Viscosity-dependent kinetics of protein conformational exchange: microviscosity effects and the need for a small viscogen.
Conformational rearrangements are critical to a variety of biological processes including protein folding and misfolding, ligand binding, enzyme catalysis, and signal transduction. Viscosity-dependent kinetics measurements can provide crucial insights into the dynamics of protein conformational exchange by highlighting the relative importance of frictional forces derived from either solvent or from internal protein interactions in activating the exchange reaction. Here, we analyze the kinetics of interconversion between the native and intermediate states of the four helix bundle FF domain recorded in solutions containing the viscogens glycerol or bovine serum albumin (BSA), using the viscosity measured from the translational diffusion of probes of different sizes. In the large viscogen BSA, we demonstrate that vastly different internal friction values are obtained using the different viscosity measures, leading to conflicting interpretations of the role of solvent friction in the interconversion. We show that this can be a consequence of the small effective hydrodynamic radius of the protein conformational transition and differences between solution micro- and macroscopic viscosities that are germane in this case. In general, correct values of internal friction can only be obtained by carrying out measurements using small viscogens.
Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto , Toronto, Ontario Canada , M5S 1A8.
Ashok
A
Sekhar
Michael P
MP
Latham
Pramodh
P
Vallurupalli
Lewis E
LE
Kay
D000818:Animals; D002352:Carrier Proteins / Q000737:chemistry*; D002417:Cattle; D005990:Glycerol / Q000494:pharmacology*; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary / Q000187:drug effects; D017434:Protein Structure, Tertiary / Q000187:drug effects; D012710:Serum Albumin, Bovine / Q000494:pharmacology*; D014783:Viscosity / Q000187:drug effects
D002352:Carrier Proteins; C491404:PRPF40A protein, human; D012710:Serum Albumin, Bovine; D005990:Glycerol