Tm1631 protein surface conservation analysis by ProBiS.

<p>Tm1631 is shown in surface representation, which is colored by degrees of structural conservation from unconserved (white) to conserved (red). The predicted binding site is encircled by a yellow dashed line.</p

Similar evolutionary patterns in nucleotide binding sites found in PDB using ProBiS.

<p>Predicted Tm1631 binding site (left) is similar to (right): (a) active site in DNA binding site of polymerase X (2w9m) with DNA ligand that was transposed from homologous protein structure 3au6; (b) allosteric site in uridine monophosphate kinase (2jjx); (c) active site of DNA-glycosylase (3fhf) with DNA ligand transposed from homologous protein structure 3knt.</p

Top-ranked similar binding sites in proteins of different folds found using the predicted binding site in Tm1631 as query to the binding site comparison approach.^a

a<p>The entire list of similar binding sites is in Table S1 in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003341#pcbi.1003341.s001" target="_blank">Text S1</a>.</p

Workflow of the function prediction for the Tm1631 protein structure of unknown function.

<p>Workflow of the function prediction for the Tm1631 protein structure of unknown function.</p

Tm1631-DNA model based on comparison of Tm1631 protein (1vpq) to known endonuclease IV-DNA complex (2nqj) from PDB.

<p>Tm1631 is white, endonuclease IV is blue, DNA is green and light-blue cartoons, sulfate ions are CPK sticks, crescent-shaped grooves in both proteins are shaded areas. Initial Tm1631-DNA model; Tyr47 and Tyr48 penetrate the DNA's extra-helical region (left). Endonuclease IV-DNA complex (right).</p

Tm1631-DNA model after 90 ns of MD.

<p>Reactive phosphate group in DNA is marked with a red asterisk. (a) Tm1631-DNA model, residues that interact with the DNA are marked. (b) Magnified view of the Tm1631-DNA interface. DNA phosphate groups and residues that interact with the DNA are represented as sticks; black dashed lines denote putative hydrogen bonds and salt bridges. (c) and (d) Schematic picture of Tm1631-DNA and endonuclease IV-DNA interactions. Similar residues in Tm1631 and endonuclease IV binding sites are in white and blue ellipses, respectively. Hydrogen bonds with DNA are shown for amino acid side chains (solid black arrows) and backbone atoms (solid cyan arrows). Stacking interactions with DNA nucleotides are dashed black lines.</p

Enzyme titration reaction scheme.

<p>E is the <i>Torpedo californica</i> acetylcholinesterase enzyme, I the m-(N,N,N-trimethylammonio) trifluoroacetophenone (TMTFA) inhibitor, and EI their complex; <i>k₀</i> is a second order association rate constant. The reaction was drawn using the <i>Reaction Scheme</i> tab of ENZO.</p

Nontrivial NOE connectivities and corresponding distances (Å) calculated from the transferred NOESY spectra for arylalkyloxy derivatives.

<p>For the sake of clarity, the atom labels do not strictly follow IUPAC rules for all compounds.</p>a<p>Distances from X-ray structure, PDB code 2VTD <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052817#pone.0052817-Humljan1" target="_blank">[8]</a>.</p>b<p>Distances from X-ray structure, PDB code 2XPC <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052817#pone.0052817-Sosi1" target="_blank">[11]</a>.</p>c<p>Overlapped.</p>d<p>Medium NOE cross-peak that can belong either to H1” or H5” due to signal overlap.</p

Autoactivation of procathepsin B.

<p>The data originally presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022265#pone.0022265-Rozman1" target="_blank">[11]</a> were used. The total amount of protein was determined by Pace et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022265#pone.0022265-Pace1" target="_blank">[13]</a> and used as a fixed value for each substrate/precursor concentration. The initial values of ES is zero and E is fitted in the interval [0, 1]. The initial value of rate constant <i>k₀</i> is set to diffusion rate value of 10⁸ M⁻¹ min⁻¹ and fixed, while initial values of <i>k₁</i> and <i>k₂</i> are 200 min⁻¹ and 7.2 min⁻¹ respectively, and fitted in the interval of [0, 10²⁰]. The sum of free active enzyme (E) and the instantaneusly dissociated complex (ES) is the measured species. Y-axis represents the concentration of cathepsin B in molar concentration and the X-axis represents time in minutes. The final estimated values of rate constants and initial concentrations of active enzyme portion for each individual curve are displayed under the <i>Evaluated Parameters</i>.</p

ENZO URL:

<p><a href="http://enzo.cmm.ki.si" target="_blank">http://enzo.cmm.ki.si</a><b>.</b> The ENZO web page provides a short introduction and links to a quick guide, examples and ENZO tool.</p