br Materials and methods br

Materials and methods
Brief discussion Indicative peptide stereochemistries are shown in Fig. 1. In the absence of second shell O atoms, the native peptide, 3GSO_P, is under-coordinated in respect to the reference (also see Fig. 3b) and may not be differentiated from the other peptides exhibiting increased side-chain mobility (3GSU_P, 3GSV_P and 3GSX_P in Fig. 1). Additionally, as shown in Fig. 2, the variance of the total coordination of the 3GSO_P models varies is substantially higher, roughly four times that of the other three peptides associated with mobile side-chains. Interestingly, the coordination difference of the DFT-relaxed 3GSO_P model from the reference falls well within the range of 3GSO_P models. It might, thus, be envisaged that the ‘flexibility’ shown by 3GSO_P to adapt to recognition by the TCR rests on the substantially higher number of second shell O atoms – almost twice as many O atoms in comparison to the rest of the variants, also see Table 1. Due to their abundance, second shell O atoms, which represent water AZD1208 Supplier coordinated around the peptide might provide adequate ‘cushioning’ to the NLV such that the peptide is able to adjust to a wide variety of TCR׳s via expulsion of waters during recognition [22]. Certainly, inclusion of the second shell O atoms in peptide structures produced a trend of total coordination vs. functional avidity of the peptide in complexation with the TCR which was reminiscent of our results on atomic coordination of pMHC-TCR complexes in the case of Tax and a number of Tax-derived variants [1,2], i.e. the agonist peptide is over-coordinated in respect to the less agonist/antagonist. As depicted in Fig. 3a, all three 3GSO_P models were over-coordinated in respect to the reference as well as compared to the rest of the variants. In fact, 3GSO_P over-coordination in respect to the variants was almost exclusively due to the C–O and, principally, the O–O partials by roughly 60% (see Fig. 3c and d respectively) as compared to the highest-coordinated of the variants.
Note on the data files All peptide structures considered in the current study have been included in .xyz format in the Structures.rar file. The pair correlation data underlying to this work are included in PRDF.rar in comma delimited format. Data comparison is provided in PRDF.xls, which comprises total and partial PDF, RDF and coordination (RDF(r)dr) data for each of the peptides studied, in respect to interatomic distance, r (Å). In each of the tabs, the first line of every column represents the peptide number density (atoms/Å3) while the second line is the peptide designation, corresponding to Table 1. The sequence of peptides is the same in each tab. In the set of tabs named ‘PDF XXX’, the peptide data have been calculated via Eq. (1), while data in the tabs named ‘RDF XXX’, the peptide data have been calculated via Eq. (2). The RDF(r)dr XXX have been calculated via Eq. (3). and to estimate the cumulative coordination for a peptide structure, the running sum of RDF(r)dr may be calculated as shown in the example tab ‘RDF(r)dr Total’ and coordination differences in respect to the column named ‘Reference’ may then be calculated also as exemplified.
Value of the data Experimental design
Materials and methods
Experimental design, materials and methods Our study sample consisted of 775 unrelated Caucasian subjects, namely 289 controls (218 males and 71 females; mean age 51.9±18.3 years) and 486 suicide completers (362 males and 124 females; mean age 49.2±17.8 years). The control group was comprised of deceased persons, in which suicide as a cause of death was excluded. Criteria for positive alcohol dependence syndrome (ADS) status were met in 72 controls and in 97 suicide completers (for the details on the ADS status determination also see Materials and methods section in [1]). Here, by means of software specifically designed for genetic analyses PLINK v1.07 [2], we performed logistic regression analyses (adjusted for covariates age, gender and ADS status) of the genotype data (raw file may be provided upon request) in order to gain more insight into the role of the studied SNPs in completed suicide phenotype [1].