Study On The Molecular Mechanism Of Coupled Folding And Binding In Self-Binding Peptides

Self-binding peptide(SBP)represents a new biomolecular phenomenon that spans between folding and binding.SBP is defined as a structurally and functionally independent,short peptide segment within a monomeric protein,which is connected to rest of the monomer via a flexible linker and fulfills biological function by dynamically associating to/disassociating from its target domain in the same monomer.It is widely known that the folding of proteins is an essential process by which a polypeptide acquires its biological function.Traditionally,the SBP phenomenon is naturally recognized as protein folding since it shares a common polypeptide chain with its target domain,where the intramolecular interaction between SBP and target is only regarded as the last step of the whole protein folding process.However,the SBP phenomenon is different significantly to classic protein folding as it can work as a molecular switch to dynamically shift between bound and unbound states –– this is a typical feature of biomolecular binding.Therefore,SBP possesses the dual characteristics of folding and binding.In order to ascertain the molecular mechanism of SBP coupling folding and binding,we herein systematically investigate four representative SBP systems,including mouse proto-oncogene Vav,human retinoic acid receptor RAR?,fruit fly scaffold module INAD and crypto 14-3-3 protein Cp14 b,by using atomistic molecular dynamics(MD)simulations,thermodynamics analyses and energetics calculations.First,we construct four unbound counterparts of SBP–target complexes by artificially breaking the linker region between SBP and target.Second,the isolated SBP peptide segments,artificial SBP–target complexes and native SBP-containing monomeric proteins are subjected to MD simulations,from which the dynamics behavior,energetics property and enthalpy/entropy effect are derived and examined in detail.The Vav protein is adopted as a representative case,with which we systematically investigate the effect of polypeptide linker on the SBP system based on its crystal structure(with linker connection)and artificial SBP–target complex(without linker connection).It is revealed that,on the one hand,SBP can be regarded as one step of classic protein folding,which packs against other parts of its parent monomer via intramolecular interaction;on theother hand,the thermodynamics property of SBP–target interaction would not be influenced substantially by breaking polypeptide linker,indicating that there is no essential difference between SBP and routine peptide–protein binding in energetics point of view.Therefore,we believe that the SBP is an intramolecular binding phenomenon driven by traditional protein folding,namely,binding-upon-folding,which can be regarded as a reversed process of the folding-upon-binding in routine peptide–protein interaction.In addition,although the linker has no substantial effect on the thermodynamics property of SBP–target interaction,it can restrict the occupation space of SBP nearby its target and enhance the encountering probability of SBP with its target,thus largely promoting the interaction efficiency between them.This is considerably different to the folding-upon-binding observed in routine peptide–protein interaction.Moreover,we also investigate the amino acid composition of SBP sequences and find that it is roughly similar with those of intrinsically disordered proteins(IDPs).Even though,there is a significant difference between the structural configuration and biological function of SBPs and IDPs,and thus the former cannot be simply attributed to a specific form of the latter.