Percentage hydrogen bonding occupancy between Thr44-Thr80 and Asp116-Ser118.

<p>Percentage hydrogen bonding occupancy between Thr44-Thr80 and Asp116-Ser118.</p

Hydrogen bond interaction network for L35P mutant.

<p>The hydrogen bond interactions between contiguous amino acid residues based on a 3.2 Å cut-off has been presented here. The paths leading from the site of mutation Pro35 to catalytic residue His114 have been shown in blue square boxes. Other hydrogen bond interactions are shown in grey circles. The bond length is given on the edge between the nodes of amino acid residues. One of the path is mediating through Leu115 which plays a role in His114 conformational switching and the other path is mediating through Thr44 similar to that of WT-ANG.</p

Cartoon representation of X-ray structure for Human Angiogenin (PDB code: 1B1I).

<p>Cartoon representation of the structure of Human Angiogenin (PDB entry 1B1I) showing its functional sites; catalytic triad residues are represented as stick models, nuclear localization signal is represented in magenta color and receptor binding site is represented in orange color. Figure produced using PyMOL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032479#pone.0032479-DeLano1" target="_blank">[53]</a>.</p

Changes in folding of residues ³¹RRR³³ for WT-ANG, S28N and L35P mutants.

<p>Comparison of the changes in the folding of the residues R31, R32 and R33 at initial condition and at 50 ns of simulation. The residues are in open conformation for WT-ANG throughout the duration of simulation. For S28N and L35P mutants, a closed conformation is dominant. Figure produced using PyMOL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032479#pone.0032479-DeLano1" target="_blank">[53]</a>.</p

Conformational switching of catalytic residue His114 in K17I and L35P mutants.

<p>Orientation of the catalytic triad residue His114 at a regular interval of 10 ns during the MD simulations of K17I and L35P mutants. In these figures, T = 0 ns is the start of production phase post-equilibration. Figure produced using PyMOL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032479#pone.0032479-DeLano1" target="_blank">[53]</a>.</p

Comparison of AutoDock and ParDOCK binding energy scores for NCI-65828 complexes with WT-ANG and ANG mutants.

<p>*(ANG in which there is no conformational change of the catalytic residue His114).</p

RMSD and RMSF profile for WT-ANG and mutants.

<p>(A) Control plots representing the stability of the models during the molecular dynamics run. The root mean square deviation (RMSD) of the backbone atoms from the equilibrated conformation (0 ns) is presented as a function of time. The RMSD time profiles for WT-ANG, K17I, S28N, P112L, L35P, K60E and V113I are shown in black, red, dark green, blue, orange, pink, and light green, respectively. (B) Root mean square fluctuation (RMSF) values of atomic positions computed for the backbone atoms are shown as a function of residue number. The RMSF values for WT-ANG, K17I, S28N, P112L, L35P, K60E and V113I are shown in black, red, dark green, blue, orange, pink, and light green, respectively.</p

Residues interacting through hydrogen bonds from the site of mutation to His114 in L35P mutant.

<p>Amino acid residues of L35P mutant through which hydrogen bonds exert influence from the site of mutation on the catalytic site His114. There were two shortest paths identified. The first mediated through Leu115 and the second mediated through Thr44. Residues have been shown as stick models in marine blue color. Catalytic triad residues have been shown as stick model and represented in green color. Hydrogen bonds between residues have been shown in red dashed-lines. (A) The ribbon representation shows the path traced by the contiguous amino acid sequence Pro35-Lys40-Gln12-His13-Leu115-Gln117-Asp116-His114-Ala106-Val113 (B) The ribbon representation shows the path traced by the contiguous amino acid sequence Pro35-Lys40-Gln12-His13-Thr44-Gln117-Asp116-His114-Ala106-Val113. Figure produced using PyMOL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032479#pone.0032479-DeLano1" target="_blank">[53]</a>.</p

Hydrogen bond interaction network for K60E mutant.

<p>The hydrogen bond interactions between contiguous amino acid residues based on a 3.2 Å cut-off has been presented here. The path leading from the site of mutation Glu60 to catalytic residue His114 has been shown in blue square boxes. Other hydrogen bond interactions are shown in grey circles. The bond length is given on the edge between the nodes of amino acid residues. The path is mediating through Thr44 similar to that of WT-ANG and there is no conformational switching of His114.</p

Hydrogen bond interaction network for WT-ANG.

<p>The hydrogen bond interactions between contiguous amino acid residues based on a 3.2 Å cut-off has been presented here. All hydrogen bond interaction paths up to catalytic residue His114 have been compared with the hydrogen bond interaction paths of other mutants. These hydrogen bond interactions are shown in blue square boxes. Other hydrogen bond interactions are shown in grey circles. The starting residues through which these paths led to His114 are shown in pink square boxes. The bond length is given on the edge between the nodes of amino acid residues. All the hydrogen bond interaction paths are mediating through Thr44 and there is no conformational switching of His114.</p