We have compared a RW model and a continuous model of Ca2+ diffusion in the dyadic cleft, using the distributions of stochastic events of single Ca2+ ions binding to single receptors as the measurement.
This class of binding proteins, both natural and synthetic, has a strong tendency to bind a preformed cleft using a convex binding interface (paratope).
We study the stochastic binding of single Ca2+ ions to receptors in the cleft using two different models of diffusion: a stochastic and discrete Random Walk (RW) model, and a deterministic continuous model.
To predict the orientation of cytochrome c in its binding cleft we used several rigid protein-protein docking software packages that are based on different approaches, namely PatchDock [ 79], ZDOCK [ 80], and ClusPro [ 81], and combined them with manual editing and evaluation of the obtained models.
We used crystal structure data of SORT1 complexed with NTS 27) to model peptide sequences into the binding cleft of SORT1 using NTS10-13 fragment -PYIL as a template, to determine a GRID for docking, and then to optimize the interactions through energy minimization (Fig. 4A C).
In addition, recent advances in the biochemical and pharmacological characterization of the integrin ligand interactions are beginning to reveal how integrins achieve specific recognition of wide variety of ligands using a small binding cleft at the subunit interface common to all integrins.
However, instead of mainly occupying the peptide binding cleft, the compounds were preferentially docked perpendicular to this cleft, extending into a hydrophobic pocket in the Zn2+ domain.
There is no obvious, clearly defined peptide binding cleft on the surface of TtrD.
The presence of the GαCT2 peptide in the cytoplasmic G protein binding cleft moves the cytoplasmic end of TM7 slightly toward the center, leading to a somewhat narrower binding cleft.
