This curve progression of binding efficiency of the individual clones pointed to decisive roles of the inter-domain region and the N-terminal part of the FH1 region for binding to the SH3 domain and the unique site, which is supported by analyzing the shorter clones (S010, S433, S440).
Details of genes studied are given in Additional File 1. Primers were designed to generate amplicons of approximately 600 bp using Primer3 [ 24] and checked for unique binding to the Vectorbase-Ensembl AgamP3 genome sequence using BLAST.
HS4 is unique in binding to the counterpart protein HPS1 and in forming a 1 1 heterodimer called BLOC-3 that is involved in late endosomal trafficking [ 14, 15, 33].
The chromosomal position can influence the protein binding to the different copies of a non-unique sequence and may therefore lead to erroneous ChIP-Chip results.
These observations suggest that the NPVYL sequence of VLDLR mediates its unique property of binding to the Pafah1b α subunits.
This hydrogen bond is not unique to isoquinolinesulfonamide type inhibitors binding to the three enzymes discussed here.
Not surprisingly, we did not detect a higher rate of nucleotide conservation in intervals showing four-way binding conservation compared to the unique D. melanogaster intervals; in fact, the uniquely-bound intervals show slightly, but significantly, greater sequence conservation across their entire lengths (Wilcoxon rank sum test, p = 2.34e-20).
Key features of this pathway, as identified in MRL/lpr mice, are (i) P140 binding to a unique receptor, the constitutively-expressed HSC70 chaperone protein; (ii) involvement of γδ T cells in a granzyme B- and caspase-dependent mechanism, leading directly or indirectly via cytotoxic effectors to apoptosis of distinct (activated) T and B lymphocytes/blasts.
PCR primers were tested In Silico using BLAT in UCSC to confirm their binding to a unique region of the genome and the absence of polymorphism.
Cooperative ATP binding to a unique pocket in the equatorial domains induces a downward rotation of the intermediate domains (Ranson et al., 2001; Ma et al., 2000).
