Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties

<div><p>Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (<i>Lethenteron japonicum</i> and <i>Petromyzon marinus</i>) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.</p> </div

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 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

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 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

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 kinetic and thermodynamic parameters for reductive nitrosylation of ferric heme-proteins.

a<p>pH 9.0 and 20.0°C. Present study.</p>b<p>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>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>e<p>pH 7.3 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Herold1" target="_blank">[39]</a>.</p>f<p>20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Herold1" target="_blank">[39]</a>.</p>g<p>pH 7.5 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Boffi1" target="_blank">[38]</a>.</p>h<p>Derived from values of <i>b</i> and [OH⁻] <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Boffi1" target="_blank">[38]</a>, at 20.0°C.</p>i<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>j<p>Derived from values of <i>b</i> and [OH⁻] <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Ascenzi6" target="_blank">[41]</a>, at 20.0°C.</p>k<p>pH 8.79 and room temperature. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Hoshino2" target="_blank">[37]</a>.</p>l<p>Derived from values of <i>l</i>_on and <i>L</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Hoshino2" target="_blank">[37]</a>, at pH 8.79 and room temperature.</p>m<p>Room temperature. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Hoshino2" target="_blank">[37]</a>.</p>n<p>In “Human Ngb Cys46–Cys55”, the Cys46 and Cys55 residues form an intramolecular disulphide bond.</p>o<p>pH 7.0 and room temperature. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Herold2" target="_blank">[74]</a>.</p>p<p>Derived from values of <i>l</i>_on and <i>l</i>_off<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Herold2" target="_blank">[74]</a>, at room temperature.</p>q<p>Derived from values of <i>b</i> and [OH⁻] <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Herold2" target="_blank">[74]</a>, at pH 7.0 and room temperature.</p>r<p>In “Human Ngb Cys46/Cys55”, the Cys46 and Cys55 residues do not form the intramolecular disulphide bond.</p>s<p>pH 7.1 and room temperature. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Hoshino2" target="_blank">[37]</a>.</p>t<p>Room temperature. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Hoshino2" target="_blank">[37]</a>.</p>u<p>pH 8.35 and room temperature. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Hoshino2" target="_blank">[37]</a>.</p>v<p>pH 7.5 and 20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Ascenzi7" target="_blank">[42]</a>.</p>w<p>20.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Ascenzi7" target="_blank">[42]</a>.</p>x<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-Ascenzi5" target="_blank">[40]</a>.</p>y<p>10.0°C. From <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Ascenzi5" target="_blank">[40]</a>.</p><p>n.d., not determined.</p

Reductive nitrosylation of Mt-trHbN(III), at 20.0°C.

<p>(A) Difference absorbance spectra of Mt-trHbN(III) <i>minus</i> Mt-trHbN(III)-NO and of Mt-trHbN(III)-NO <i>minus</i> Mt-trHbN(II)-NO (open and fillrd circles, respectively), at pH 9.0. (B) Normalized averaged time courses of Mt-trHbN(III) reductive nitrosylation, at pH 9.0. The NO concentration was 2.5×10⁻⁵ M (trace a) and 2.0×10⁻⁴ 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.e013" target="_blank">Eqns (5a)</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811.e015" target="_blank">(5c)</a> allowed the determination of the following values of parameters α, <i>l</i>, and <i>b</i>: trace a - α = 0.61, <i>l</i> = 6.0 s⁻¹, and <i>b</i> = 2.5×10⁻³ s⁻¹; and trace b - α = 0.89, <i>l</i> = 2.6×10¹ s⁻¹, and <i>b</i> = 2.4×10⁻³ s⁻¹. (C) Dependence of <i>l</i> on [NO] for Mt-trHbN(III) reductive nitrosylation, at pH 9.0. The continuous line was generated from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811.e016" target="_blank">Eqn. (6)</a> with <i>l</i>_on = (1.4±0.2)×10⁵ M⁻¹ s⁻¹ and <i>l</i>_off = 1.6±0.2 s⁻¹. (D) Dependence of α on [NO] for Mt-trHbN(III) reductive nitrosylation, at pH 9.0. The continuous line was generated from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811.e017" target="_blank">Eqn. (7)</a> with <i>L</i> = (1.6±0.2)×10⁻⁵ M. (E) Dependence of <i>b</i> on [NO] for Mt-trHbN(III) reductive nitrosylation, at pH 9.0. The average <i>b</i> value is 2.5×10⁻³ s⁻¹ (dashed line). (F) Dependence of <i>b</i> on [OH⁻] for Mt-trHbN(III) reductive nitrosylation. The continuous line was generated from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811.e018" target="_blank">Eqn. (8)</a> with <i>b</i>_OH− = (1.7±0.2)×10² M⁻¹ s⁻¹ and <i>b</i>_H2O = (6.4±0.7)×10⁻⁴ s⁻¹. The Mt-trHbN(III) concentration was 1.5×10⁻⁶ M. Where not shown, standard deviation is smaller than the symbol. For details, see text.</p

Consensus phylogenetic tree of major globin groups from the three kingdoms of life.

<p>This phylogenetic tree was based on the alignment of 150 sequences representing the following groups of globins: 10 plant non symbiotic 3/3 Hbs, 5 plant symbiotic 3/3 Hbs, 15 bacterial 3/3 globin-coupled sensors (GCSs), 4 3/3 protoglobins (Pgbs), 9 bacterial 2/2 Hb1s, 19 bacterial 2/2 Hb2s, 10 bacterial 2/2 Hb3s, 2 <i>Chlamydomonas reinhardtii</i> 2/2 Hbs, 2 ciliate 2/2 Hbs, 3 plant 2/2 Hbs, <i>Thalassiosira pseudonana</i> 2/2 Hb, 20 bacterial 3/3 flavohemoglobins (FHbs), 19 bacterial 3/3 single-domain Hbs, 9 eukaryote 3/3 FHbs, 1 diplomonad <i>Giardia lamblia</i> 3/3 Hb, and 1 mycetozoan <i>Dictyostelium discoideum</i> 3/3 Hb, <i>Cyanidioschyzon merolae</i> and <i>Thalassiosira pseudonana</i> 3/3 single-domain globins, and 3 vertebrate (<i>i.e.</i>, human, bird, and fish) 3/3 neuroglobins (Ngbs), cytoglobins (Cygbs), α- and β-globins and myoglobins (Mbs), and 2 urochordate 3/3 Hbs. Modified from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811-Vinogradov1" target="_blank">[1]</a> (Copyright (2005) National Academy of Sciences, U S A).</p

Mt-trHbN(II) nitrosylation at 20.0°C.

<p>(A) Difference absorbance spectrum of Mt-trHbN(II) <i>minus</i> Mt-trHbN(II)-NO, at pH 7.0. (B) Difference absorbance spectrum of Mt-trHbN(II) <i>minus</i> Mt-trHbN(II)-NO, at pH 9.0. (C) Normalized averaged time courses of Mt-trHbN(II) nitrosylation, at pH 7.0. The NO concentration was 5.0×10⁻⁶ M (trace a) and 1.2×10⁻⁵ 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.e002" target="_blank">Eqn. (1)</a> allowed the determination of the following values of <i>k</i> = 9.2×10¹ s⁻¹ (trace a) and 2.8×10² s⁻¹ (trace b). (D) Normalized averaged time courses of Mt-trHbN(II) nitrosylation, at pH 9.0. The NO concentration was 5.0×10⁻⁶ M (trace a) and 1.2×10⁻⁵ 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.e002" target="_blank">Eqn. (1)</a> allowed the determination of the following values of <i>k</i> = 7.4×10¹ s⁻¹ (trace a) and 1.9×10² s⁻¹ (trace b). (E) Dependence of the pseudo-first-order rate-constant <i>k</i> for Mt-trHbN(II) nitrosylation on the NO concentration, at pH 7.0. The analysis of data according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811.e003" target="_blank">Eqn. (2)</a> allowed the determination of <i>k</i>_on = (2.1±0.3)×10⁷ M⁻¹ s⁻¹. (F) Dependence of the pseudo-first-order rate-constant <i>k</i> for Mt-trHbN(II) nitrosylation on the NO concentration, at pH 9.0. The analysis of data according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102811#pone.0102811.e003" target="_blank">Eqn. (2)</a> allowed the determination of <i>k</i>_on = (1.6±0.3)×10⁷ M⁻¹ s⁻¹. The Mt-trHbN(II) concentration was 1.5×10⁻⁶ M. The NO concentration was 1.0×10⁻⁴ M (panels A and B). Where not shown, the standard deviation is smaller than the symbol. For details, see text.</p