Statistical mechanics of warm and cold unfolding in proteins

We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm unfolding, thus qualitatively reproducing the known thermodynamics of proteins.Comment: 5 pages, REVTex, 4 Postscript figure

Viscoelastic Transition and Yield Strain of the Folded Protein

For proteins, the mechanical properties of the folded state are directly related to function, which generally entails conformational motion. Through sub-Angstrom resolution measurements of the AC mechanical susceptibility of a globular protein we describe a new fundamental materials property of the folded state. For increasing amplitude of the forcing, there is a reversible transition from elastic to viscoelastic response. At fixed frequency, the amplitude of the deformation is piecewise linear in the force, with different slopes in the elastic and viscoelastic regimes. Effectively, the protein softens beyond a yield point defined by this transition. We propose that ligand induced conformational changes generally operate in this viscoelastic regime, and that this is a universal property of the folded state

Statistical mechanics of base stacking and pairing in DNA melting

We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at moderately low pH this transition is moved down to experimentally accessible temperatures. These measurements confirm that the Ising model approach is indeed a good description of base stacking. On the other hand, comparison with the experiments points to the limitations of the simple zipper model description of base pairing.Comment: 13 pages with figure

A Model for the Thermodynamics of Globular Proteins

Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water interactions. The model contains both hot and cold folding transitions. In addition it predicts a critical point at a given temperature and chemical potential of the surrounding water. The universality class of this critical point is new

Local Cooperativity Mechanism in the DNA Melting Transition

We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which mimic the geometrical constraints in the real molecule. This microscopic mechanism intrinsically accounts for the cooperativity related to the free energy penalty of bubble nucleation. The model describes both the unpairing and unstacking parts of the spectroscopically determined experimental melting curves. Furthermore, the model explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor (NN) type. We compute the partition function for the model through the transfer matrix formalism, which we also generalize to include non local chain entropy terms. This part introduces a new parametrization of the Yeramian-like transfer matrix approach to the Poland-Scheraga description of DNA melting. The model is exactly solvable in the homogeneous thermodynamic limit, and we calculate all observables without use of the grand partition function. As is well known, models of this class have a first order or continuous phase transition at the temperature of complete strand separation depending on the value of the exponent of the bubble entropy.Comment: Extended version of Phys. Rev. E pape

Optical simulations for the Wolter-I collimator in the VERT-X calibration facility

The VERT-X X-ray calibration facility, currently in prototypal realization phase supported by ESA, will be a vertical X-ray beamline able to test and calibrate the entire optical assembly of the ATHENA X-ray telescope. Owing to its long focal length (12 m), a full-illumination test of the entire focusing system would require a parallel and uniform X-ray beam as large as the optical assembly itself (2.5 m). Moreover, the module should better be laid parallel to the ground in order to minimize the effects of gravity deformations. Therefore, the ideal calibration facility would consist of a vertical beam, with the source placed at very large distance (>> 500 m) under high vacuum (10-6 mbar). Since such calibration systems do not exist, and also appear to be very hard to manufacture, VERT-X will be based on a different concept, i.e., the raster scan of a tightly (≈ 1 arcsec) collimated X-ray beam, generated by a microfocus source and made parallel via a precisely shaped Wolter-I mirror. In this design, the mirror will be made of two segments (paraboloid + hyperboloid) that, for the X-ray beam collimation to be preserved, will have to be accurately finished and maintain their mutual alignment to high accuracy during the scan. In this paper, we show simulations of the reflected wavefront based on physical optics and the expected final imaging quality, for different polishing levels and misalignments for the two segments of the VERT-X collimator