Protein Stability Changes upon Mutations.

<p>Where, “WT” is the wild-type amino acid in the protein, “NEW” is the new amino acid after Mutation, “SVM2/DGG” is the stability (decrease/ increase), “RI” is the Reliability Index, and “T” is the temperature in celsius degrees.</p

Sequence homology-based results from Sorting Intolerant from Tolerant (SIFT) server for SNPs.

<p><b>a</b>) Predictions threshold for intolerance positions 1 through 100. <b>b</b>) Predictions threshold for intolerance positions 101 through 200. The type of amino acids in both figure are shown in color code i.e. Non polar (black), uncharged polar (green), basic (red), acidic (blue). Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction. ‘Seq Rep’ is the fraction of sequences that contain one of the basic amino acids. A low fraction indicates the position is either severely gapped or unalignable and has little information. Expect poor prediction at these positions.</p

RMSD and total energy of native structure (4HHB) and mutant modeled structures.

<p>The total energy of native structure (4HHB) after energy minimization is −334380.5 kJ/mol (score: 0.69) and before energy minimization it was 29644578.1 kJ/mol (score: −3.31).</p

The ß-chain of the HHB protein's molecular dynamics (MD) simulation showing truncated octahedron boundary explicit water solvated and hydrogen atoms in color.

<p>The MD simulations system used in calculations are; <b>a</b>) water box without the protein, <b>b</b>) water box surrounding the entire protein (middle) and <b>c</b>) tertiary structure of the wild type <i>ß</i>-chain of HHB protein showing disease causing mutations i.e. green <i>HbE</i>26 Glu→Lys (E→K), orange <i>HbD</i>121 Glu→Gln (E→Q), blue <i>HbC</i>6 Glu→Lys (E→K) and <i>HbS</i>6 Glu→Val (E→V) on 3 helixes using predict mesh modeling. The visual inspection also allow to identify the side chain of a histidine residue involved in the hydrogen bonding with surrounding molecules and in that case the δ nitrogen of the histidine (HSB) is protonated residue.</p

The crystal structure of human deoxyhaemoglobin at 1.74 A resolution.

<p>The haems are located toward the proximal region; the partition between the mean planes of N (porphyrin) and C (porphyrin) being 0.16(6) A and 0.10(6) A, respectively at the alpha and beta haems. At the alpha haems, the normal's to the average pyrrole planes are skewed evenly toward the haem centre, by about three degrees relative to the haem normal, and there is a folding of about four degrees of the haem about an axis running between the methene carbons that are between the pyrrole rings bearing like-type side-chains. At the beta haems, there is no such folding (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025876#pone-0025876-g005" target="_blank">Figure 5a</a>) having α1-Chain A (pale green), <i>β</i>2-Chain B (yellow), <i>β</i>1-Chain C (violet) and α2-Chain D (grey) which has four haems in each chain but this study was focused on <i>β</i>2-Chain B similar to the isotropic displacement model (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0025876#pone-0025876-g005" target="_blank">Figure 5b</a>).</p

The superimpose alignments of crystal structure of human deoxyhaemoglobin native protein structure (4HBB) with mutant modelled protein i.e. <i>HbE</i>, <i>HbD</i>, <i>HbC</i> and <i>HbS</i>.

<p>The structural modeling of proteins are flat ribbon model1 <i>β</i>2 Chain B (Brown) and Schematic model2 <i>β</i>2 Chain (blue). Four different amino acid mutations occur in the <i>β</i>2 Chain B, <b>a</b>) <i>HbE</i> contains <i>β</i>6Glu→Lys (E→K) located in the <i>β</i> Helix1, <b>b</b>) <i>HbD</i> contains <i>β</i>121Glu→Gln (E→Q) on located in the <i>β</i> Helix9, <b>c</b>) <i>HbC</i> contains <i>β</i>26Glu→Lys (E→K) in the <i>β</i> Helix2 and <b>d</b>) <i>HbS</i> contains <i>β</i>6Glu→Val (E→V) in the β Helix1.</p

Total energy of before and after mutation residue on <i>β</i>2 Chain B.

<p>Where “E” is the energy, “−E/KT” is the frequency that is proportional to exp, “T” is the temperature and “K” is the Boltzmann constant.</p

Differents structures of hBDs: hBD-1 (panel A), hBD2 (Panel B), and hBD3mutant and wild type (panel C and D).

<p>Differents structures of hBDs: hBD-1 (panel A), hBD2 (Panel B), and hBD3mutant and wild type (panel C and D).</p

Clinical data of patients diagnosed with colon cancer via colonoscopy.

<p>Clinical data of patients diagnosed with colon cancer via colonoscopy.</p

Human beta defensin (hBD) protein expression in colon cancer tissues.

<p>Tissues were immunostained using specific hBD antibodies (Panel 2A). hBD- positive cells in the tissues were estimated as follows: 0 points, no positive color; 1 point, <20% positive staining; 2 points, 21‑50% positive staining; 3 points, 51–75% positive staining; and 4 points, >75% positive staining. This is presented in Panel B.</p