Structural contexts of cryptic intermediates/metastable states characterized to present in the proteins using experimental methods and/or OneG computational tool.

<p>*CI denotes Cryptic intermediates;</p>#<p>ED denotes Experimental data;</p>$<p>MS denotes Metastable states.</p

Calculation of k_rc of NHs in proteins from their 3D structures.

<p>Correlation between k_rc values estimated by manual calculation and the OneG program for NHs in proteins (A) Ubiquitin (1UBQ) and (B) Cardiotoxin III (2CRT) at pH 7.0, 298 K.</p

The values of ΔG_U, ΔG_HX and ΔG_HX* (free energy of exchange corrected to effect of <i>cis-trans</i> proline isomerisation) of sixteen different proteins are herein listed.

@<p>Parentheses contain references from which the values of the free energies of the proteins have been referred.</p><p>The values of ΔG_HX* of the proteins have been calculated using the OneG program. Free energy values of the proteins were represented in kcal/mol.</p

Comparison of the actual and the predicted conformations (by OneG program) of Xaa-Pro peptide bonds in Ubiquitin, Rnase A and Cardiotoxin III.

<p>*The manual distance measurements for determining the conformations of the Xaa-pro peptide bonds in proteins were carried-out using PyMol molecular visualization tool <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone.0032465-DeLano1" target="_blank">[23]</a>.</p

Comparison of the actual and the predicted (by OneG program) cysteine and cystine residues in Cardiotoxin III and Cytochrome C.

#<p>Cys denotes Cysteine residue.</p><p>*The manual distance measurements for determining the cysteine and cystine residues in proteins were carried-out using PyMol molecular visualization tool <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone.0032465-DeLano1" target="_blank">[23]</a>.</p

Figurative representation of cryptic intermediates of Cytochrome C.

<p>The cryptic intermediates detected by experimental methods and predicted by OneG are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone-0032465-g004" target="_blank">Figure 4A</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone-0032465-g004" target="_blank">Figure 4B</a>, respectively. The backbone structures of the protein and residues representing each intermediate are shown in ribbon and stick models, respectively. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone-0032465-g004" target="_blank">Figure 4A</a> shows cryptic intermediates, proposed on the basis of experimental methods, in blue, green, yellow and red colours. The residues (for which exchange kinetics were observed by experiments) representing each intermediate are shown in sticks. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone-0032465-g004" target="_blank">Figure 4B</a> shows residues constituting three distinct intermediates as predicted by OneG program, in blue, magenta and yellow colours.</p

Possible existence of cryptic intermediates of CTX III.

<p>The five β-strands (S1–S5), three loops and a globular head in the structure of CTX III (2CRT) are shown by ribbon diagram. The blue and red sticks represent residues in the cryptic intermediates I & II, respectively, as predicted by OneG program.</p

Figurative representation of cryptic intermediates of apocytochrome b₅₆₂.

<p>Three cryptic intermediates of the protein detected by experimental methods and predicted by OneG are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone-0032465-g005" target="_blank">Figure 5A</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone-0032465-g005" target="_blank">Figure 5B</a>, respectively. The intermediates are denoted by blue, green and red colour codes in both cases. The backbone structures of the protein and residues representing each intermediate are shown in ribbon and stick models, respectively. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032465#pone-0032465-g005" target="_blank">Figure 5A</a> shows residues for which exchange kinetic data were reported in the literature.</p

Isolation and characterization of bioactive compounds of <i>Clematis gouriana</i> Roxb. ex DC against snake venom phospholipase A₂ (PLA₂) computational and <i>in vitro</i> insights

<p>Bioactive compounds were isolated from <i>Clematis gouriana</i> Roxb. ex DC. The compounds were separated, characterized, the structures elucidated and submitted to the PubChem Database. The PubChem Ids SID 249494134 and SID 249494135 were tested against phospholipases A₂ (PLA₂) of <i>Naja naja</i> (Indian cobra) venom for PLA₂ activity. Both the compounds showed promising inhibitory activity; computational data also substantiated the results. The two compounds underwent density functional theory calculation to observe the chemical stability and electrostatic potential profile. Molecular interactions between the compounds and PLA₂ were observed at the binding pocket of the PLA₂ protein. Further, this protein–ligand complexes were simulated for a timescale of 100 ns of molecular dynamics simulation. Experimental and computational results showed significant PLA₂ inhibition activity.</p