Distribution of echolucent and echogenic carotid plaques according to the extent of coronary artery disease in the entire study population

<p><b>Copyright information:</b></p><p>Taken from "Carotid Ultrasound Assessment of Patients with Coronary Artery Disease: A Useful Index for Risk Stratification"</p><p></p><p>Vascular Health and Risk Management 2005;1(2):131-136.</p><p>Published online Jan 2005</p><p>PMCID:PMC1993944.</p><p>© 2005 Dove Medical Press Limited. All rights reserved</p> Data adapted from . VD, vessel disease. : black bars = echogenic carotid plaque group; white bars = echolucent carotid plaque group

Dynamic cross-correlation maps calculated for the wild-type and the mutant LOX-1 proteins

<p><b>Copyright information:</b></p><p>Taken from "Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant"</p><p>http://www.biomedcentral.com/1472-6807/7/73</p><p>BMC Structural Biology 2007;7():73-73.</p><p>Published online 7 Nov 2007</p><p>PMCID:PMC2194713.</p><p></p> Panels A and C reports the intra-subunit motion correlations in the wild-type, while panels B and D the intra-subunit motion correlations in the mutant. The black and grey squares represent the Cmotion correlations wit

Secondary structure evolution, as a function of time, for the LOX-1 region (140–165) including strands 0 (red bar with middle point around 150) and 1 (red bar with middle point around 156)

<p><b>Copyright information:</b></p><p>Taken from "Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant"</p><p>http://www.biomedcentral.com/1472-6807/7/73</p><p>BMC Structural Biology 2007;7():73-73.</p><p>Published online 7 Nov 2007</p><p>PMCID:PMC2194713.</p><p></p> Colour code identifying the secondary structure is shown in the figure

Four snapshots of the final unperturbed simulation E taken at different times, showing the opening of the protein

<p><b>Copyright information:</b></p><p>Taken from "The open state of human topoisomerase I as probed by molecular dynamics simulation"</p><p></p><p>Nucleic Acids Research 2007;35(9):3032-3038.</p><p>Published online 16 Apr 2007</p><p>PMCID:PMC1888835.</p><p>© 2007 The Author(s)</p> The snapshots are displayed in two different orthogonal orientations (left and right). Core subdomains I, II and III are rendered in yellow, blue and red, respectively. Linker and C-terminal domains are rendered in green and cyan, respectively. The five active site residues are represented in ball and stick. The hinge residue Glu445 is indicated by an arrow in panel D

Snapshot of the final configuration of simulation E, showing only the core subdomain III, the C-terminal, and the linker domain regions of the protein

<p><b>Copyright information:</b></p><p>Taken from "The open state of human topoisomerase I as probed by molecular dynamics simulation"</p><p></p><p>Nucleic Acids Research 2007;35(9):3032-3038.</p><p>Published online 16 Apr 2007</p><p>PMCID:PMC1888835.</p><p>© 2007 The Author(s)</p> Helices 8, 9 and 16 and the catalytic Arg590 are highlighted in the figure to evidentiate the hydrophobic interactions between the C-terminal portion of helix 8 and helix 16. The hinge residue Glu445 is also indicated by an arrow

Average per-residue RMSD of hTop1 for the final unperturbed simulation E represented as a function of the residue number

<p><b>Copyright information:</b></p><p>Taken from "The open state of human topoisomerase I as probed by molecular dynamics simulation"</p><p></p><p>Nucleic Acids Research 2007;35(9):3032-3038.</p><p>Published online 16 Apr 2007</p><p>PMCID:PMC1888835.</p><p>© 2007 The Author(s)</p> The average per-residue RMSD have been calculated overlapping the protein on the initial position of the core subdomains I and II (black line), the core subdomain III (red line), the linker (green line) or the C-terminal domain (blue line)

Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch

Here we couple experimental and simulative techniques to characterize the structural/dynamical behavior of a pH-triggered switching mechanism based on the formation of a parallel DNA triple helix. Fluorescent data demonstrate the ability of this structure to reversibly switch between two states upon pH changes. Two accelerated, half microsecond, MD simulations of the system having protonated or unprotonated cytosines, mimicking the pH 5.0 and 8.0 conditions, highlight the importance of the Hoogsteen interactions in stabilizing the system, finely depicting the time-dependent disruption of the hydrogen bond network. Urea-unfolding experiments and MM/GBSA calculations converge in indicating a stabilization energy at pH 5.0, 2-fold higher than that observed at pH 8.0. These results validate the pH-controlled behavior of the designed structure and suggest that simulative approaches can be successfully coupled with experimental data to characterize responsive DNA-based nanodevices

NSC314622 in aprotic solvents.

<p>Comparison of the TD-DFT transitions of NSC314622, in CCl4 and DMSO, with the experimental UV-Vis absorption peaks, cfr <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073881#pone-0073881-g002" target="_blank">Fig. 2</a>.</p>a<p>v.str: very strong, str: strong, w: weak, sh: shoulder.</p

IQN and TPT binding pocket.

<p>Superposition of TPT and IQN into the DNA in the ternary complex. Thr718, Asn722 and Arg364 are shown.</p

Analysis of the helix bundle.

<p>Atomic distance between the centre of masses of helices 17–19 (<b>A</b>), 19–20 (<b>B</b>) and 19–21 (<i>C</i>). The black and red lines represent the distances calculated in the binary and ternary complexes, respectively.</p