the rapidity density of charged hadrons produced by semihard interactions, and
analyze the extent of perturbative rescattering among partons.Comment: 6 pages, 4 figures, uses RevTeX 4.0; revised version with minor
corrections and one updated figur
Dileptons from hot heavy static photons
We compute the production rate of lepton pair by static photons at finite
temperature at two-loop order. We treat the infrared region of the gluon phase
space carefully by using a hard thermal loop gluon propagator. The result is
free of infrared and collinear divergences and exhibits an enhancement which
produces a result of order instead of as would be
expected from ordinary perturbation theory.Comment: 14 pages, 2 figure
Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations
We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N [subscript G] is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε ε[subscript s] with slow internal dynamics. The cohesion strength ε[subscript s] of this freezing transition depends on N G . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N [subscript G] . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi
Fishing for folding nuclei in lattice models and proteins
Systematic studies of kinetics using minimal protein models reveal multiple folding nuclei for sequences that reach the native state in a single step. The diversity of the folding nuclei depends on sequence and topology