Perturbation-response scanning: Ligand entry-exit mechanisms of ferric binding protein
Atılgan, Canan and Atılgan, Ali Rana (2008) Perturbation-response scanning: Ligand entry-exit mechanisms of ferric binding protein. (Submitted)
A new tool, termed perturbation-response scanning (PRS), for the analysis of remote control strategies utilized by proteins is introduced, and its predictive power is shown on the ligand release mechanisms of haemophilus influenzae Ferric binding protein (FBP). The approach relies on systematic use of computational perturbation/response techniques based on linear response theory. By sequentially exerting directed forces on single-residues along the chain and recording the resulting relative changes in the residue coordinates, we find that for a large number of the cases, residue-by-residue displacements as determined from the X-ray structures are faithfully reproduced for the apo FBP. Once a stabilizing ligand is integrated to the system in the holo form, only a few residues remain that are particularly successful in reproducing the experimental displacements. It is possible to manipulate the bound form of the protein towards the unbound form by either directly perturbing the Fe binding residues, or by controlling the distant loop residues that show large displacements upon binding. The latter are charged residues, providing binding locations for ions which are known to influence Fe+3 release kinetics. By perturbing any one of these residues, the tip of the cap that opens the exit of the Fe+3 is made to operate coherently, irrespective of the direction of the perturbation. The analysis, based on the structural features of the protein, provides alternative strategies for ferric iron release.
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