Values of the second-order rate constant for nitrosylation of ferrous globins.

a<p>pH 7.0 and 20.0°C. Present study.</p>b<p>pH 9.0 and 20.0°C. Present study.</p>c<p>pH 7.2 and 22.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Ascenzi8" target="_blank">[43]</a>.</p>d<p>pH 7.0 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Abbruzzetti1" target="_blank">[53]</a>.</p>e<p>pH 7.0 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Rohlfs1" target="_blank">[49]</a>.</p>f<p>pH 7.0 and 20.0°C From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Chiancone1" target="_blank">[50]</a>.</p>g<p>pH 9.2 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Ascenzi6" target="_blank">[41]</a>.</p>h<p>pH 7.0 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Moore1" target="_blank">[48]</a>.</p>i<p>pH 7.5 and room temperature. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-VanDoorslaer1" target="_blank">[51]</a>.</p>j<p>pH 7.0 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Cassoly1" target="_blank">[47]</a>.</p>k<p>pH 6.5 and room temperature. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Hoshino1" target="_blank">[36]</a>.</p>l<p>pH 7.0 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Ascenzi9" target="_blank">[55]</a>.</p>m<p>pH 7.0 and 10.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Fasano1" target="_blank">[52]</a>.</p

Values of λ_max and ε of the absorption spectra in the Soret region of ferric and ferrous derivatives of Mt-trHbN, Mt-trHbO, and Cj-trHbP, 20.0°C.

<p>Values of λ_max and ε of the absorption spectra in the Soret region of ferric and ferrous derivatives of Mt-trHbN, Mt-trHbO, and Cj-trHbP, 20.0°C.</p

Nitrite-mediated nitrosylation of Mt-trHbN(II), at 20.0°C.

<p>(A) Difference absorbance spectrum of Mt-trHbN(II) <i>minus</i> Mt-trHbN(II)-NO, at pH 7.4. (B) Normalized averaged time courses of nitrite-mediated nitrosylation of Mt-trHbN(II), at pH 7.4. The nitrite concentration was 2.5×10⁻³ M (trace a) and 1.0×10⁻² M (trace b). The time course analysis according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811.e007" target="_blank">Eqn. (3)</a> allowed the determination of the following values of <i>h</i> = 4.0×10⁻² s⁻¹ (trace a) and 1.6×10⁻¹ s⁻¹ (trace b). (C) Dependence of <i>h</i> on [NO₂⁻] for nitrite-mediated nitrosylation of Mt-trHbN(II), at pH 7.4. The continuous line was generated from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811.e008" target="_blank">Eqn. (4)</a> with <i>h</i>_on = (1.6±0.2)×10¹ M⁻¹ s⁻¹. (D) pH-Dependence of <i>h</i>_on for the nitrite-mediated nitrosylation of Mt-trHbN(II). The slope of the continuous line was −1.00±0.01. The Mt-trHbN(II) concentration was 1.5×10⁻⁶ M. Where not shown, standard deviation is smaller than the symbol. For details, see text.</p

Values of the second-order rate constant for the nitrite-mediated nitrosylation of ferrous globins.

a<p>pH 7.4 and 20.0°C. Present study.</p>b<p>pH 7.0; unknown temperature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Sturms1" target="_blank">[31]</a>.</p>c<p>pH 7.4 and 25.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Tiso2" target="_blank">[34]</a>.</p>d<p>pH 7.6 and 25.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Helbo1" target="_blank">[90]</a>.</p>e<p>pH 7.4 and 25.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Tiso1" target="_blank">[32]</a>.</p>f<p>pH 7.4 and 25.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Huang1" target="_blank">[25]</a>.</p>g<p>pH 7.4 and 25.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Petersen1" target="_blank">[29]</a>.</p>h<p>pH 7.0 and 25.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Li1" target="_blank">[33]</a>.</p>i<p>In “Human Ngb Cys46–Cys55”, the Cys46 and Cys55 residues form an intramolecular disulphide bond.</p>j<p>In “Human Ngb Cys46/Cys55”, the Cys46 and Cys55 residues do not form the intramolecular disulphide bond.</p>k<p>pH 7.4 and 25.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Li1" target="_blank">[33]</a>.</p>l<p>pH 7.4 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Ascenzi4" target="_blank">[35]</a>.</p

Sequence alignment of human kallikreins (panel A) and three-dimensional structure of PSA (panel B).

<p>Sequence alignment (panel A) is built with those human kallikreins for which the three-dimensional structure is available at the Protein Data Bank. The protein sequences were obtained from the NCBI database (<a href="http://www.ncbi.nlm-nih.gov" target="_blank">http://www.ncbi.nlm-nih.gov</a>). The progressive multiple alignment of PSA (also named kallikrein 3; NCBI entry number: CAD30845.1), kallikrein 1 (also named tissue kallikrein; KLK1; NCBI entry number: AAH05313.1), kallikrein 2 (KLK2; NCBI entry number: AAF08276.1), kallikrein 4 (KLK4; NCBI entry number: AAD38019.1), kallikrein 6 (KLK6; NCBI entry number: AAP35498.1), kallikrein 7 (KLK7; NCBI entry number: NP_644806.1), and human plasma kallikrein (HPK; NCBI entry number: AAF79940.1) was performed by the Clustal-Omega program (<a href="http://www.ebi.ac.uk/Tools/msa/clustalo" target="_blank">http://www.ebi.ac.uk/Tools/msa/clustalo</a>). Only the trypsin-like serine protease domain of HPK has been aligned. The “*” symbol means that the residues are identical in all the aligned sequences; the ":" symbol indicate conserved substitutions, and the "." symbol means semi-conserved substitutions. The amino acid sequence of bovine chymotrypsinogen (BCTRP; NCBI entry number: 681083A) has been reported as the template. Three-dimensional structure of PSA (panel B). In both panels, the image was produced using UCSF Chimera molecular graphics package <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102470#pone.0102470-Pettersen1" target="_blank">[26]</a>. The “kallikrein loop” is in yellow <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102470#pone.0102470-Menez1" target="_blank">[24]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102470#pone.0102470-Tang1" target="_blank">[27]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102470#pone.0102470-Fernndez1" target="_blank">[28]</a>, amino acid residues forming the catalytic triad are in red, and amino acid residues affecting the pH dependence of the catalytic parameters are in cyan.</p

Three-dimensional structure of Mt-trHbN, Mt-trHbO, and Cj-trHbP.

<p>(Top) Ribbon views of Mt-trHbN, Mt-trHbO, and Cj-trHbP, including the heme-Fe group (red) and the protein matrix cavity/tunnel systems (blue mash). (Bottom) The heme-Fe pocket of Mt-trHbN, Mt-trHbO, and Cj-trHbP. The heme group is colored in red. The heme ligand (a cyanide ion in all the three structures) and the side chains of residues in the B10, CD1, E7 and F8 topological positions are highlighted. Atomic coordinates were taken from the PDB entries 1S56 (Mt-trHbN), 1NGK (Mt-trHbO), and 2IG3 (Cj-trHbP). All pictures have been drawn with the Swiss-PdbViewer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Guex1" target="_blank">[91]</a>.</p

Values of the second-order rate constant for the nitrite-reductase activity of ferrous heme-proteins.

a<p>pH 7.0; unknown temperature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Sturms1" target="_blank">[42]</a>.</p>b<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Tiso2" target="_blank">[45]</a>.</p>c<p>CysE20Ser mutant. pH 7.4 and 20°C. Present study.</p>d<p>pH 7.6 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Helbo1" target="_blank">[49]</a>.</p>e<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Tiso1" target="_blank">[43]</a>.</p>f<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Huang1" target="_blank">[37]</a>.</p>g<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Tiso1" target="_blank">[43]</a>.</p>h<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Petersen1" target="_blank">[40]</a>.</p>i<p>pH 7.0 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Li1" target="_blank">[44]</a>.</p>j<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Tiso1" target="_blank">[43]</a>. In “Human neuroglobin CysCD4-CysD5”, the CysCD4 and CysD5 residues form an intramolecular disulphide bond.</p>k<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Tiso1" target="_blank">[43]</a>. In “Human neuroglobin CysCD4/CysD5”, the CysCD4 and CysD5 residues do not form the intramolecular disulphide bond.</p>l<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Tiso1" target="_blank">[43]</a>.</p>m<p>pH 7.4 and 20°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Ascenzi8" target="_blank">[46]</a>.</p>n<p>pH 7.4 and 25°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Li1" target="_blank">[44]</a>.</p

Values of the second-order rate constant for peroxynitrite isomerization by ferric heme-proteins.

a<p>pH 7.4 and 20°C. Present study.</p>b<p>pH 7.0 and 20°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Ascenzi7" target="_blank">[32]</a>.</p>c<p>pH 7.0 and 20°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Coppola1" target="_blank">[31]</a>.</p>d<p>pH 7.0 and 20°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Herold2" target="_blank">[22]</a>.</p>e<p>pH 7.5 and 20°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Herold4" target="_blank">[24]</a>.</p>f<p>pH 7.5 and 20°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Herold2" target="_blank">[22]</a>.</p>g<p>pH 7.2 and 22°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Ascenzi4" target="_blank">[28]</a>.</p>h<p>pH 7.0 and 20°C. Cardiolipin was 1.6×10^–4 M. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Ascenzi5" target="_blank">[29]</a>.</p

Normalized averaged time courses of the NO₂^–-mediated nitrosylation of Ma-Pgb*-Fe(II), in the absence and presence of CO, at pH 7.4 and 20°C, λ = 430 nm.

<p>The NO₂^– concentration was 2.5×10^–3 M (traces a and b) and 8.0×10^–3 M (trace c). The CO concentration was 1.0×10^–4 M (trace a). CO inhibits the NO₂^–-mediated nitrosylation of Ma-Pgb*-Fe(II) (trace a). The time course analysis according to Eqn. 1 allowed the determination of the following parameters: trace b, α₁ = 0.58±0.05, <i>k</i>_obs1 = (2.3±0.2) ×10^–2 s^–1, α₂ = 0.42±0.04, and <i>k</i>_obs2 = (3.2±0.3)×10^–3 s^–1; trace c, α₁ = 0.56±0.05, <i>k</i>_obs1 = (7.9±0.8)×10^–2 s^–1, α₂ = 0.44±0.04, and <i>k</i>_obs2 = (9.0±0.1)×10^–3 s^–1. For details, see text.</p

Ma-Pgb* fold.

<p>(Panel A) The secondary structure elements are labeled A–H’. The 20 <i>N</i>-terminal residues and the extended CE and FG loops that seal the heme pocket and prevent the access of small ligands to the heme distal cavity are in orange. The pre-A Z-helix is in green. The heme (red) is displayed edge on. The proximal HisF8 residue is shown on the left hand side of the heme. The picture includes the mutated SerE20 residue, located at the <i>C</i>-terminus of the E-helix. The HisF8 and SerE20 side chains and residues building up the heme distal pocket are drawn as skeletal models (C atoms yellow, N atoms blue, and O atoms red) and labeled. (Panel B) Mono views of “tunnel 1” (top) and “tunnel 2” (bottom) access sites in Ma-Pgb*. Helices flanking the tunnel entries are labelled. The heme group (seen through the tunnel apertures) is shown in red. The protein is correctly oriented in both images, to bring each tunnel in the direction of sight. The images are rotated by 90°. The pictures have been drawn by UCSF - Chimera <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Pettersen1" target="_blank">[55]</a>. For details, see ref. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095391#pone.0095391-Nardini1" target="_blank">[11]</a>.</p