br Experimental design materials and

Experimental design, materials and methods
Conflict of interest
Acknowledgment We wish to thank the Academy of Finland (Center of Excellence in Biomembrane Research, project no. 2721130), and the European Research Council (Advanced Grant project CROWDED-PRO-LIPIDS) for financial support. For computational resources, we wish to thank the CSC–IT Center for Science (Espoo, Finland).
Data Our work on the transcriptional regulatory Tax protein of the human T-cell leukemia virus type 1 (HTLV-1) [1–3], indicated that the immunological outcome of a number of functionally diverse variant ampar [4] recognized by the human A6 TCR, was highly correlated to their atomic coordination differences in respect to Tax [5]: over-coordination signified an agonist while under-coordination indicated an antagonist or null peptide. Additionally, gas-phase molecular orbital interactions on protonated tertiary structures revealed that the atomic coordination of agonist peptides resulted in the presence of a stable ammonium group on their N termini which was altogether unattainable for antagonists, and this finding was consistent across the range of conditions studied in regard to peptide formal charge and protonation of side chain groups [5,6]. Interestingly, we also attained data indicating that the atomic coordination of the peptide on the isolated pMHC (in the absence of TCR) may also serve as a metric of functional avidity, as we reported for the case of human cytomegalovirus (HCMV) variants [7].
Materials and Methods
Note on the data files The unprotonated peptide tertiary structures have been included in the file Structures.rar in.xyz format. Structure designation follows from the residue substitution on each peptide, e.g. the file corresponding to the peptide taken from the 1QRN structure is named “P6A.xyz”. Underlying pair correlation data are included in PRDF.rar in comma delimited format. Atomic coordination is compared in PRDF.xls, which comprises total and partial PDF, RDF and RDF(r)dr data in respect to the interatomic distance, r (°A). Each of the tabs in PRDF.xls represents a pair correlation partial and lists the underlying PDF (Eq. (3)), RDF (Eq. (4)) and RDF(r)dr (Eq. (5)) data as well as the running sum of RDF(r)dr (coordination) and variant differences in respect to Tax along with graphical representations of these differences.
Data Representative vertebrate CAPN3 sequences were aligned using MOE Ver. 2014.09 and GENETYX Ver. 12 software. Based on the alignment in this data, Figs. 5, 6, and 7 and Table 3 of Ref. [1] were made.
Experimental design, materials and methods Sequence data were retrieved from NCBI (http://www.ncbi.nlm.nih.gov.eleen.top/) and Ensemble (http://asia.ensembl.org/) databases. Representative vertebrates that have complete or close to complete amino acid sequence(s) for CAPN3 were selected for alignment. These sequences were aligned by Protein Align function of MOE Ver.2014.09 software using default parameters, and then refined using Parallel Editor of GENETYX Ver.12.
Acknowledgements
Value of the data Data, experimental design, materials and methods
Acknowledgments We thank P. Wilmarth (OHSU) for assistance with proteomics analyses. Proteomics studies were supported by a Research Core award from the OHSU School of Medicine, and NIH Grants P30EY010572, P30CA069533, and S10OD012246. This work was supported by Grants from the National Institutes of Health (R01HL101972 to O.J.T.M.), the American Heart Association (13POST13730003 to J.E.A. and 13EIA12630000 to O.J.T.M). The authors have no conflicts of interest to declare.
Specifications Table
Value of the data
Data Bioinformatic tools were applied in order to search for overrepresented cellular processes GO terms in the groups of protein showing increased or decreased abundance, to elucidate their putative biological functions. Lists of over-represented GO terms, where all proteins (indicated by the corresponding gene) enriched for a specific functional category are shown, were generated for each condition comparison (Table 1). Information about the GO Term ID, database and p-value are also available along with the hyperlink to the AmiGO2 application, where further details about each GO term are available. A similar list was created after categorization of the semantically related terms (Table 1).