Polypeptide folding with off-lattice Monte Carlo dynamics: the method

The MC dynamics of an off-lattice all-atom protein backbone model with rigid amide planes are studied. The only degrees of freedom are the dihedral angle pairs of the C-atoms. Conformational changes are generated by Monte Carlo (MC) moves. The MC moves considered are single rotations (simple moves, SM's) giving rise to global conformational changes or, alternatively, cooperative rotations in a window of amide planes (window moves, WM's) generating local conformational changes in the window. Outside the window the protein conformation is kept invariant by constraints. These constraints produce a bias in the distribution of dihedral angles. The WM's are corrected for this bias by suitable Jacobians. The energy function used is derived from the CHARMM force field. In a first application to polyalanine it is demonstrated that WM's sample the conformational space more efficiently than SM's.Abbreviations CPU Central Processing Unit - MC Monte Carlo - MCD Monte Carlo Dynamics - MD Molecular Dynamics - RMS Root-Mean-Square - RMSD Root-Mean-Square-Deviation - SM Simple Move - WM Window Move     

Generation of rhythmic and arrhythmic behaviour of Crassulacean acid metabolism in Kalanchoë daigremontiana under continuous light by varying the irradiance or temperature: Measurements in vivo and model simulations

Leaves of Kalanchoë daigremontiana Hamet et Perr. at a photon flux density (PFD) above 220 mol·m^–2s^–1 (400–700 nm) or at leaf temperatures above 27.0 °C showed a rapid loss of rhythmicity, and a more or less pronounced damping-out of the endogenous circadian rhythm of CO₂ exchange under continuous illumination. This rhythm was reinitiated after reduction of the PFD by 90–120 mol·m^–2·s^–1 or reduction of leaf temperature by 3.5–11.0 °C under otherwise unchanged external conditions. The reduction in the magnitude of the external control parameter of the Crassulacean acid metabolism (CAM) rhythm (i.e. PFD or leaf temperature) set the phase of the new rhythm. The maxima of CO₂ uptake occurred about 5, 28, 51, 75 h after the reduction. Simulations with a CAM model under comparable conditions showed a similar behaviour. The influence of temperature on the endogenous CAM rhythm observed in K. daigremontiana in vivo could be simulated by incorporating into the model temperature-dependent switch modes for passive efflux of malate from the vacuole to the cytoplasm. Thus, the model indicates that tonoplast function plays an important role in regulation of the endogenous CAM rhythm in K. daigremontiana.Abbreviations CAM Crassulacean acid metabolism - PAR photosynthetically active radiation - PFD photon flux density This work was supported by a grant to F.B. and U.L. from Teilprojekt B5 in the Sonderforschungsbereich 199 of the Deutsche Forschungsgemeinschaft (Bonn, Germany) and by a grant to T. E. E. G. from the Sudienstiftung des deutschen Volkes (Bonn, Germany). Erika Ball is thanked for processing of time-course data for the analysis of Fourier spectra.     

A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. I. Methodology

A Bayesian approach to the statistical mapping of Quantitative Trait Loci (QTLs) using single markers was implemented via Markov Chain Monte Carlo (MCMC) algorithms for parameter estimation and hypothesis testing. Parameter estimators were marginal posterior means computed using a Gibbs sampler with data augmentation. Variables sampled included the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable for linkage, and the parameters (allele frequency, QTL substitution effect, recombination rate, polygenic and residual variances). Several MCMC algorithms were derived for computing Bayesian tests of linkage, which consisted of the marginal posterior probability of linkage and the marginal likelihood of the QTL variance associated with the marker.     

Prerequisite for His4 in deltorphin A for highδ opioid receptor selectivity

Summary Analysis of deltorphin A position 4 analogues included: backbone constrained N MeHis, spinacine (Spi), N MePhe and the tetrahydroisoquinoline-3-carboxylic acid (Tic); spatially confined side-chain (Phg); and imidazole alkylation ofl- andd-His⁴ enantiomers. High selectivity was lost with the following replacements: N MeHis⁴, N MePhe⁴ and Phg⁴ reduced binding and the constrained residues also increasedµ binding; ring closure between the side-chain and amino group to yield Spi⁴ or Tic⁴ increasedµ affinity. Imidazole methylation of His⁴ marginally affected opioid binding and doubled selectivity; alkylatedd-His⁴-derivatives generally maintained selectivity in spite of decreased affinities. Thus, His⁴ imidazole preserves selectivity by facilitating high binding and by repulsion at theµ receptor. Several low energy conformers of deltorphin A indicated that the His⁴ imidazole preferred a spatial orientation parallel to the phenolic side-chain of Tyr¹ suggestive that this conformation might contribute to high affinity and selectivity.     

Presence of double‐stranded RNAs and virus‐like particles in the entomopathogenic fungus Metarhizium anisopliae

Nucleic acids from 41 strains of Metarhizium anisopliae, obtained from different parts of the world were extracted and examined by electrophoresis. Strong bands of double‐stranded RNA (dsRNA) were detected in two isolates from Brazil, V215 and V291, which had, respectively, 13 and 9 distinct bands ranging in size from ca. 0.75 to 3.5 kb. Icosahedral virus‐like particles (VLPs) (ca. 33 nm in diameter) were observed by transmission electron microscopy in extracts of these isolates. The VLPs and dsRNA were both absent from a clone of the isolate V291 which had been subcultured successively on solid medium. Bioassays against the aphid Myzus persicae showed no detectable difference in virulence between the clone of V291 which contained dsRNA and the clone that did not.     

Modeling of protein loops by simulated annealing.

A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms.     

Antibiotic production by strains of Gliocladium virens and its relation to the biocontrol of cotton seedling diseases

Strains of the fungal antagonist Gliocladium virens were separated into two distinct groups on the basis of secondary metabolite production in vitro. Strains of the ‘P’ group produced the antibiotics gliovirin and heptelidic acid but not the antibiotic gliotoxin and its companion, dimethylgliotoxin. Strains of the ‘Q’ group produced gliotoxin and dimethylgliotoxin but not gliovirin or heptelidic acid. Strains from both groups produced the antibiotic viridin and phytotoxin viridiol. Gliovirin was very inhibitory to Pythium ultimum but had no activity against Rhizoctonia solani, and strains that produce it were more effective seed treatment biocontrol agents of disease incited by P. ultimum. Conversely, gliotoxin was more active against R. solani than against P. ultimum, and strains that produced it were more effective seed treatments for controlling disease incited by R. solani. These results indicate that the antibiotic profiles of strains should be considered when screening strains for biocontrol efficacy, and that it may be necessary to treat seeds with a combination of strains in order to broaden the disease control spectrum.     

Integrating experimental data with molecular simulations to investigate RNA structural dynamics

Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule Förster resonance energy transfer, or even thermal or mechanical denaturation experiments probe RNA dynamics at different time and space resolutions. Their combination with accurate atomistic molecular dynamics (MD) simulations paves the way for quantitative and detailed studies of RNA dynamics. First, experiments provide a quantitative validation tool for MD simulations. Second, available data can be used to refine simulated structural ensembles to match experiments. Finally, comparison with experiments allows for improving MD force fields that are transferable to new systems for which data is not available. Here we review the recent literature and provide our perspective on this field.