Gristick, H. B. et al. Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site.
The structural basis for this has been nicely worked out by Steve Blacklow and colleagues (Structure of an LDLR-RAP Complex Reveals a General Mode for Ligand Recognition by Lipoprotein Receptors. Fisher C, Beglova N, Blacklow SC. Mol Cell. 2006 Apr 21 22 2):277-83).
Citing the nucleosome core particle, the same group (50) also proposed that the binding of arginines to regions of high negative electrostatic potential in narrow minor grooves (51), a consequence of isoelectric focusing (52), provides an important mode for protein−DNA recognition (50).
Grooves formed by aromatic hydrophobic residues on amyloid fibril surfaces may therefore offer a generic mode of recognition for amyloid dyes.
For example, syn-inosine has been observed to form an HG-type bp with protonated adenine at near-neutral pH, which affords a possible mode of recognition for I·A+ mispairs.
Single nucleotide segments accommodated 67% of the binding sites in T. thermophilus whereas only 33% of the binding sites have single nucleotide segments in E. coli.> The mode of recognition for protein-RNA complexes belonging to different organisms has been further studied with a typical complex, AspRS-tRNAAsp using molecular dynamics simulations as described in the Methods section.
Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products.
Importantly, the as-prepared TMICMs with thermo-responsive "specific recognition sites" also exhibited excellent temperature-dependent switching modes for selective recognition and separation of the template molecule (ciprofloxacin).
Strikingly, although ZIKV and dengue virus (DENV) apo-helicases share conserved residues for RNA binding, their different manners of motor domain rotations result in distinct individual modes for RNA recognition.
If, in the first situation, the same mode of recognition of ancestral acceptor stems (major groove/major groove) with complementary second base pairs helped to decrease mis-aminoacylation as Figure 6 suggests, then one would predict for the second situation that, symmetrically, the acceptor stems with the same second base pair need different modes of recognition to minimize the risk of confusion.
