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Combined Kinetic and Thermodynamic Analysis of -Helical Membrane Combined kinetic and thermodynamic analysis of ␣-helical membrane protein unfolding Paul Curnow† and Paula J. Booth† Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom Edited by Alan R. Fersht, University of Cambridge, Cambridge, United Kingdom, and approved October 11, 2007 (received for review May 30, 2007) The analytical toolkit developed for investigations into water- the equilibrium constant. The reaction can be approximated to soluble protein folding has yet to be applied in earnest to mem- a two-state process; both kinetic- and equilibrium-derived free- brane proteins. A major problem is the difficulty in collecting energy values are linear with SDS concentration and with kinetic data, which are crucial to understanding any reaction. Here, comparable gradients (m values), and extrapolate to remarkably we combine kinetic and thermodynamic studies of the reversible similar free-energy changes at zero denaturant. Analysis of the unfolding of an ␣-helical membrane protein to provide a definitive kinetic m-values gives information on the transition state. Thus, value for the reaction free energy and a means to probe the we obtain a robust value for the free-energy change and infor- transition state. Our analyses show that the major unfolding step mation on the transition state for the formation of the final fold in the SDS-induced denaturation of bacteriorhodopsin involves a of an ␣-helical membrane protein. This advances understanding reduction in ␣-helical structure and proceeds with a large free- of this final folding step that is notoriously difficult to achieve in energy change; both our equilibrium and kinetic measurements vitro. predict that the free energy of unfolding in the absence of denaturant is ؉20 kcal⅐mol؊1, with an associated m-value of 25 Results -kcal⅐mol؊1. The rate of unfolding in the absence of denaturant, Equilibrium Measurements. Equilibrium measurements of unfold H O ؊15 ؊1 ku 2 , is surprisingly very slow (Ϸ10 s ). The kinetics also give ing were performed as in refs. 8 and 9 by titrating bR in information on the transition state for this major unfolding step, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/3-[(3- with a value for ␤ (mf/[mf ؉ mu]) of Ϸ0.1, indicating that the cholamidopropyl)dimethylammonio]-1-propanesulfonate transition state is close to the unfolded state. We thus present a (CHAPS) micelles with increasing concentrations of SDS (ex- basis for mapping the structural and energetic properties of mem- pressed throughout as bulk mole fraction SDS, ␹SDS) and brane protein folding by mutagenesis and classical kinetics. monitoring the loss of the native purple chromophore (bR560). The overall free energy of unfolding was then determined by bacteriorhodopsin ͉ folding ͉ free energy ͉ transition state fitting the entire dataset to a two-state equation (Fig. 1a) as well as by linearly extrapolating individual free-energy values around the transition region (Fig. 1b). These two analyses were consis- he folding and assembly of integral membrane proteins is a tent (Table 1), with the latter, linear method giving a free energy fundamental process within biological systems, yet surpris- T ⌬ H2O ϩ Ϯ of unfolding in the absence of denaturant, Gu of 20.57 ingly few quantitative studies of membrane protein folding have Ϫ Ϫ 0.20 kcal⅐mol 1 with mH2O of Ϫ28.30 Ϯ 0.27 kcal⅐mol 1. The been performed. Many transmembrane ␣-helical proteins are u transition midpoint (K ϭ 1) was found to be at 0.725 ␹ , unstable once they are displaced from the biological membrane, U SDS higher than the value of Ϸ0.60 ␹ found in work using and our limited understanding of the factors affecting folding SDS SDS/DMPC/CHAPSO micelles (8). The DMPC/CHAPS system and stability presents a major barrier to studies of structure and used here may impart greater stability to the protein. function. CD spectroscopy was used to determine changes in secondary Bacteriorhodopsin (bR), a light-driven proton pump from the structure on unfolding (Fig. 1a Inset). At low SDS, the percent- purple membrane (PM) of Halobacterium salinarum, is the ␣ ␤ ␤ ␣ age of secondary structure present as -helix, -sheet, -turn, current paradigm for studies of -helical membrane protein and random coil, respectively, was 78%, 7%, 9%, and 6%. These folding (1, 2). The native purple chromophore is formed by the values are characteristic of native bR. A sharp transition was covalent attachment of the cofactor retinal at K216 and offers a observed at Ͼ0.73 ␹SDS and the secondary structure composition direct, quantitative measure of the folded state of the protein changed to 53%, 21%, 9%, and 17% of the motifs above. These because it is strongly influenced by retinal isomerization and values correlate with those found during formation of the noncovalent binding pocket interactions (i.e., refs. 3 and 4). partially unfolded apoprotein bO at high SDS concentrations (5, The unfolding and refolding of bR in lipid/detergent mixtures 10). The sloping baseline seen in the absorbance signal (0–0.6 was first reported in the seminal work of London and Khorana ␹SDS) was not associated with a change in the CD spectra. The (5). bR was found to unfold in SDS from the native purple state reduction in helicity on SDS unfolding, monitored at 226 nm, by way of an intermediate to give denatured apoprotein, bacte- agrees well with the loss of bR560 (Fig. 1a). (Note that the rioopsin (bO), and bR was efficiently reconstituted from bO by unfolding time used means that the SDS-unfolded state in the replacing SDS with renaturing micelles. The kinetics of refolding CD measurements corresponds to bO440 below.) have been investigated in considerable detail (1, 6, 7). A recent equilibrium study of this denaturation of bR (8) has also Kinetic Measurements. Spectral changes during bR unfolding over demonstrated that the free-energy change of unfolding could be short time scales (milliseconds to seconds) were analyzed by measured. A full kinetic and thermodynamic study of unfolding and folding is, however, vital for a complete understanding of the reaction mechanism, but it has yet to be achieved. Here, we Author contributions: P.C. and P.J.B. designed research; P.C. performed research and present such a study and probe the reversible unfolding of bR in analyzed data; and P.C. and P.J.B. wrote the paper. greater detail and over wider time scales than before. We The authors declare no conflict of interest. identify a series of intermediate states as well as the point when This article is a PNAS Direct Submission. helical structure is lost. We further highlight the intermediate †To whom correspondence may be addressed. E-mail: [email protected] or paula. states involved in the major unfolding step of bR and determine [email protected] the free-energy change for this step from both kinetic rates and © 2007 by The National Academy of Sciences of the USA 18970–18975 ͉ PNAS ͉ November 27, 2007 ͉ vol. 104 ͉ no. 48 www.pnas.org͞cgi͞doi͞10.1073͞pnas.0705067104 Downloaded by guest on September 29, 2021 BIOPHYSICS Fig. 2. Fast unfolding kinetics. (a) Changes in bR spectra over time on Fig. 1. SDS-induced equilibrium unfolding of bR monitored by absorbance addition of 0.882 ␹ . After an immediate red shift to 600 nm (solid black line; and CD spectroscopy. (a) The reduction in the native chromophore band at 560 SDS recorded at 16 ms), the signal decays to a 490-nm band (dashed line; recorded nm (open circles) and helical secondary structure, as reflected by the intensity at 208 ms). This subsequently decays to a band at 440 nm (dotted line; recorded at 226 nm (filled triangles). A data were fit to a two-state equation (solid 560 at 11.58 s). The gray lines show intermediate traces, demonstrating the single line). Error bars where shown represent deviation from the mean average of isosbestic point between each species. Arrows indicate loss or gain of band duplicate experiments. (Inset) CD spectra of bR (solid line) and unfolded bO (at during reaction. (b) Changes at individual band maxima over time: 600 nm 0.82 ␹ , dashed line). (b) Linear dependence of the free-energy change (⌬G ) SDS u (open circles), 490 nm (filled inverted triangles), and 440 nm (open triangles). with respect to SDS. using stopped-flow mixing and diode array detection. On mixing decays sequentially through the 600-nm and 490-nm states to with ␹SDS Ͼ0.72, the native bR band at 560 nm broadens and give bO440. This conclusion is reinforced by a global data analysis shifts to 600 nm within the 16-ms experimental dead time (Fig. of the spectra in Fig. 2a in which the data were best fit to a 3 3 2a). This 600-nm band (bR600) then decays coincident with the sequential reaction model with three species (A B C) (data appearance of a band at 490 nm (bR490) with a single isosbestic not shown). These three species corresponded to bR600,bR490, point at 530 nm. Subsequently, bR490 decays to a band at 440 nm and bO440 respectively. with a single isosbestic point at 480 nm. This 440-nm band arises Single-wavelength measurements, with increased data density, from denatured protein that has lost secondary structure as well were used for more accurate determination of unfolding rates. as retinal binding pocket structure and interactions with retinal Decay of bR560 was found to fit well to the sum of two ϭ Ϫ1 ϭ Ϫ1 (see below) and is termed bO440. No wavelength shifts or exponential functions (Fig. 3a): ku1 14.9 s and ku 0.54 s photodegradation of the native bR band were observed in at 0.882 ␹SDS, in good agreement with the rates of formation of Ϫ1 Ϫ1 control samples recorded at ␹SDS Ͻ0.70 (data not shown).
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