Folding thermodynamics of three beta-sheet peptides: A model study

We study the folding thermodynamics of a beta-hairpin and two three-stranded beta-sheet peptides using a simplified sequence-based all-atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic attraction. The native populations obtained for these three sequences are in good agreement with experimental data. We also show that the apparent native population depends on which observable is studied; the hydrophobicity energy and the number of native hydrogen bonds give different results. The magnitude of this dependence matches well with the results obtained in two different experiments on the beta-hairpin.Comment: 17 pages, 7 figures, to appear in Protein

Hydrogen Bonds, Hydrophobicity Forces and the Character of the Collapse Transition

We study the thermodynamic behavior of a model protein with 54 amino acids that is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the Ramachandran torsion angles as its only degrees of freedom. The force field is based on hydrogen bonds and effective hydrophobicity forces. We study how the character of the collapse transition depends on the strengths of these forces. For a suitable choice of these two parameters, it is found that the collapse transition is first-order-like and coincides with the folding transition. Also shown is that the corresponding one- and two-helix segments make less stable secondary structure than the three-helix sequence.Comment: 14 pages, 8 figure

Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space

We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conformation-dependent) Gaussian distribution that favors approximately local deformations of the chain. The degree of bias is controlled by a parameter b. The method is tested on a reduced model protein with 54 amino acids and the Ramachandran torsion angles as its only degrees of freedom, for different b. Without excessive fine tuning, we find that the effective step size can be increased by a factor of three compared to the unbiased b=0 case. The method may be useful for kinetic studies, too.Comment: 14 pages, 4 figure

Modeling of Protein Folding and Genetic Networks

Models for potein folding are developed and applied to peptides and small proteins with both α-helix and β-sheet structure. The energy functions, in which effective hydrophobicity forces and hydrogen bonds are taken to be the two central terms, are sequence-based and deliberately kept simple. The geometric representations of the protein chains are, by contrast, detailed and have torsion angles as the degrees of freedom. The thermodynamic properties of the models are studied using Monte Carlo methods and quantitative comparisons with experiments are carried out. To improve the sampling of compact states, a semi-local Monte Carlo update in the backbone torsion angles is developed. In addition, the thesis includes a study of a simple model for genetic networks, the Kauffman model

Miljööversikt - luftens kvalitet i Kvarkenområdet

Denna miljööversikt ska ge information om Kvarkenområdets miljötillstånd och öka miljömedvetenheten bland allmänheten. Du kommer att få läsa om luftens kvalitet och vilka faktorer som påverkar den.I miljööversikten presenteras resultat från ett urval av de mätningar som utförs för att bevaka luftens kvalitet. Uppgifterna kommer från nationell, regional och lokal miljöövervakning.I Sverige utförs de nationella undersökningarna av luftkvalitet av Svenska Miljöinstitutet AB (IVL). I Finland har Finlands Meteorologiska Institut (FMI) motsvarande ansvar.Kommuner, Länsstyrelsen i Västerbottens län och Västra Finlands miljöcentral ansvarar för den lokal och regionala övervakning. Kommunerna mäter luftkvaliteten i stadskärnorna.Regionala inventeringsrapporter import från MDP 2015-05</p