Quantitative analysis of chromatin compaction in living cells using FLIM-FRET

FRET analysis of cell lines expressing fluorescently tagged histones on separate nucleosomes demonstrates that variations in chromosome compaction occur during mitosis

The spatial effect of protein deuteration on nitroxide spin-label relaxation:implications for EPR distance measurement

This work was supported by a Wellcome Trust Senior Fellowship (095062) to T.O.-H. The Authors would also like to acknowledge funding from The MRC – United Kingdom, Grant G1100021.Pulsed electron-electron double resonance (PELDOR) coupled with site-directed spin labeling is a powerful technique for the elucidation of protein or nucleic acid, macromolecular structure and interactions. The intrinsic high sensitivity of electron paramagnetic resonance enables measurement on small quantities of bio-macromolecules, however short relaxation times impose a limit on the sensitivity and size of distances that can be measured using this technique. The persistence of the electron spin-echo, in the PELDOR experiment, is one of the most crucial limitations to distance measurement. At a temperature of around 50 K one of the predominant factors affecting persistence of an echo, and as such, the sensitivity and measurable distance between spin labels, is the electron spin echo dephasing time (Tm). It has become normal practice to use deuterated solvents to extend Tm and recently it has been demonstrated that deuteration of the underlying protein significantly extends Tm. Here we examine the spatial effect of segmental deuteration of the underlying protein, and also explore the concentration and temperature dependence of highly deuterated systems.Publisher PDFPeer reviewe

The 3-dimensional architecture of the Upsilon Andromedae planetary system

The Upsilon Andromedae system is the first exoplanetary system to have the relative inclination of two planets' orbital planes directly measured, and therefore offers our first window into the 3-dimensional configurations of planetary systems. We present, for the first time, full 3-dimensional, dynamically stable configurations for the 3 planets of the system consistent with all observational constraints. While the outer 2 planets, c and d, are inclined by about 30 degrees, the inner planet's orbital plane has not been detected. We use N-body simulations to search for stable 3-planet configurations that are consistent with the combined radial velocity and astrometric solution. We find that only 10 trials out of 1000 are robustly stable on 100 Myr timescales, or about 8 billion orbits of planet b. Planet b's orbit must lie near the invariable plane of planets c and d, but can be either prograde or retrograde. These solutions predict b's mass is in the range 2 - 9 $M_{Jup}$ and has an inclination angle from the sky plane of less than 25 degrees. Combined with brightness variations in the combined star/planet light curve ("phase curve"), our results imply that planet b's radius is about 1.8 $R_{Jup}$, relatively large for a planet of its age. However, the eccentricity of b in several of our stable solutions reaches values greater than 0.1, generating upwards of $10^{19}$ watts in the interior of the planet via tidal dissipation, possibly inflating the radius to an amount consistent with phase curve observations.Comment: 17 pages, 10 figures, accepted for publication in ApJ; revised statement in Section 1.1, references added, results unchange

Constraints, Histones, and the 30 Nanometer Spiral

We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic rod that is free to twist and that writhes subject to mechanical constraints. We find that the number of constraints required to stabilize the nuclesome configuration is determined by the length of the segment, the number of times the DNA wraps around the histone spool, and the specific constraints utilized. While it can be shown that four constraints suffice, in principle, to insure stability of the nucleosome, a proper choice must be made to guarantee the effectiveness of this minimal number. The optimal choice of constraints appears to bear a relation to the existence of a spiral ridge on the surface of the histone octamer. The particular configuration that we investigate is related to the 30 nanometer spiral, a higher-order organization of DNA in chromatin.Comment: ReVTeX, 15 pages, 18 figure

Polymer reptation and nucleosome repositioning

We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem arises in the case of globular aggregates of proteins (histones) that are wound by DNA in the chromosomes of plants and animals; these beads (nucleosomes) are multiply wrapped and yet are able to reposition themselves over long distances, while remaining bound by the DNA chain.Comment: 9 pages, including 2 figures, to be published in Phys. Rev. Let