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Protein-peptide interactions play essential roles in many cellular processesand their structural characterization is the major focus of currentexperimental and theoretical research. Two decades ago, it was proposed toemploy the steered molecular dynamics to assess the strength of protein-peptideinteractions. The idea behind using steered molecular dynamics simulations isthat the mechanical stability can be used as a promising and an efficientalternative to computationally highly demanding estimation of binding affinity.However, mechanical stability defined as a peak in force-extension profiledepends on the choice of the pulling direction. Here we propose an uncommonchoice of the pulling direction along resultant dipole moment vector, which hasnot been explored in simulations so far. Using explicit solvent all-atom MDsimulations, we apply steered molecular dynamics technique to probe mechanicalresistance of protein-peptide system pulled along two different vectors. Anovel pulling direction, along the resultant dipole moment vector, results instronger forces compared to commonly used peptide unbinding along center ofmasses vector. Our results demonstrate that resultant dipole moment is one ofthe factors influencing the mechanical stability of protein-peptide complex.

Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes