Measuring unfolding of proteins in the presence of denaturant using fluorescence correlation spectroscopy |
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Authors: | Chattopadhyay Krishnananda Saffarian Saveez Elson Elliot L Frieden Carl |
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Affiliation: | Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA. |
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Abstract: | IFABP is a small (15 kDa) protein consisting mostly of antiparallel beta-strands that surround a large cavity into which ligands bind. We have previously used FCS to show that the native protein, labeled with fluorescein, exhibits dynamic fluctuation with a relaxation time of 35 micros. Here we report the use of FCS to study the unfolding of the protein induced by guanidine hydrochloride. Although the application of this technique to measure diffusion coefficients and molecular dynamics is straightforward, the FCS results need to be corrected for both viscosity and refractive index changes as the guanidine hydrochloride concentration increases. We present here a detailed study of the effects of viscosity and refractive index of guanidine hydrochloride solutions to calibrate FCS data. After correction, the increase in the diffusion time of IFABP corresponds well with the unfolding transition monitored by far ultraviolet circular dichroism. We also show that the magnitude of the 35 micros phase, reflecting the conformational fluctuation in the native state, decreases sharply as the concentration of denaturant increases and the protein unfolds. Although FCS experiments indicate that the unfolded state at pH 2 is rather compact and native-like, the radius in the presence of guanidine hydrochloride falls well within the range expected for a random coil. |
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Keywords: | IFABP, rat intestinal fatty acid binding protein FCS, fluorescence correlation spectroscopy Gdn, guanidine hydrochloride fluorescein, 5-iodo acetamido fluorescein Alexa488, Alexa488 maleimide V60Flu, fluorescein covalently linked to Cys-60 of the V60C mutant of IFABP V60Alexa, Alexa488 covalently linked to Cys-60 of the V60C mutant of IFABP F62Flu, fluorescein covalently linked to Cys-62 of the F62C mutant of IFABP F62Alexa, Alexa488 covalently linked to Cys-62 of the F62C mutant of IFABP and tR, chemical relaxation time |
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