Distribution of molecular size within an unfolded state ensemble using small-angle X-ray scattering and pulse field gradient NMR techniques.
The size distribution of molecules within an unfolded state of the N-terminal SH3 domain of drk (drkN SH3) has been studied by small-angle X-ray scattering (SAXS) and pulsed-field-gradient NMR (PFG-NMR) methods. An empirical model to describe this distribution in the unfolded state ensemble has been proposed based on (i) the ensemble-averaged radius of gyration and hydrodynamic radius derived from the SAXS and PFG-NMR data, respectively, and (ii) a histogram of the size distribution of structures obtained from preliminary analyses of structural parameters recorded on the unfolded state. Results show that this unfolded state, U(exch), which exists in equilibrium with the folded state, F(exch), under non-denaturing conditions, is relatively compact, with the average size of conformers within the unfolded state ensemble only 30-40% larger than the folded state structure. In addition, the model predicts a significant overlap in the size range of structures comprising the U(exch) state with those in a denatured state obtained by addition of 2 M guanidinium chloride.
Choy
Wing-Yiu
WY
Protein Engineering Network Centers of Excellence and Department of Medical Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
Mulder
Frans A A
FA
Crowhurst
Karin A
KA
Muhandiram
D R
DR
Millett
Ian S
IS
Doniach
Sebastian
S
Forman-Kay
Julie D
JD
Kay
Lewis E
LE
D000818:Animals; D004330:Drosophila; D029721:Drosophila Proteins / Q000737:chemistry*; D016521:Electrophoresis, Gel, Pulsed-Field; D019791:Guanidine / Q000494:pharmacology; D019476:Insect Proteins / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D011489:Protein Denaturation / Q000187:drug effects; D017510:Protein Folding; D012542:Scattering, Radiation; D012984:Software; D014965:X-Rays; D018909:src Homology Domains / Q000187:drug effects
D029721:Drosophila Proteins; D019476:Insect Proteins; C080530:drk protein, Drosophila; D019791:Guanidine