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 $\theta$-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 $\sim e^2 g^3$ instead of $\sim e^2 g^4$ 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