Abstract
Electrostatic interactions are important for understanding molecular interactions, since they are long-range interactions and can guide binding partners to their correct binding positions. To investigate the role of electrostatic forces in molecular recognition, we calculated electrostatic forces between binding partners separated at various distances. The investigation was done on a large set of 275 protein complexes using recently developed DelPhiForce tool and in parallel, evaluating the total electrostatic force via electrostatic association energy. To accomplish the goal, we developed a method to find an appropriate direction to move one chain of protein complex away from its bound position and then calculate the corresponding electrostatic force as a function of separation distance. It is demonstrated that at large distances between the partners, the electrostatic force (magnitude and direction) is consistent among the protocols used and the main factors contributing to it are the net charge of the partners and their interfaces. However, at short distances, where partners form specific pair-wise interactions or de-solvation penalty becomes significant, the outcome depends on the precise balance of these factors. Based on the electrostatic force profile (force as a function of distance), we group the cases into four distinctive categories, among which the most intriguing is the case termed “soft landing.” In this case, the electrostatic force at large distances is favorable assisting the partners to come together, while at short distance it opposes binding, and thus slows down the approach of the partners toward their physical binding.
Highlights
IntroductionElectrostatics plays an important role in molecular biology since it contributes to protein folding and stability (Strickler et al, 2006; McCammon, 2009; Tsai et al, 2016), protein-protein interactions (Zhang et al, 2011), ion binding (Petukh and Alexov, 2014; Petukh et al, 2015a), dimerization (Zhang et al, 2013; Campbell et al, 2014), protein-DNA/RNA interactions (Ghaemi et al, 2017), and protein-microtubule binding (Li et al, 2016a,b)
In case of a microtubule binding domain (MTBD) which binds to microtubule (MT), we demonstrated that the electrostatic force of interaction is attractive when the MTBD is not physically bound to MT, but becomes repulsive when there is a physical contact between MTBD and MT (Li et al, 2016b)
This work investigated the role of electrostatic force in molecular recognition, and we would like to emphasize that the focus is on recognition, rather on binding
Summary
Electrostatics plays an important role in molecular biology since it contributes to protein folding and stability (Strickler et al, 2006; McCammon, 2009; Tsai et al, 2016), protein-protein interactions (Zhang et al, 2011), ion binding (Petukh and Alexov, 2014; Petukh et al, 2015a), dimerization (Zhang et al, 2013; Campbell et al, 2014), protein-DNA/RNA interactions (Ghaemi et al, 2017), and protein-microtubule binding (Li et al, 2016a,b). As the partners approach each other, other energy terms become significant and the outcome of the binding depends on their balance
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