The new program DYANA...

Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading and installing large program packages and databases. Results: SWISS-MODEL Workspace is a web-based integrated service dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure databases necessary for modelling are accessible from the workspace and are updated in regular intervals. Tools for template selection, model building, and structure quality evaluation can be invoked from within the workspace. Workflow and usage of the workspace are illustrated by modelling human Cyclin A1 and human Transmembrane Protease

This paper was followed by two others from Stouch and coworkers, on the diffusion of small molecules in lipid membranes [70,97]. The membrane model explored in these studies is a fully hydrated DMPC bilayer, which was shown to compare favorably to most available experimental data [61]. The first paper deals with the diffusion proces of benzene. Four simulations were conducted; three of them with a single benzene molecule placed at different positions in the membrane, and another simulation with four benzene molecules present at the same time (fig. 6). Diffusion rates could be extracted by computing the mean square displacement (MSD) of the (unconstrained) molecules. For purely Brownian motion, the slope of the MSD curve at long times is proportional to the diffusion constant. The total simulation time, including equilibration, exceeded 4 ns. During the simulations it turned out that the benzene molecules did not have a strong preference for a particular part of the membrane. However, the rate of diffusion was found to depend on their location in the membrane, the benzene molecules diffusing 2-3 times slower in the headgroup region than in the center of the bilayer. The authors further concluded that the mechanism of diffusion is, at least partly, due to jumps of the benzene molecules between voids in the lipid matrix, similar to the diffusion process as observed in soft polymers. Since the number of free volume voids increases towards the bilayer interior, the higher diffusion rate originates from a higher probability of jumps. In a subsequent paper [70] the effect of temperature on the diffusion rates and mechanism was studied. Comparison of four 1ns simulations ranging in temperature from 310 to 340 K revealed that the effect of temperature on the diffusion process ...

This article summarizes the present state of the transfer operator approach to biomolecular conformations with special emphasis on the conceptual and mathematical foundations.

Statistical methods for analyzing large data sets of molecular configurations within the chemical concept of molecular conformations are described. The strategies are based on dependencies between configurations of a molecular ensemble; the article concentrates on dependencies induced by a) correlations between the molecular degrees of freedom, b) geometrical similarities of configurations, and c) dynamical relations between subsets of configurations. The statistical technique realizing aspect a) is based on an approach suggested by Amadei et al. (Proteins, 17 (1993)). It allows to identify essential degrees of freedom of a molecular system and is extended in order to determine single configurations as representatives for the crucial features related to these essential degrees of freedom. Aspects b) and c) are based on statistical cluster methods. They lead to a decomposition of the available simulation data into conformational ensembles or subsets with the property that all...

A hybrid Monte Carlo method with adaptive temperature choice is presented, which exactly generates the distribution of a mixed-canonical ensemble composed of two canonical ensembles at low and high temperature. The analysis of resulting Markov chains with the reweighting technique shows an efficient sampling of the canonical distribution at low temperature, whereas the high temperature component facilitates conformational transitions, which allows shorter simulation times. The algorithm was tested by comparing analytical and numerical results for the small n-butane molecule before simulations were performed for a triribonucleotide. Sampling the complex multi-minima energy landscape of this small RNA segment, we observe enforced crossing of energy barriers.

In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na + ions and 12992 water molecules. After equilibration and a nanosecond production run the OmpF trimer exhibits a C-ff root mean square deviation from the crystal structure of 0.23 nm and a stable secondary structure. No evidence is found for large-scale motions of the L3 loop. We investigate the pore dimensions, conductance and the properties of water inside the pore. This water forms a complicated pattern, even when averaged over 1 ns of simulation time. Around the pore constriction zone the water dipoles are highly structured in the plane of the membrane, oriented by the strong transversal electric øeld. In addition, there is a net orientation along the pore axis pointing from the extracellular to the intracellular side of the bilayer. The dioeusion coeOEcients of water ins...

ABSTRACT Isolated pore-lining helices derived from three types of K-channel have been analyzed in terms of their structural and dynamic features in nanosecond molecular dynamics (MD) simulations while spanning a lipid bilayer. The helices were 1) M1 and M2 from the bacterial channel KcsA (Streptomyces lividans), 2) S5 and S6 from the voltage-gated (Kv) channel Shaker (Drosophila melanogaster), and 3) M1 and M2 from the inward rectifier channel Kir6.2 (human). In the case of the Kv and Kir channels, for which x-ray structures are not known, both short and long models of each helix were considered. Each helix was incorporated into a lipid bilayer containing 127 palmitoyloleoylphosphatidylcholine molecules, which was solvated with �4000 water molecules, yielding �20,000 atoms in each system. Nanosecond MD simulations were used to aid the definition of optimal lengths for the helix models from Kv and Kir. Thus the study corresponds to a total simulation time of 10 ns. The inner pore-lining helices (M2 in KcsA and Kir, S6 in Shaker) appear to be slightly more flexible than the outer pore-lining helices. In particular, the Pro-Val-Pro motif of S6 results in flexibility about a molecular hinge, as was suggested by previous in vacuo simulations (Kerr et al., 1996, Biopolymers. 39:503–515). Such flexibility may be related to gating in the corresponding intact channel protein molecules. Analysis of H-bonds revealed interactions with both water and lipid molecules in the water/bilayer interfacial region. Such H-bonding interactions may lock the helices in place in the bilayer during the folding of the channel protein (as is implicit in the two-stage model of membrane protein folding). Aromatic residues at the extremities of the helices underwent complex motions on both short (�10 ps) and long (�100 ps) time scales.

Molecular dynamics simulations allow a direct study of the structure and dynamics of membrane proteins and lipids. We describe the behavior of aromatic residues and lipid properties in POPE and POPC bilayer models with the E. coli OmpF trimer, single alamethicin and Influenza M2 helices, 4-helix M2 bundles and two alamethicin 6-helix channel models. The total simulation time is over 24 nanoseconds, of systems containing solvent, protein and between 104 and 340 lipids. Various types of adjustment between lipids and proteins occur, depending on the size of the protein and the degree of hydrophobic mismatch between lipid and protein. Single helices cause little measurable effect on nearby lipids whereas the 4-helix bundles, 6-helix channel models and OmpF cause a significant lowering of order parameters in nearby lipid chains, an increased difference between odd and even chain dihedrals in the magnitude of the trans dihedral fractions and dihedral transition rates, in most cases a decreased gauche population and a decrease in bilayer thickness. An increased tilt of the lipid chains near the proteins can account for most of the observed decrease in order parameters.

this paper has been supported by the Natural Sciences and Engineering Research Council (Canada), the Protein Engineering Network of Centres of Excellence, and a University of Calgary Research Grant. JLM and DPT would like to thank Paul Lu and the CISS2 team, as well as all of the C3 sites that participated in the CISS2 experiment