immunostaining-for-dna-modifications-computational-analysis-confocal

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

For several decades, 5-methylcytosine (5mC) has been thought to be the only DNA modification with a functional significance in metazoans. The discovery of ...

University of Nottingham

The water dynamics near nanoscale fluorinated (CF(3)(CF(2))(7)(CH(2))(2)SiH(3)) monolayers (plates) as well as possible dewetting transitions in-between two such plates have been studied with molecular dynamics simulations in this paper. A "weak water depletion" is found near the single fluorinated surface, with an average water density in the first solvation shells 6-8% lower than its hydrogenated counterpart. The fluorinated molecules are also found to be water impermeable, consistent with experimental findings. More surprisingly, a dewetting transition is found in the interplate region with a critical distance D(c) of 10 A (3-4 water diameters) for double plates with 8 x 8 molecules each (plate size approximately 4 nm x 4 nm). This transition, although occurring on a microscopic length scale, is reminiscent of a first-order phase transition from liquid to vapor. The unusual superhydrophobicity of fluorocarbons is found to be related to their larger size (or surface area) as compared to hydrocarbons, which "dilutes" their physical interactions with water. The water-plate interaction profile shows that the fluorinated carbons have a 10-12% weaker water-plate interaction than their hydrogenated counterparts in the nearest solvation shell, even though the fluorocarbons do have a stronger electrostatic interaction with water due to their larger partial charges. However, the van der Waals interactions dominate the water-plate interaction within the nearest shell, with up to 90% contributions to the total interaction energy, and fluorocarbons have a noticeably weaker (by 10-15%) van der Waals interaction with water in the nearest shell than do hydrocarbons. Both the slightly weaker water-plate interaction and larger surface area contribute to the stronger dewetting transition in the current fluorinated carbon plates.

Hydration and dewetting near fluorinated superhydrophobic plates.

Biomolecular simulations enabled by massively parallel supercomputers such as BlueGene/L promise to bridge the gap between the currently accessible simulation time scale and the experimental time scale for many important protein folding processes. In this study, molecular dynamics simulations were carried out for both the wild-type and the mutant hen lysozyme (TRP62GLY) to study the single mutation effect on lysozyme stability and misfolding. Our thermal denaturing simulations at 400-500 K with both the OPLSAA and the CHARMM force fields show that the mutant structure is indeed much less stable than the wild-type, which is consistent with the recent urea denaturing experiment (Dobson et al. Science 2002, 295, 1719-1722; Nature 2003, 424, 783-788). Detailed results also reveal that the single mutation TRP62GLY first induces the loss of native contacts in the beta-domain region of the lysozyme protein at high temperatures, and then the unfolding process spreads into the alpha-domain region through Helix C. Even though the OPLSAA force field in general shows a more stable protein structure than does the CHARMM force field at high temperatures, the two force fields examined here display qualitatively similar results for the misfolding process, indicating that the thermal denaturing of the single mutation is robust and reproducible with various modern force fields.

Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields.

We propose a mechanism, based on a > or =10-micros molecular dynamics simulation, for the surprising misfolding of hen egg-white lysozyme caused by a single mutation (W62G). Our simulations of the wild-type and mutant lysozymes in 8 M urea solution at biological temperature (with both pH 2 and 7) reveal that the mutant structure is much less stable than that of the wild type, with the mutant showing larger fluctuations and less native-like contacts. Analysis of local contacts reveals that the Trp-62 residue is the key to a cooperative long-range interaction within the wild type, where it acts like a bridge between two neighboring basic residues. Thus, a native-like cluster or nucleation site can form near these residues in the wild type but not in the mutant. The time evolution of the secondary structure also exhibits a quicker loss of the beta-sheets in the mutant than in the wild type, whereas some of the alpha-helices persist during the entire simulation in both the wild type and the mutant in 8 M urea (even though the tertiary structures are basically all gone). These findings, while supporting the general conclusions of a recent experimental study by Dobson and coworkers [Klein-Seetharam J, Oikama M, Grimshaw SB, Wirmer J, Duchardt E, Ueda T, Imoto T, Smith LJ, Dobson CM, Schwalbe H (2002) Science 295:1719-1722], provide a detailed but different molecular picture of the misfolding mechanism.

Destruction of long-range interactions by a single mutation in lysozyme.

We study discrete surface breathers in two-dimensional lattices of inductively coupled split-ring resonators with capacitive nonlinearity. We consider both conservative (Hamiltonian) and analyze the properties of the modes localized in space and periodic in time (discrete breathers) located in the corners and on the edges of the lattice. We find that surface breathers in the Hamiltonian systems have lower energy than their bulk counterparts and they are generally more stable.

Surface magnetoinductive breathers in two-dimensional magnetic metamaterials.

DNA methylation (5-methylcytosine (5mC)) patterns are often altered in cancers. Ten-eleven translocation (Tet) proteins oxidise 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). In addition to their presumptive specific biological roles, these oxidised forms of 5mC may serve as intermediates in demethylation process. According to several reports, 5hmC levels are strongly decreased in cancers; however, the distribution of 5fC and 5caC in malignant tissue has not been studied.

Maria Eleftheriou

Division of Cancer and Stem Cells,
School of Medicine,
Centre for Biomolecular Sciences,
Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences

University of Nottingham

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Maria Eleftheriou

Division of Cancer and Stem Cells,School of Medicine,Centre for Biomolecular Sciences,Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences

University of Nottingham

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Division of Cancer and Stem Cells,
School of Medicine,
Centre for Biomolecular Sciences,
Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences