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We have shown that highly stable binding proteins for a wide spectrum of targets can be generated through mutagenesis of the Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus.
Two principally different applications are considered, (1) effects monitoring with biological components as targets for bioeffective substances, among them endocrine disruptors; and (2) immunochemical analysis employing antibodies as binding proteins for a wide variety of analytes such as pesticides.
Binding proteins for a diverse set of model targets could be isolated from this library; our chosen targets included a small organic molecule (fluorescein), a 12 amino acid peptide fragment from the C-terminus of β-catenin, the model proteins hen egg lysozyme and streptavidin, and immunoglobulins from chicken and mouse.
Reverse docking approach, the opposite of the direct docking method firstly proposed by Chen et al. [ 11], could identify probable binding proteins for a specific small molecule.
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Calcium-Response Factor (CaRF) is a novel nuclear protein first identified as a binding protein for a calcium-response element (CaRE1) in Bdnf promoter IV [14].
Nucleolin expressed at the cell surface is a binding protein for a variety of ligands implicated in tumorigenesis and angiogenesis.
Cell surface expressed gC1q-R can serve as a receptor for diverse proinflammatory ligands, and as a binding protein for a number of functional antigens of viral and bacterial origin.
Instances found in genome annotations include orthologues of the S. pneumoniae TIGR4 CDS SP_0243, encoding the extracellular binding protein for a putative iron ABC transporter, which is disrupted by the insertion of a RUP element in all the other pneumococcal genomes except S. pneumoniae AP200, 670-6B and TIGR4 itself.
ABA is perceived by soluble PYR/PYL/RCAR (pyrabactin resistance1/PYR1-like/regulatory component of ABA receptor) receptors that belong to the START superfamily of ligand-binding proteins (for a review see 81).
The other class of virally-encoded chemokine binding proteins for which a complex structure has been determined is the M3 decoy receptor from murine herpesvirus-68, whose structure with, and without CCL2, a member of the CC chemokine family has been determined[36].
The use of small binding proteins for pretargeting may also offer a new perspective.
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