Backbone RMSD and per-residue RMSF values of native and mutant structures of the TSPO protein.

<p><b>(A)</b> The RMSD values of native and mutant structures are shown as a function of time. <b>(B)</b> Central alpha carbon RMSF per residue of native, and mutant systems are shown. Transmembrane domains are depicted with grey cylinders. Blue, red and green lines indicate native, A147T and R162H mutations, respectively.</p

Distribution of coding nsSNPs, coding sSNPs, intronic SNPs, and UTR SNPs in the human TSPO gene.

<p>Distribution of coding nsSNPs, coding sSNPs, intronic SNPs, and UTR SNPs in the human TSPO gene.</p

Identification of deleterious nsSNPs in human TSPO gene.

<p>Out of 52 nsSNPs analysed using a wide array of sequence and structure based computational methods, 21 were predicted to be deleterious. Non-deleterious (blue), and deleterious (red), nsSNPs were plotted onto topology model of human TSPO which was generated with PROTTER [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195627#pone.0195627.ref018" target="_blank">18</a>]. Cholesterol recognition/interaction amino acid consensus sequence (CRAC) domain is highlighted in black.</p

Two known loci with significant age-difference in genetic effects on late stage AMD.

<p>Shown are the genome-wide significant (P_Agediff < 5 x 10⁻⁸) lead variant at the CFH locus and two of the 34 known variants from Fritsche et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194321#pone.0194321.ref013" target="_blank">13</a>], which revealed significant age-dependency (P_Agediff < 0.05/34, corrected for 34 known lead variants from Fritsche et al). Age-stratified analyses included 17,031 younger (7,959 cases, 9,072 controls) and 16,587 older (7,934 cases, 8,653 controls) individuals.</p

Analysis of protein stability by the cycloheximide protein degradation assay of wt and mutant TSPO proteins.

<p><b>(A)</b> TSPO is localized to mitochondria in primary dermal fibroblasts. <b>(B)</b> Lysates of human primary fibroblast cells were subjected to Western blotting to detect endogenous TSPO. <b>(C)</b> Fibroblasts from carriers of wt and homozygous A147T and R162H mutations of TSPO were treated with cycloheximide (25 μg/ml) for the indicated times, and endogenous TSPO was then detected by specific rabbit anti-TSPO antibody. Equal amounts of protein were subjected to Western blot analyses, as determined by comparing the amount of beta 1 tubulin. <b>(D)</b> Densitometry results for endogenous TSPO after treatment with cycloheximide were quantified as percentage of the initial TSPO protein level (0h of CHX treatment) and normalized to the intensity of beta 1 tubulin, and then plotted. Data are shown as mean ± SEM from three independent experiments.</p

Spatial superposition of the native and mutant TSPO structures.

<p>Native human TSPO structure depicted in grey, was aligned with <b>(A)</b> A147T (red), and <b>(B)</b> R162H (blue) TSPO mutant structures, respectively. Mutation at position A147T destabilized the whole protein, especially the loop LP1, which is involved in ligand binding pocket and loop LP2. Mutation R162H, on the other hand, affected the conformation of the C-terminus only.</p

List of nsSNPs in TSPO gene and their predicted Provean, SIFT, PolyPhen2, PhD-SNP, SNAP2, SNPs&GP, FATHMM, and iMutant3 scores. (N = non-deleterious, D = deleterious).

<p>List of nsSNPs in TSPO gene and their predicted Provean, SIFT, PolyPhen2, PhD-SNP, SNAP2, SNPs&GP, FATHMM, and iMutant3 scores. (N = non-deleterious, D = deleterious).</p

Average structural properties calculated for full length wt, A147T, and R162H TSPO models and corresponding standard deviations (in parentheses).

<p>Average structural properties calculated for full length wt, A147T, and R162H TSPO models and corresponding standard deviations (in parentheses).</p

Manhattan and QQ plot of sex-difference P-Values.

<p>Shown are the sex-difference P-Values for late AMD by their position on the genome (Manhattan plot) as well as their distribution (QQ plot). The 34 known genetic regions identified by Fritsche et al [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194321#pone.0194321.ref013" target="_blank">13</a>] are colored blue in the Manhattan plot.</p

Gene prioritization scoring for two AMD regions that were undetected by Fritsche et al.

<p>We queried 11 genes in the 2 narrow AMD regions (index and proxies, r² ≥ 0.5 and ±500 kb) for biological evidence. Detailed results are shown in the supplement for the expression data (<b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194321#pone.0194321.s005" target="_blank">S5 Table</a></b>) and the functional annotation (<b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194321#pone.0194321.s004" target="_blank">S4 Table</a></b>) as well as for the mouse data (<b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194321#pone.0194321.s006" target="_blank">S6 Table</a></b>).</p