Two-state folding, folding through intermediates, and metastability in a minimalistic hydrophobic-polar model for proteins

Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are permutations of each other. Despite the simplicity of the model, the knowledge of the free-energy landscape in dependence of a suitable system order parameter enables us to reveal complex folding characteristics known from real bioproteins and synthetic peptides, such as two-state folding, folding through weakly stable intermediates, and glassy metastability.     

Identification of characteristic protein folding channels in a coarse-grained hydrophobic-polar peptide model

Folding channels and free-energy landscapes of hydrophobic-polar heteropolymers are discussed on the basis of a minimalistic off-lattice coarse-grained model. We investigate how rearrangements of hydrophobic and polar monomers in a heteropolymer sequence lead to completely different folding behaviors. Studying three exemplified sequences with the same content of hydrophobic and polar residues, we can reproduce within this simple model two-state folding, folding through intermediates, as well as metastability.     

Differences in solution behavior among four semiconductor-binding peptides

Recent experiments have identified peptides that adhere to GaAs and Si surfaces. Here, we use all-atom Monte Carlo simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all with 12 residues. At room temperature, we find that all four peptides are largely unstructured, which is consistent with experimental data. At the same time, we find that one of the peptides is structurally different and more flexible, as compared to the others. This finding points at structural differences as a possible explanation for differences in adhesion properties among these peptides. By also analyzing designed mutants of two of the peptides, an experimental test of this hypothesis is proposed.     

On the Picard principle for Δ?+?μ

Given a (local) Kato measure?μ on ${{\mathbb{R}^d} \setminus \{0\},\,d \ge 2}$ , let ${{\mathcal H}_0^{\Delta+\mu}(U)}$ be the convex cone of all continuous real solutions u?≥ 0 to the equation Δu?+?u μ?=?0 on the punctured unit ball U satisfying ${\lim_{|x|\to 1} u(x)=0}$ . It is shown that ${{\mathcal H}_0^{\Delta+\mu}(U)\ne \{0\}}$ if and only if the operator ${f\mapsto \int_U G(\cdot,y)f(y)\,d\mu(y)}$ , where G denotes the Green function on U, is bounded on ${\mathcal L^2(U,\mu)}$ and has a norm which is at most one. Moreover, extremal rays in ${{\mathcal H}_0^{\Delta+\mu}(U)}$ are characterized and it is proven that Δ?+?μ satisfies the Picard principle on U, that is, that ${{\mathcal H}_0^{\Delta+\mu}(U)}$ consists of one ray, provided there exists a suitable sequence of shells in U such that, on these shells,?μ is either small or not too far from being radial. Further, it is shown that the verification of the Picard principle can be localized. Several results on L ²-(sub)eigenfunctions and 3G-inequalities which are used in the paper, but may be of independent interest, are proved at the end of the paper.     

Defect passivation by hydrogen reincorporation for silicon quantum dots in SiC/SiOx hetero-superlattice

The SiC/SiO_x hetero-superlattice (HSL) consisting of alternating near-stoichiometric SiC barrier layers for the electrical transport and silicon rich SiO_x matrix layers for the quantum dot formation is a promising approach to the realization of silicon quantum dot (Si–QD) absorbers for 3rd generation solar cells. However, additional defect states are generated during post deposition annealing needed for the Si–QD formation causing an increase in sub-band gap absorption and a decrease in PL intensity. Proper passivation of excess defects is of major importance for both the optical and electrical properties of the SiC/SiO_x HSL Si–QD absorber. In this work, we investigate the effectiveness of the hydrogen reincorporation achieved with hydrogen plasma in a plasma-enhanced chemical vapor deposition (PECVD) reactor, hydrogen dissociation catalysis in hot-wire chemical vapor deposition (HWCVD) reactor and annealing in forming gas atmosphere (FGA). Both the HSL samples and single layer reference samples are tested. The passivation quality of the hydrogen reincorporation was examined by comparing electrical and optical properties measured after deposition, after annealing and after passivation. In addition, the formation of Si–QDs in SiC/SiO_x HSL was evaluated using high resolution transmission electron microscopy. We demonstrated that hydrogen can be successfully reincorporated into the annealed HSL sample and its single layer reference samples. FGA passivation is most effective for SiO_1.2 single layers and HSL samples. Passivation with PECVD appeared to be only effective for SiC single layers.     

On the existence of Evans potentials

It is shown that, for every noncompact parabolic Riemannian manifold $X$ and every nonpolar compact $K$ in  $X$ , there exists a positive harmonic function on $X\setminus K$ which tends to $\infty $ at infinity. (This is trivial for $\mathbb{R }$ , easy for  $\mathbb{R }^2$ , and known for parabolic Riemann surfaces.) In fact, the statement is proven, more generally, for any noncompact connected Brelot harmonic space  $X$ , where constants are the only positive superharmonic functions and, for every nonpolar compact set  $K$ , there is a symmetric (positive) Green function for $X\setminus K$ . This includes the case of parabolic Riemannian manifolds. Without symmetry, however, the statement may fail. This is shown by an example, where the underlying space is a graph (the union of the parallel half-lines $\left[0,\infty \right)\times \{0\}, \left[0,\infty \right)\times \{1\}$ , and the line segments $\{n\}\times [0,1], n=0,1,2,\dots $ ).     

Jensen Measures in Potential Theory

It is shown that, for open sets in classical potential theory and??more generally??for elliptic harmonic spaces Y, the set J _x (Y) of Jensen measures (representing measures with respect to superharmonic functions on?Y) for a?point x????Y is a?simple union of closed faces of the compact convex set $M_x(\mathcal P(Y))$ of representing measures with respect to potentials on?Y, a?set which has been thoroughly studied a?long time ago. In particular, the set of extreme Jensen measures can be immediately identified. The results hold even without ellipticity (thus capturing also many examples for the heat equation) provided a?rather weak approximation property for superharmonic functions holds. Equally sufficient are a?certain transience property and a?weak regularity property. More important, each of these properties turns out to be necessary and sufficient for obtaining (in the classical case) that J _x (Y) coincides with the set of all compactly supported probability measures in $M_x(\mathcal P(Y))$ .     

Restricted Mean Value Property for Balayage Spaces with Jumps

It is shown that, for α-stable processes (Riesz potentials) or—more generally—for balayage spaces with jumps, “one-radius” results for harmonicity can be obtained under fairly weak assumptions.     

Polymer adsorption on a fractal substrate: numerical study

We study the adsorption of flexible polymer macromolecules on a percolation cluster, formed by a regular two-dimensional disordered lattice at critical concentration p(c) of attractive sites. The percolation cluster is characterized by a fractal dimension d(s) (p(c))=91/49. The conformational properties of polymer chains grafted to such a fractal substrate are studied by means of the pruned-enriched Rosenbluth method. We find estimates for the surface crossover exponent governing the scaling of the adsorption energy in the vicinity of transition point, φ(s)(p(c))=0.425±0.009, and for adsorption transition temperature, T(A)(p(c))=2.64±0.02. As expected, the adsorption is diminished when the fractal dimension of the substrate is smaller than that of a plain Euclidean surface. The universal size and shape characteristics of a typical spatial conformation which attains a polymer chain in the adsorbed state are analyzed as well.