A theoretical study of the stability of disulfide bridges in various β-sheet structures of protein segment models

Electron structure calculations are used to explore stabilization effects of disulfide bridges in a (Ala–Cys–Ala–Cys–Ala)2 β-sheet model both in the parallel and the anti-parallel (103142 and 143102) arrangements. Stabilities were calculated using a redox reaction involving a weak oxidizing agent (1,4-benzoquinone). The results show that both inter- and intra-strand disulfide SS-bridges stabilize the β-sheet backbone fold. However, inter-strand SS-bridges give more stability than their intra-strand counterparts. For both single and double disulfide linked conformations, stabilization was larger for the parallel than for the anti-parallel β-sheet arrangements

The Phase Diagram of an Anisotropic Potts Model

A study is made of an anisotropic Potts model in three dimensions where the coupling depends on both the Potts state on each site but also the direction of the bond between them using both analytical and numerical methods. The phase diagram is mapped out for all values of the exchange interactions. Six distinct phases are identified. Monte Carlo simulations have been used to obtain the order parameter and the values for the energy and entropy in the ground state and also the transition temperatures. Excellent agreement is found between the simulated and analytic results. We find one region where there are two phase transitions with the lines meeting in a triple point. The orbital ordering that occurs in $LaMnO_3$ occurs as one of the ordered phases.Comment: 30 pages, 19 figures, one tabl

Impairment of a model peptide by oxidative stress: Thermodynamic stabilities of asparagine diamide C(alpha)-radical foldamers

Electron structure calculations on N-acetyl asparagine N-methylamide were performed to identify the global minimum from which radicals were formed after H-abstraction by the OH radical. It was found that the radical generated by breaking the C–H bond of the alpha-carbon was thermodynamically the most stable one in the gas- and aqueous phases. The extended ((beta)L and (beta)D) backbone conformations are the most stable, but syn–syn or inverse gamma-turn ((gamma)L) and gamma-turn ((gamma)D) have substantial stability too. The highest energy conformers are the degenerate eL and eD foldamers. Clearly, the most stable beta foldamer is the most likely intermediate for racemization

Thermodynamic characteristics of the classical n-vector magnetic model in three dimensions

The method of calculating the free energy and thermodynamic characteristics of the classical n-vector three-dimensional (3D) magnetic model at the microscopic level without any adjustable parameters is proposed. Mathematical description is perfomed using the collective variables (CV) method in the framework of the $\rho^4$ model approximation. The exponentially decreasing function of the distance between the particles situated at the N sites of a simple cubic lattice is used as the interaction potential. Explicit and rigorous analytical expressions for entropy,internal energy, specific heat near the phase transition point as functions of the temperature are obtained. The dependence of the amplitudes of the thermodynamic characteristics of the system for $T>T_c$ and $T<T_c$ on the microscopic parameters of the interaction potential are studied for the cases $n=1,2,3$ and $n\to\infty$. The obtained results provide the basis for accurate analysis of the critical behaviour in three dimensions including the nonuniversal characteristics of the system.Comment: 25 pages, 5 figure

Helix compactness and stability: Electron structure calculations of conformer dependent thermodynamic functions

Structure, stability, cooperativity and molecular packing of two major backbone forms: 310-helix and β-strand are investigated. Long models HCO-(Xxx)n-NH2 Xxx = Gly and (l-)Ala, n ⩽ 34, are studied at two levels of theory including the effect of dispersion forces. Structure and folding preferences are established, the length modulated cooperativity and side-chain determined fold compactness is quantified. By monitoring ΔG°β→α rather than the electronic energy, ΔEβ→α, it appears that Ala is a much better helix forming residue than Gly. The achiral Gly forms a more compact 310-helix than any chiral amino acid residue probed here for l-Ala

Hydrogen bonds: relation between lengths and electron densities at bond critical points

The electron densities for a number of molecules with either inter- or intra-molecular hydrogen bonds are analyzed using the theory of atoms in molecules. The levels of theory used include second order Møller Plesset and density functional methods. The molecules investigated ranges from small molecules/ions to an alanine octa-peptide. The hydrogen bond length, BL, varies from 1.15 to 3.01 Å and $\rho_{b}$, the electron density at the bond critical point, spans the interval 0.0033 to 0.168 (au). We find that the data may be represented by the relation $\rho_{b} = A \exp (-B\times {\it BL}$), where A and B are empirical constants. The relation is compared to a similar relation derived from solid state experiments. Since the $\rho_{b}$ values are related to the bond strengths, this general relationship may useful for hydrogen bond studies

Latest results from the European Mars simulation wind tunnel facility

The Mars Simulation wind tunnel at Aarhus University is a unique ESA and EU supported simulation facility designed for studies of the Martian environment. Specifically it is capable of recreating the key physical parameters such as temperature, pressure (composition), wind flow and importantly the suspension of dust particulates. This facility is available to the scientific community for collaborative research. Preliminary results from the first year of facility operations will be presented