Physics-Based Potentials for Coarse-Grained Modeling of Protein–DNA Interactions

Physics-based potentials have been developed for the interactions between proteins and DNA for simulations with the UNRES + NARES-2P force field. The mean-field interactions between a protein and a DNA molecule can be divided into eight categories: (1) nonpolar side chain–DNA base, (2) polar uncharged side chain–DNA base, (3) charged side chain–DNA base, (4) peptide group–phosphate group, (5) peptide group–DNA base, (6) nonpolar side chain–phosphate group, (7) polar uncharged side chain–phosphate group, and (8) charged side chain–phosphate group. Umbrella-sampling molecular dynamics simulations in explicit TIP3P water using the AMBER force field were carried out to determine the potentials of mean force (PMF) for all 105 pairs of interacting components. Approximate analytical expressions for the mean-field interaction energy of each pair of the different kinds of interacting molecules were then fitted to the PMFs to obtain the parameters of the analytical expressions. These analytical expressions can reproduce satisfactorily the PMF curves corresponding to different orientations of the interacting molecules. The results suggest that the physics-based mean-field potentials of amino acid–nucleotide interactions presented here can be used in coarse-grained simulation of protein–DNA interactions

Effect of Spikelet position on starch content (A and B) and amylose content (C and D) in wheat grains in winter wheat in growing seasons 2010/2011 (left) and 2011/2012 (right).

<p>US, upper spikelets; MS, middle spikelets; BS, basal spikelets.</p

Effect of spikelet position on starch content (A) and amylase (B) accumulation in wheat grain in the growing season 2010/2011.

<p>US: Upper spikelets; MS: Middle spikelets; BS: Basal spikelets.</p

Correlation coefficients between grain weight and the proportion of volume distribution and number distribution of starch granules at different spikelet positions.

<p>Correlation coefficients between grain weight and the proportion of volume distribution and number distribution of starch granules at different spikelet positions.</p

Effect of Spikelet position on the proportion by volume distribution of starch granules in wheat grain (d.f. = 17).

<p>Means within cultivar followed by a different letter are significantly different at <i>P</i><0.05. US, Upper spikelets; MS, Middle spikelets; BS, Basal spikelets.</p><p>Effect of Spikelet position on the proportion by volume distribution of starch granules in wheat grain (d.f. = 17).</p

Vaclav Stefan Teplicky on the origins and analysis of 17th century Utraquist prayer books

<p>D1, 75 plants m^-2; D2, 225 plants m^-2; D3, 375 plants m^-2; D4, 525 plants m^-2.</p

Mean daily temperature and sunshine durations from anthesis to maturity of wheat.

<p>Mean daily temperature and sunshine durations from anthesis to maturity of wheat.</p

Kernel numbers per spikelet (A and B), weight per spikelet (C and D), and grain weight per spikelet (E and F) in winter wheat in growing seasons 2010/2011 (left) and 2011/2012 (right).

<p>Kernel numbers per spikelet (A and B), weight per spikelet (C and D), and grain weight per spikelet (E and F) in winter wheat in growing seasons 2010/2011 (left) and 2011/2012 (right).</p

Golf - is it posh or for all?

Playing golf became a part of lifestyle of new dominant social and cultural groups but thanks to democratization tendencies and use as a business tool it opens up for more wide range of Czech society. Simultaneously the sporty heritors of golf tradition from the past before November 1989 last till today creating a core of Czech golfers space and teach newcomers the secrets of golf rules and etiquette. There are various groups in Czech golf space which differ from each other in the spirit of game, costs, but also in form of capital acquired. The first group is the mentioned one with long golf heredity. These players are holders of ideas in sense of golf rules, etiquette and skills. It was mainly social capital witch they obtained in golf space before November 1989 in their connections to golf community, nowadays it is according to their skills and traditional club membership symbolic capital. Together with this group it was a then power and wealth elite who started golf playing before November 1989. What its members drew from this activity was a symbolic capital when using golf playing as a demonstration of their wealth while nowadays it is mainly social capital which they can use. Newcomers into golf environment are mainly top executive managers and businessmen encountering golf as a part of..

Schematic diagram indicating the specific spikelet and grain positions analyzed in detail.

<p>Fertile and sterile spikelets are classified by whether or not there are grains in the spikelets. SS, sterile spikelets (SSN, number of sterile spikelets per spike); FS, fertile spikelets (FSN, number of fertile spikelets per spike); GNS, grain number per spikelet; SGW, single-grain weight; GWS, grain weight per spikelet.</p