Pairs. The highest scored matched spectra were validated manually, and to each spectral match a confidence was allocated. A high-confidence match indicates that for the longer peptide almost all and for shorter peptides a minimum of three fragments were matched and all major peaks in the spectrum were accounted for. A low-confidence match indicates that one peptide matched essentially all observed fragments and a second peptide had up to three fragments matched with most of peaks in spectrum explained. Reverse peptide sequences were used as a decoy search. All matches had to be highest ranking and unambiguous in the target and decoy search.XWALK web server v. 0.6 [70] (http://www.xwalk.org), in vali?dation mode. Thresholds for RWJ 64809 web calculation were set to 40 A to ensure proper calculation but all reported SAS distances were ?within the developer-suggested 34 A cut-off. Where Euclidian distances are discussed in the text these refer to Ca a distances measured in UCSF CHIMERA [78] on the atomic Cartesian coordinate set for the model as provided with this publication (electronic supplementary material).rsob.royalsocietypublishing.org6.10. Coiled-coil fragment modelsMultiple sequence alignments of the newly defined coiled-coil segments (d2 and d4 in table 1) with close homologues were obtained by submission to the COILS/PCOILS server within ?the Bioinformatics Toolkit Tubingen suite [91] in December 2013, with PSI-BLAST enabled and default settings retained otherwise. For identifying potential `break-points’ for fragmenting the model, these automatically obtained coiled-coil predictions and heptad periodicity position assignments by COILS/PCOILS were also considered; however, they were supplemented (and often overruled) with manual multiple sequence analysis heuristics, and with secondary structure predictions obtained via the Genesilico metaserver [93] (http:// www.genesilico.pl/meta2). (There are various structurally documented examples of disrupted heptad periodicity in nonetheless regular coiled-coil segments in known structures, and conversely structural disruptions that are not easily correlated to disruptions in heptad periodicity). Specifically, we assigned potential break-points where at least one, and usually several, signs of aperiodicity were noted in the sequence alignment: (i) five or more consecutive alignment positions in which highly polar amino acids dominated; (ii) disrupted helix predictions according to three or more secondary structure prediction methods from different research groups; (iii) four or more consecutive positions that featured only RRx-001 site hydrophobic amino acids; (iv) secondary structure `parsing’ gaps or amino acids [94] present in more than one third of the homologues; (v) strong indications of disruption of the sequence repeat pattern (not spanning multiples of seven positions) as revealed through alignment analyses with HHrep, HHrepID, and/or the COILS/PCOILS outputs at the Bioinformatics Toolkit site [91] corroborated by other heuristics. Ideally, we would like the fragment boundaries to coincide with locations where the coiled-coil structure features substantive disruptions, e.g. inserted loops. Owing to the scarcity of reference structures, there are no tested methods for identifying such locations. Our heuristics reflect a common-sense procedure to this end, without claiming that all irregularities can be identified this way or that all breaks in the model will precisely match a coiled-coil disruption. Accordi.Pairs. The highest scored matched spectra were validated manually, and to each spectral match a confidence was allocated. A high-confidence match indicates that for the longer peptide almost all and for shorter peptides a minimum of three fragments were matched and all major peaks in the spectrum were accounted for. A low-confidence match indicates that one peptide matched essentially all observed fragments and a second peptide had up to three fragments matched with most of peaks in spectrum explained. Reverse peptide sequences were used as a decoy search. All matches had to be highest ranking and unambiguous in the target and decoy search.XWALK web server v. 0.6 [70] (http://www.xwalk.org), in vali?dation mode. Thresholds for calculation were set to 40 A to ensure proper calculation but all reported SAS distances were ?within the developer-suggested 34 A cut-off. Where Euclidian distances are discussed in the text these refer to Ca a distances measured in UCSF CHIMERA [78] on the atomic Cartesian coordinate set for the model as provided with this publication (electronic supplementary material).rsob.royalsocietypublishing.org6.10. Coiled-coil fragment modelsMultiple sequence alignments of the newly defined coiled-coil segments (d2 and d4 in table 1) with close homologues were obtained by submission to the COILS/PCOILS server within ?the Bioinformatics Toolkit Tubingen suite [91] in December 2013, with PSI-BLAST enabled and default settings retained otherwise. For identifying potential `break-points’ for fragmenting the model, these automatically obtained coiled-coil predictions and heptad periodicity position assignments by COILS/PCOILS were also considered; however, they were supplemented (and often overruled) with manual multiple sequence analysis heuristics, and with secondary structure predictions obtained via the Genesilico metaserver [93] (http:// www.genesilico.pl/meta2). (There are various structurally documented examples of disrupted heptad periodicity in nonetheless regular coiled-coil segments in known structures, and conversely structural disruptions that are not easily correlated to disruptions in heptad periodicity). Specifically, we assigned potential break-points where at least one, and usually several, signs of aperiodicity were noted in the sequence alignment: (i) five or more consecutive alignment positions in which highly polar amino acids dominated; (ii) disrupted helix predictions according to three or more secondary structure prediction methods from different research groups; (iii) four or more consecutive positions that featured only hydrophobic amino acids; (iv) secondary structure `parsing’ gaps or amino acids [94] present in more than one third of the homologues; (v) strong indications of disruption of the sequence repeat pattern (not spanning multiples of seven positions) as revealed through alignment analyses with HHrep, HHrepID, and/or the COILS/PCOILS outputs at the Bioinformatics Toolkit site [91] corroborated by other heuristics. Ideally, we would like the fragment boundaries to coincide with locations where the coiled-coil structure features substantive disruptions, e.g. inserted loops. Owing to the scarcity of reference structures, there are no tested methods for identifying such locations. Our heuristics reflect a common-sense procedure to this end, without claiming that all irregularities can be identified this way or that all breaks in the model will precisely match a coiled-coil disruption. Accordi.
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Cathepsins
