title: Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides.
abstract: Understanding the rate at which various parts of a molecular chain come together to facilitate the folding of a biopolymer (e.g., a protein or RNA) into its functional form remains an elusive goal. Here we use experiments, simulations, and theory to study the kinetics of internal loop closure in disordered biopolymers such as single-stranded oligonucleotides and unfolded proteins. We present theoretical arguments and computer simulation data to show that the relationship between the timescale of internal loop formation and the positions of the monomers enclosing the loop can be recast in a form of a universal master dependence. We also perform experimental measurements of the loop closure times of single-stranded oligonucleotides and show that both these and previously reported internal loop closure kinetics of unfolded proteins are well described by this theoretically predicted dependence. Finally, we propose that experimental deviations from the master dependence can then be used as a sensitive probe of dynamical and structural order in unfolded proteins and other biopolymers.
authors.affiliation: Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, USA.
authors.forename: Ryan R
authors.initials: RR
authors.lastname: Cheng
authors.forename: Takanori
authors.initials: T
authors.lastname: Uzawa
authors.forename: Kevin W
authors.initials: KW
authors.lastname: Plaxco
authors.forename: Dmitrii E
authors.initials: DE
authors.lastname: Makarov
mesh_terms: D003198:Computer Simulation; D007700:Kinetics; D008958:Models, Molecular; D009841:Oligonucleotides / Q000737:chemistry*; D011108:Polymers / Q000737:chemistry; D017433:Protein Structure, Secondary; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013997:Time Factors
chemical_list: D009841:Oligonucleotides; D011108:Polymers; D011506:Proteins