Summary of the clustering analysis.

<p>Summary of the clustering analysis.</p

Hydrogen bond network for the wild type at three different temperatures.

<p>(A) 300 K, (B) 305 K and (C) 310 K.</p

Effect of mutation on the main-chain flexibility profiles of (A) DNA-free(B) DNA-bound p53 at various temperatures.

<p>Flexibility profiles determined from Cα atoms of DNA-free and DNA-bound p53 comparing WT (black solid line) and R248Q (red solid line) variants at 300, 305 and 310 K.</p

Binding energy decomposition per residue for WT and R248Q p53-DNA complexes at 300, 305 and 310 K.

<p>Binding energies are given relative to the energy of the DNA−bound WT p53 complex at 300 K. Residues 119, 120, 248 and 277 from p53 contributed the most to temperature-induced changes in binding energy. At least eight DNA residues involved in close contacts with the protein contributed significantly to binding.</p

Plot of the dynamic correlation between DNA and contact sites.

<p>Correlation between DNA and selected side-chain atoms of p53 involved in (A) major groove, (B) phosphate and (C) minor groove contacts for WT (black solid line) and R248Q p53 (red solid line). Small values of <i>d</i> represent a strong correlation between atoms, while large values indicate weak correlation. For arginine residues, Nη1, Nη2, and Nε atoms of the guanidinium group give rise to similar plots – a single atom is depicted for each residue, except for the minor groove contact. Each data point corresponds to an average over 5 equilibrated trajectory segments of 0.2 ns.</p

Clustering analysis for the wild type at 300 K.

<p>DBI exhibited local minima at cluster counts of 7, 12, 15 and 17. The percentage of variance explained by the data (sum of squares regression/total sum of squares, <i>i.e.</i>, SSR/SST) started to plateau after 14 clusters. Therefore, 17 clusters were extracted from the trajectory.</p

Main-chain flexibility profiles of (A) WT p53 and (B) R248Q p53 at various temperatures.

<p>Flexibility profiles determined from Cα atoms of DNA-bound (black solid line) and DNA-free (red solid line) WT and R248Q p53 at 300, 305 and 310 K. Regions of interest (loop L1 and loop between S10 and H2) are highlighted in grey.</p

Abscisic acid binding by the PYR1 ligand pocket induces gate-latch-locking.

<p>(A) – Structure of the apo-PYR1, gate open [PDB ID 3K3K, chain A]. (B) – Structure of ABA-bound PYR1, gate closed [PDB ID 3K3K, chain B]. The lock mechanism involves both direct and water/ions-mediated interactions of residues from gate (residues 85–89) and latch (residues 115–117), as well as hydrophobic interactions and hydrogen bonds throughout the binding pocket's surface. Residues which contribute to hydrogen binding in gate and latch are labeled and shown by orange sticks, while hydrophobic residues in the neighborhood of ABA (colored yellow) are shown by purple sticks. The allosteric rearrangement of gate and latch loops forms a surface for successful PP2C binding. Upon the binding, a conserved PP2C tryptophan 385 (not shown) is inserted between gate and latch and forms water-mediated hydrogen bond with ABA <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003114#pcbi.1003114-Nishimura1" target="_blank">[9]</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003114#pcbi.1003114-Melcher1" target="_blank">[11]</a>.</p

Normalized main-chain flexibility profiles of PYR1 monomers

<p> (solid lines) over-imposed on B-factors of the corresponding starting crystallographic structures (chains A and B from PDB entry 3K3K <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003114#pcbi.1003114-Nishimura1" target="_blank">[9]</a>, dashed lines). In the plot, red color represents PYR1 in ABA-bound, closed-lid conformation and blue color represents ABA-free, open lid conformation.</p

Normalized main-chain flexibility profile of PYR1 monomer bound to HAB1 (solid lines) over-imposed on B-factors of the starting crystallographic structure 3QN1 (dashed lines).

<p>Normalized main-chain flexibility profile of PYR1 monomer bound to HAB1 (solid lines) over-imposed on B-factors of the starting crystallographic structure 3QN1 (dashed lines).</p