raw data for plos one

<p>pdb structures for plos one published data</p

Structure refinement of the U2/U6 small-nuclear RNA.

<p>(A) Superposition of 20 structures calculated by refining against NMR, secondary structure, and knowledge-based restraints. The RMS deviation is 9.87±0.87 Å. (B-D) Upon the incorporation of the maps at 35 Å, 25 Å, and 15 Å resolutions, the RMS deviation for the 20-model bundle can be improved to 5.05±0.17 Å, 4.05±0.19 Å, and 3.25 ± 0.11 Å, respectively. (E) Upon the incorporation of an artificial, cube-shaped density map restraint, the structural convergence deteriorates to 10.84±1.02 Å. (F) Histogram showing the relationship between RMS deviation value and the resolution of the input map.</p

Structure refinement of ribosome-binding element from turnip crinkle virus genome.

<p>(A) Superposition of 20 structures, obtained by refining against NMR, secondary structure, and knowledge-based restraints. The RMS deviation for the bundle is 13.24±0.56 Å. (B) When incorporating of SAXS and P-P envelope distance restraints, the structural convergence is improved to 8.20±0.44 Å. (C) With the incorporation of additional map restraints, the RMS deviation is further lowed to 2.35±0.05 Å, for the 20-structure bundle. (D) By allowing only translation movement for the RNA duplexes but not the rotational movement, refined against both NMR and map restraints, the convergence of the calculated structures can be improved to 0.76±0.03 Å. The structure for generating the density map (the first model of PDB structure 2KRL) is colored red. The RMS difference between the structure calculated and the reference structure is 2.65±0.27 Å and 0.94±0.04 Å for (C) and (D), respectively.</p

PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape

<div><p>Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.</p></div

xplor-nih script

<p>xplor-nih script for RNA structure refinement </p

Induced fit pathway revealed by conformation switching between open, holo-closed and apo-closed states.

<p>The parameters are , , , using potential. (A–B) shows the typical trajectories in time for Q fractions and RMSDs. (C) the free energy profile as a function of . (D) the two dimensional free energy profile as a function of and . There is a direct route from the open basin to the holo-closed basin implying a clear induced fit pathway. The apo-closed basin is not on the way to the holo-closed basin, but is, in fact, off pathway. In addition, we can identify two transition states between O, A, H basins which are located at () = (0.3,0.8) and (0.7,0.65).</p

Functional landscapes of K6-, K27-, K29- and K33-diUbs.

<p>Upper subfigures are the free energy profiles of K6, K27, K29 and K33 linked diUbs plotted as a function of and . Lower subfigures are the free energy profiles of K11, K63 and K48 linkages, shown as references. They represent compact, open and the multi-state functional landscapes, respectively.</p

Experimental structures of diUbs with different linkages.

<p>Only five linkage types have been structurally characterized (summarized in Table 1 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003691#pcbi.1003691.s018" target="_blank">Text S1</a>). The corresponding structures are shown with the distal Ub unit (contributes a carboxyl group of G76 to form the linkage) in yellow and the proximal Ub unit (contributes an -amino group of lysine) in red, above a schematic cartoon. The formation of Ub interfaces is mainly contributed by two hydrophobic patches. One is the I44 patch (color in blue) consisting of L8, I44, V70, another is the I36 patch (colored in green) involving L8, I36, L71 and L73. These experimental structures include: compact structure of K6-linked diUb (2XK5, 3ZLZ), compact structure of K11-linked diUb (3NOB, 2XEW), open and compact structures of M1-linked diUb (2W9N, 3AXC, respectively), open and compact structures of K63-linked diUb (2JF5 and 3H7P, 3DVG, respectively), and four distinct structures of K48-diUb consisting of open (1F9J), closed (1AAR) and two compact conformations (1TBE, 3AUL, 3NS8 and 2PE9, respectively).</p

Schematic and actual representations of the folding landscape and functional landscape.

<p>A schematic energy landscape and a schematic free energy landscape are shown in (A) and (B), respectively. The unfolded state and folded states are denoted as U and F, respectively. (C) The actual free energy landscapes is shown by the high-dimensional free energy profile as a function of , , and (in unit of Å) under modest ligand concentrations (). The dashed arrows represent functional transitions between the open, apo-closed and holo-closed states. The route that is hidden in two-dimensional free energy profiles can be visible in the four-dimensional free energy profiles. For better view of the functional landscape, the conformational regions with beyond 15 Å are not shown.</p

Influence of ligand concentration on kinetic mechanism and transition rate constant.

<p>(A) Fractional flux of IF route () as a function of ligand concentration. Increasing ligand binding interactions can facilitate MBP to activate its conformation following an induced fit pathway. Intriguingly, is always kept on high values () during all the ligand concentrations. This strongly supports that the induced fit pathway is the predominant activation route of the system. (B) Transition rate constants as a function of ligand concentration. and increased as ligand concentration increased. However, increased more sharply than and . Our simulation results give strong support that if the transition rate between ligand-free major state and ligand-binding active state is sufficiently high, then the enzyme will mostly follow the direct conformational transition route, resulting in a predominant induced fit mechanism.</p