Sieber and Allemann [ 72] found that R (348) can't directly interact with the nucleobases, but can determine the DNA binding specificity of the basic helix-loop-helix proteins (BHLH) E12 by directly interacting with both the phosphate backbone and the carboxylate of E 345) resulting in locking the side chain conformation of E 345).
For interactions between protein amino acid residues and DNA bases, Yang et al. showed that the evolutions of the transcription factors and the DNA binding sites of the basic helix-loop-helix family, homeo family, high-mobility group family, and transient receptor potential channels family are significantly correlated across eukaryotes [ 10].
The drastic decrease in lysis efficiency for POPC/PS5% liposomes indicates that the mechanism determining the binding of the highly basic toxin to the anionic membrane includes nonspecific electrostatic attraction.
N-terminal interactions have also been observed with the binding of the myelin basic protein, a natural Aβ inhibitor in the brain.
The authors present a model in which binding of these basic residues to acidic membrane phospholipids re-orientates the talin head and, therefore, the integrin β-subunit, leading to separation of the transmembrane helices of the two integrin (Lau et al, 2009) and subsequent integrin activation.
Phosphorylation or acetylation that can block FoxO activity may alter the binding of the C-terminal basic region to DNA to prevent transcriptional activity [ 27].
If any of the proteins in question would be involved in the post LARGE modification, mutations should not result in loss of ligand binding as the basic ligand binding LARGE glycan scaffold would still be preserved and present.
This structural observation suggests that the occluded state of the TMD that is induced by binding of a basic SBP may couple the substrate-loading to the formation of the ATPase catalytic site.
In the absence of Myb domain-directed binding, the basic domain of TRF2 may promote this process in a similar manner.
A role for PA in this process is suggested by the binding of a basic domain of Dsh to PA in vitro through a cluster of basic amino acids that are also required for Dsh membrane localization in vivo.
