Structural And Dynamical Exploration Of The Molecular Mechanism Of Self-Binding Peptides

It is well known that traditional peptide-mediated protein-protein recognition and interactions orchestrate various cellular processes in signaling and regulatory networks. Apart from it, peptide within monomeric protein can also mediate the biological function of its parent protein by adopting a so-called “self-binding” approach. Here, we call such peptide segments “self-binding peptides(SBPs)”, on the one hand, they can fulfill their biological functions by dynamically binding to/unbinding from their cognate targets; on the other hand, the segment is integrated into the target in primary sequence via a flexible polypeptide linker. Therefore, SBPs can be thought as a new and special kind of biomolecular phenomenon that spans between the folding and binding. SBPs exhibit a broad spectrum of biological functions in living world. They are found to serve commonly as functional mediator of their parent proteins within cell regulatory networks, and can bind to their cognate targets in a transient, reversible manner through fine-tuned molecular mechanism. In this study, we attempt to systematically investigate the thermodynamic property and dynamic behavior of SBPs in structural level, and then elucidate the molecular mechanism and biological implication underlying SBPs.We have deployed a fold of structure-based studies around SBPs. First, the SBP concept was for the first time introduced and defined to describe such biomolecular phenomenon. On this basis, in order to identify whether this phenomenon is naturally a folding or a binding, we systematically performed atomistic molecular dynamics(MD) simulations and post binding energy analysis for typical SBP-target system and their peptide-protein complex counterpart in comparison. Results show that SBP is almost a binding phenomenon, but the polypeptide linker has folding effect.Second, we have employed long-term, atomistic MD simulations to elucidate the molecular mechanism of SBP binding and recognition by its cognate target. Several SBP systems were investigated in detail to reconstruct the complete structural dynamics from their unbound state to the final bound state. The simulations revealed a two-step binding mechanism for SBPs: the electrostatic interactions and the desolvation effect are the predominant chemical forces in the first phase of SBP binding that results in a nonspecific, metastable encounter complex, and the second phase involves a slow process of conformational rearrangement and optimization by refining the complicated network of nonbonded interactions involved in the encounter complex, which finally recovers the specific, native bound state.Third, we have designed theoretical experiment on mutating linker sequence and modifying cognate target region to investigate these effects on SBP-target binding, and then compared these changes with experimental data. Results show that changing the linker’s structural feature can alter the energy landscape of SBP binding, and modifying target’s active site can affect the binding affinity of SBP-target.