To examine the effect of the TM helix orientation on the interaction of the JM sequence with the membrane surface, we performed similar experiments as described above to determine whether PIP2 affected the fluorescence intensity of the Alexa probe incorporated at the C-terminus of the TM JM (WT) peptide.
The linear programming model (1 - 10) infers the pathways given the source, the target and the whole network G V,E,D,C,T), where V is the set of proteins and DNAs, E is the set of protein-protein interactions and protein-DNA interactions, D defines the dissipation indix on each edge, C defines the capacity of each edge, and T defines the orientations of the interactions.
Although Met164 contacts the "opposite bases" (G19 and A2) in both structures, the orientation of the interaction is also different.
The surface charge properties of Pc and Cyt f, which vary significantly between the different species, influence the relative orientation of the interaction partners in the well-defined complex.
To model the FAK-NT-p53 peptide interaction, the DOCK 6.0 software analyzed >10,000 possible orientations of this interaction, based on the scores of the resulting interfaces using electrostatics (ES) and van der Waals (vWS) energies.
We have also incorporated one-headed myosin-V smooth muscle myosin rod chimeras (M5SH) into myosin rod filaments, allowing us to determine the orientation of the actomyosin interaction, finding that the stepsize of myosin-II depends on the angle between the cofilament and the actin filament [20].
The ANN results suggest broad trends regarding peptide orientation and the interaction of charged residues as a function of their position in the peptide.
For both Binary and Linear models, there may be an orientation bias: the interaction of two factors may depend on the relative orientation of the two binding sites.
Small orientation bias was found in the cases of Nanog-Esrrb, Sox2-Oct4 and cMyc-E2f1, where the free energy that penalizes one orientation is about 20% of the interaction free energy, and no such bias was detected for STAT3-Klf4 and Oct4-Zfx.
The observations are interpreted based on a slip system analysis, considering the relative effects of the initial grain orientation and the interaction between neighbouring grains as well.
