Overview of the assembled Muller elements of <i>D</i>. <i>hydei</i>.

<p>Overview of the assembled Muller elements of <i>D</i>. <i>hydei</i>.</p

Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics

<div><p>Proteins accomplish their physiological functions with remarkably organized dynamic transitions among a hierarchical network of conformational substates. Despite the essential contribution of water molecules in shaping functionally important protein dynamics, their exact role is still controversial. Water molecules were reported either as mediators that facilitate or as masters that slave protein dynamics. Since dynamic behaviour of a given protein is ultimately determined by the underlying energy landscape, we systematically analysed protein self energies and protein-water interaction energies obtained from extensive molecular dynamics simulation trajectories of barstar. We found that protein-water interaction energy plays the dominant role when compared with protein self energy, and these two energy terms on average have negative correlation that increases with increasingly longer time scales ranging from 10 femtoseconds to 100 nanoseconds. Water molecules effectively roughen potential energy surface of proteins in the majority part of observed conformational space and smooth in the remaining part. These findings support a scenario wherein water on average slave protein conformational dynamics but facilitate a fraction of transitions among different conformational substates, and reconcile the controversy on the facilitating and slaving roles of water molecules in protein conformational dynamics.</p></div

Overview of the system.

<p><i>D</i>. <i>hydei</i> and <i>D</i>. <i>mojavensis</i> are members of <i>repleta</i> species group, and <i>D</i>. <i>melanogaster</i> and <i>D</i>. <i>simulans</i> are members of <i>melanogaster</i> subgroup. For each species pair we performed MK tests to identify the targets of parallel recurrent protein adaptation. Maine and Panama population genomes and transcriptomes of <i>D</i>. <i>hydei</i> and <i>D</i>. <i>melanogaster</i> were used to study parallel population differentiation between species.</p

Estimates of mean 1-kb <i>F</i>_<i>ST</i> for Maine vs. Panama population samples.

<p>Estimates of mean 1-kb <i>F</i>_<i>ST</i> for Maine vs. Panama population samples.</p

Number of genes harboring non-synonymous SNP <i>F</i>_<i>ST</i> outliers.

<p>Number of genes harboring non-synonymous SNP <i>F</i>_<i>ST</i> outliers.</p

Density of <i>F</i>_<i>ST</i> estimates from 1-kb windows between Panama and Maine populations.

<p>The 1%, 2.5%, and 5% tail cutoffs are indicated with hash marks.</p

Nucleotide diversity (π) and sequence coverage of each chromosome.

<p>Nucleotide diversity (π) and sequence coverage of each chromosome.</p

The relationship between <i>r</i> (correlation coefficient between <i>E_p</i> and <i>E_p</i>_–<i>w</i>) and net effects of water molecules on local PES () for three different time scales.

<p>a) , b) and c). Data for all eight time scales studied are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060553#pone.0060553.s006" target="_blank">Fig. S6</a>.</p

Pearson correlation coefficient <i>r</i> between <i>E_p</i> and <i>E_p</i>_–<i>w</i> for barstar.

<p>Time scale values are obtained by first reducing time scales() with femto-second and then taking logarithm (e.g. 1 corresponds to 10 , 2 corresponds to 100 , 3 corresponds to 1 , etc.) Time scales mentioned in figures hereafter are the same. (a) ensemble average of as a function of time scales. (b) Distributions of at 10 (square), 1 (circle), 100 (upwards triangles) and 10 (downwards triangles).</p

Effect of Methylation on the Photodynamical Behavior of Arylazoimidazoles: New Insight from Theoretical ab Initio Potential Energy Calculations and Molecular Dynamics Simulations

Arylazoimidazoles are a series of azobenzene derivatives possessing the ability to undergo photoinduced trans–cis isomerization. Their isomerization quantum yields are found to be dependent on the excitation wavelength and chemical substituents. The current work investigated the ultrafast nonadiabatic decay behaviors of three arylazoimidazoles (Pai-H, Tai-H, and Tai-Me) after being photoexcited to the S₁ and S₂ states by means of high-level ab initio potential energy calculations and on-the-fly surface hopping dynamical simulations in gas phase to explore the effect of the methylation. The results found that the Pai-H with no methylation substituents only decay along a NNC bending reaction pathway for both the S₁ and S₂ states. The Tai-H with a methylation substituent on the six-membered ring can decay along both the NNC bending and twisting motion pathways for the S₁ and S₂ states. The Tai-Me has methylation substituents on both the six- and five-membered rings prefers to decay by a twisting motion in the S₁ state, while a NNC bending channel is activated following excitation to the S₂ state. The position and numbers of methylation substituents has important influence on the dynamical behaviors of arylazoimidazoles. The current work provides fundamental knowledge of the arylazoimidazoles and will be helpful for advanced and further exploration and application