Structural Insights into the Evolution of a Sexy Protein: Novel Topology and Restricted Backbone Flexibility in a Hypervariable Pheromone from the Red-Legged Salamander, <i>Plethodon shermani</i>

<div><p>In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions – such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake “three-finger” topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique adaptation may establish new paradigms for how receptor:ligand pairs co-evolve, in particular with respect to sexual conflict.</p></div

Rates of molecular evolution on PMF-G.

<p>Putty model of PMF-G, with backbone width proportional to residue variability (Shannon-Weaver index in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096975#pone-0096975-g004" target="_blank">Figure 4D</a>), and color-coded according to the likely mode of molecular evolution (based on data from Wilburn et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096975#pone.0096975-Wilburn1" target="_blank">[20]</a>; backbone, black; purifying selection, blue; neutral selection, yellow; positive selection, 0.01≤p<0.05, orange; positive selection, p<0.01, red).</p

Summary of mass spectral analysis in PMF-G disulfide bonding pattern determination.

<p>Mass spectral analyses was performed on the three-disulfide species of PMF-G purified by RP-HPLC. Differential treatment included proteolytic enzyme (Enz; chymotrypsin [C] or AspN [A]), reduction with dithiothreitol (DTT), and alkylation with iodoacetamide (addition of a carboxyamidomethyl (CAM) group). Observed monoisotopic masses were compared to theoretical masses with no free sulfhydryls, and mass shifts used to determine peptide modification. All assignments were confirmed by analysis of the fragmented ion series.</p

Homology modeling of major PMF isoforms.

<p>Homology models of four additional PMF isoforms that are highly expressed in <i>P. shermani</i> (isoform H, accession #JF274289; isoform I, accession #JF274304; isoform E3, accession #JF274344; isoform A1, accession #JF274380). Models are color coded according to amino acid conservation relative to PMF-G, which is included as a reference in the first panel (same residue, blue; conservative substitution, green; nonconservative substitution, red; insertion, yellow).</p

Restraints and statistics of the PMF-G structural ensemble.

<p>Restraints and statistics of the PMF-G structural ensemble.</p

Surface models of PMF-G.

<p>(a) Alignment of PMF-G with a representative TFP (1IQ9), color coded by residue type (acidic, red; basic, blue; hydrophilic, purple; nonpolar, green; cysteine, yellow), with disulfide bonds denoted by the black lines; (b) secondary structure schematic comparing PMF-G (left) and a representative TFP (right; 1IQ9); (c) backbone model of PMF-G (20 lowest-energy conformers) with partially transparent surface rendering (both color coded N- to C-terminus, blue to red); (d) full surface rendering of PMF-G color coded by residue type (same color code as a); (e) surface rendering of 1IQ9 (same color code as a).</p

Measurements of structural and sequence variability in PMF.

<p>(a) Backbone amide (H_N) exchange H/D exchange rates measured by half life (in hours), with proline residues omitted; (b) Root mean squared fluctation (RMSF) per residue in the PMF structural ensemble (blue) and predicted from the random coil index (red); (c) spectral density functions at 0, ω_N, and ω_H; J(0) is sensitive to fast (ns) and slow (µs-ms) motions, J(ω_N) to motiions on time scales faster than (1/ω_N = 2 ns), and J(ω_H) to motions faster than ¹H (1/ω_H = 0.2 ns); (d) Sequence variability (Shannon entropy index) at each residue measured for all Class I PMFs, shaded according to likelihood of positive selection at each position (red p<0.01, orange p<0.05; yellow = neutral selection). Seven out of the nine non-conserved amino acids in finger 3 display signatures of positive selection, suggesting combined structural flexibility and rapid evolution in this region.</p

NMR-derived structural ensemble of PMF-G.

<p>(a) Backbone model of PMF-G with the twenty lowest-energy conformers, color coded from N- to C-terminus (blue to red), and peptide finger numbers denoted (1–3); (b) disulfide bonds in PMF-G from underside view (same color scheme as a) and a representative TFP (1IQ9, carbons in magenta, sulfurs in green).</p