Statistical mechanics elucidates constraints on the ultimate accuracy of biochemical sensing
Charles Day
In biology textbooks, the way proteins work is often depicted by what looks like a set of puzzle pieces. A small piece, a regulator molecule, say, fits into a large piece, an enzyme, say. The enzyme's shape then changes to one that fits snugly around a medium-sized piece, the enzyme's substrate. ... [Phys. Today 61, 14 (2008)] published Wed Jul 2, 2008.
Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides
Zanxia Cao and Haiyan Liu
We propose a method that may allow data about the conformational equilibriums of peptides to enter the parameter calibration phase in force field developments. The method combines free energy perturbation with techniques for extensive sampling in the conformational space. It predicts shifts in compu ... [J. Chem. Phys. 129, 015101 (2008)] published Tue Jul 1, 2008.
Prolonged irradiation of enhanced cyan fluorescent protein or Cerulean can invalidate F[o-umlaut]rster resonance energy transfer measurements
Birgit Hoffmann, Thomas Zimmer, Nikolaj Klocker, Laimonas Kelbauskas, Karsten Konig et al.
Since its discovery, green fluorescent protein (GFP) and its variants have proven to be a good and convenient fluorescent label for proteins: GFP and other visible fluorescent proteins (VFPs) can be fused selectively to the protein of interest by simple cloning techniques and develop fluorescence wi ... [J. Biomed. Opt. 13, 031205 (2008)] published Tue Jul 1, 2008.
Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides
Zanxia Cao and Haiyan Liu
We propose a method that may allow data about the conformational equilibriums of peptides to enter the parameter calibration phase in force field developments. The method combines free energy perturbation with techniques for extensive sampling in the conformational space. It predicts shifts in compu ... [J. Chem. Phys. 129, 015101 (2008)] published Tue Jul 1, 2008.
Dynamical changes of hemoglobin and its surrounding water during thermal denaturation as studied by quasielastic neutron scattering and temperature modulated differential scanning calorimetry
H. Jansson and J. Swenson
We have investigated the dynamical behavior of both the protein hemoglobin and its surrounding water during the denaturation process using modulated temperature differential scanning calorimetry, quasielastic neutron scattering, and frequency dependent conductivity measurements. To distinguish betwe ... [J. Chem. Phys. 128, 245104 (2008)] published Mon Jun 30, 2008.
Dynamical changes of hemoglobin and its surrounding water during thermal denaturation as studied by quasielastic neutron scattering and temperature modulated differential scanning calorimetry
H. Jansson and J. Swenson
We have investigated the dynamical behavior of both the protein hemoglobin and its surrounding water during the denaturation process using modulated temperature differential scanning calorimetry, quasielastic neutron scattering, and frequency dependent conductivity measurements. To distinguish betwe ... [J. Chem. Phys. 128, 245104 (2008)] published Mon Jun 30, 2008.
Spontaneous emergence of sequence-dependent rosettelike folding of chromatin fiber
Ph. St-Jean, C. Vaillant, B. Audit, and A. Arneodo
In the crowded environment of the eukaryotic nucleus, the presence of intrinsic structural defects is shown to predispose chromatin fiber to spontaneously form rosettelike structures. These multilooped patterns self-organize through entropy-driven clustering of sequence-induced fiber defects by depl ... [Phys. Rev. E 77, 061923 (2008)] published Fri Jun 27, 2008.
Shaping robust system through evolution
Kunihiko Kaneko
Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness of the phenotype. Here we study how this dynamical system is ... [Chaos 18, 026112 (2008)] published Fri Jun 27, 2008.