Manipulating the ensemble of unfolding pathways for proteins

M.C. Demirel A.R. Atilgan
 School of Engineering & Polymer Research Center, Bogazici University,
Bebek 80815, Istanbul, Turkey
 

The equilibrium dynamics of proteins is satisfactorily described by simple analytical methods [1]. To characterize unfolding behavior and to orchestrate [2] the unfolding pathway, we derived the following set of equations:

Firstly, the distorted shape of the native structure caused by the most cooperative, slowest mode of motion is obtained and compared with moleculardynamics (MD) results [3]. The equivalent force field that stabilizes this distortion is determined. Secondly, the native structure is perturbed by nonconservative, incremental forces that drive unfolding. The evolution of the structure is monitored at each force increment. We characterized the unfolding transition states of chymotrypsin inhibitor 2 (CI2) and bovine pancreatic trypsin inhibitor (BPTI) for different environmental conditions that stimulate different loading organizations.

 In case of CI2, for instance, a manipulation is achieved in such a way that five hydrogen bonds that enhance the stability of the hydrophobic core are gradually broken. The ensemble of the transition state, that exhibits a weakening in the hydrophobic core and complete loss of native interactions in the packing region, is obtained. These results conform with experiments and molecular dynamics simulations [4].

This newly proposed approach is particularly promising for characterizing the unfolding dynamics and reconstructing the unfolding potential energy surfaces of large proteins. With the proposed methodology, one can manipulate the enzymatic activity [5] and can alter the unfolding pathway so as to design highly flexible intermediates via which drug diffuses into membranes [6]. Furthermore, our formulation can monitor unbinding processes of ligands to proteins [7] and results are associated nicely with micromanipulationthrough atomic force microscopy [8].

 
References

 
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