Also among Oct4 binding proteins we found various molecules involved in positive regulation of transcription, including several activators and coactivators and chromatin-modifying enzymes such as Myst2, a histone H4 acetyltransferase (Doyon et al., 2006; Sterner and Berger, 2000).
When we compared binding of different concentrations of fusion protein, we found that the IgM backbone strongly increased binding to plate-bound PD-1 by approximately 100-fold compared with IgG.
Given this evidence that CaRF is a direct sequence-specific DNA binding protein, we wanted to find endogenous gene targets of CaRF.
In in vitro competition assays with recombinant proteins, we found that binding between Daple and Dvl was reduced with increasing amounts of His-Gαi3.
Using a variant of NP1 with cobalt ferrite magnetic metal core (NP1-MNP) to pull down associated proteins, we found direct binding of LC3β and p62, two key proteins involved in autophagosome formation, with silica nanoparticles.
Of the Gram-negative binding proteins (GNBP), we found induction of GNBP2 and GNBP3 (Supplementary file 2).
Based on the presence of sequence motifs G1 G4, HflX is classified as a GTP binding protein, and we find that E. coli HflX hydrolyses both ATP and GTP (to be published elsewhere).
Using this high-resolution imaging approach to detect protein binding we found that under saturating conditions the fluorescence intensity between Ni-NTA beads (Qiagen) varied less than 16% and we found that about 7% of the beads did not bind recombinant protein.
When several known factor Xa inhibitors were overlaid within the protein binding site, we found that they all bind within the groove formed by the S1 and S4 sub-pocket of fXa (Figure 10B).
They also reported increased expression in yolk protein genes (Yp1 and Yp2 ) and an odorant binding protein (Obp99a ), which we found to be significantly affected by mating in our study as well (Table S1).
