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Bacteriorhodopsin photocycle at cryogenic temperatures reveals distributed barriers of conformational substates Andrei K. Dioumaev and Janos K. Lanyi* Department of Physiology and Biophysics, University of California, Irvine, CA 92697 Communicated by Hans Frauenfelder, Los Alamos National Laboratory, Los Alamos, NM, April 26, 2007 (received for review January 24, 2007) The time course of thermal reactions after illumination of 100% humidified bacteriorhodopsin films was followed with FTIR spec- troscopy between 125 and 195 K. We monitored the conversion of the initial photoproduct, K, to the next, L intermediate, and a shunt reaction of the L state directly back to the initial BR state. Both reactions can be described by either multiexponential kinetics, which would lead to apparent end-state mixtures that contain increasing amounts of the product, i.e., L or BR, with increasing temperature, or distributed kinetics. Conventional kinetic schemes that could account for the partial conversion require reversible reactions, branching, or parallel cycles. These possibilities were tested by producing K or L and monitoring their interconversion at a single temperature and by shifting the temperature upward or downward after an initial incubation and after their redistribution. The results are inconsistent with any conventional scheme. Instead, we attribute the partial conversions to the other alternative, distributed kinetics, observed previously in myoglobin, which arise from an ensemble of frozen conformational substates at the cryogenic temperatures. In this case, the time course of the reac- tions reflects the progressive depletion of distinct microscopic substates in the order of their increasing activation barriers, with a distribution width for K to L reaction of 7 kJ/mol. low-temperature kinetics distributed kinetics photointermediates infrared FTIR V arious kinds of evidence show that macromolecules exist as populations of conformational substates (1–6). The most dra- matic of these evidences is that below 200 K the reactions that follow photodissociation of the CO–myoglobin complex cannot be described by conventional kinetics that would arise from a single barrier. Instead, the time course follows a nonexponential path that suggests an ensemble of barriers, and from its analysis it was concluded (6–9) that the protein, like glasses and spin glasses, assumes a large number of slightly differing conformational sub- states. At ambient temperature, these substates rapidly equilibrate to produce a thermally averaged homogeneous state, but at cryo- genic temperatures they are distinct and noninterconvertible. More direct methods, such as x-ray scattering (7) and Mo ¨ssbauer spec- troscopy (for review, see ref. 1) and spectroscopic and kinetic hole burning (10–12), have indeed detected such populations of slightly differing conformations. Conformational heterogeneity will result in nonconventional, distributed kinetics. A multibarrier ‘‘energy landscape’’ must be a property of all proteins (1–3), but its consequences for enzyme kinetics at cryogenic temperatures are difficult to explore with- out the technical advantages of the photodissociation and re- binding of the CO–myoglobin complex, and a few other such reactions (for reviews, see ref. 1) that can be initiated by illumination in the frozen state. The photocycle of bacteriorho- dopsin, a proton pump (for reviews, see refs. 13–15), is also a light-driven reaction. It is described by the sequence, BR–h3 K 7 L 7 M 1 7 M 2 7 M 2 7 N 7 N 7 O 3 BR, containing the various spectrally identified configurational transitions of the photoisomerized 13-cis,15-anti-retinal chromophore and the protein that recover the initial state, in 10 ms. Bacteriorho- dopsin would be another obvious candidate for such studies. There are several reports of the bacteriorhodopsin photocycle at cryogenic temperatures, which contain clues for the existence of conformational substates. Spectral and kinetic anomalies near 100 K had suggested the existence of multiple K photoproducts (16, 17), which come to a steady-state mixture only at temper- atures above 200 K (16), in a suggested analogy with myoglobin. Similar findings were reported for the low-temperature batho- product of 13-cis bacteriorhodopsin (17). In a different ap- proach, optical hole burning (18) indicated the existence of vibrational substates that give rise to inhomogeneous band broadening in this protein. We report here real-time FTIR monitoring of the K 3 L reaction at cryogenic temperatures. In this reaction, the initially twisted photoisomerized 13-cis,15-anti-retinal of the primary photoproduct relaxes and the protonated Schiff base regains its hydrogen bond to Asp-85 that was transiently lost in K (19–22). In the temperature range examined, there is also a shunt from the L state to the BR state that bypasses the normal photocycle (23), not observable at ambient temperature. Analysis of the observed kinetics according to conventional concepts, such as equilibration, branching, and parallel reactions, leads to unresolvable contradictions. Instead, the observations can be well accounted for with distributed kinetics, in which between 125 and 195 K an apparently increasing fraction of the protein undergoes reaction at increasing temperatures, reflect- ing the heterogeneous barriers of microscopic conformational substates. Results Blue-light (500 20 nm) illumination of bacteriorhodopsin films at temperatures below 155 K produces photostationary states that contain mostly the K intermediate because any L generated from K by a thermal reaction will be reconverted to the BR state by the blue light (24), and the temperature is too low for the L 3 M reaction (16, 25). Once the actinic light is off, the L state is built up from K through a thermal reaction. The difference FTIR spectra in Fig. 1 were measured during illumination (in red) and after 200 min (in blue) at the indicated temperatures. Fig. 1 illustrates that after blue-light illumination, virtually no K 3 L reaction is observable within 200 min at 125 K (Fig. 1a), but a partial transformation of K to L is evident at 155 K (Fig. 1b). The derived spectra of K and L shown in Fig. 2 agree with earlier published spectra for L (e.g., refs. 26 and 27) and K when measured at these temperatures (28). The characteristic changes (20, 26) are (i) in the CAO stretch region where the overlapping negative CAO stretch bands of the protonated Asp-96 and Asp-115 at 1,740 cm 1 are shifted in L to higher and lower Author contributions: A.K.D. and J.K.L. designed research; A.K.D. performed research; A.K.D. analyzed data; and A.K.D. and J.K.L. wrote the paper. The authors declare no conflict of interest. *To whom correspondence should be addressed. E-mail: [email protected]. © 2007 by The National Academy of Sciences of the USA www.pnas.orgcgidoi10.1073pnas.0703859104 PNAS June 5, 2007 vol. 104 no. 23 9621–9626 BIOPHYSICS

Bacteriorhodopsin photocycle at cryogenic temperatures reveals distributed barriers of conformational substates

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Bacteriorhodopsin photocycle at cryogenictemperatures reveals distributed barriersof conformational substatesAndrei K. Dioumaev and Janos K. Lanyi*

Department of Physiology and Biophysics, University of California, Irvine, CA 92697

Communicated by Hans Frauenfelder, Los Alamos National Laboratory, Los Alamos, NM, April 26, 2007 (received for review January 24, 2007)

The time course of thermal reactions after illumination of 100%humidified bacteriorhodopsin films was followed with FTIR spec-troscopy between 125 and 195 K. We monitored the conversion ofthe initial photoproduct, K, to the next, L intermediate, and a shuntreaction of the L state directly back to the initial BR state. Bothreactions can be described by either multiexponential kinetics,which would lead to apparent end-state mixtures that containincreasing amounts of the product, i.e., L or BR, with increasingtemperature, or distributed kinetics. Conventional kinetic schemesthat could account for the partial conversion require reversiblereactions, branching, or parallel cycles. These possibilities weretested by producing K or L and monitoring their interconversion ata single temperature and by shifting the temperature upward ordownward after an initial incubation and after their redistribution.The results are inconsistent with any conventional scheme. Instead,we attribute the partial conversions to the other alternative,distributed kinetics, observed previously in myoglobin, which arisefrom an ensemble of frozen conformational substates at thecryogenic temperatures. In this case, the time course of the reac-tions reflects the progressive depletion of distinct microscopicsubstates in the order of their increasing activation barriers, witha distribution width for K to L reaction of �7 kJ/mol.

low-temperature kinetics � distributed kinetics � photointermediates �infrared � FTIR

Various kinds of evidence show that macromolecules exist aspopulations of conformational substates (1–6). The most dra-

matic of these evidences is that below �200 K the reactions thatfollow photodissociation of the CO–myoglobin complex cannot bedescribed by conventional kinetics that would arise from a singlebarrier. Instead, the time course follows a nonexponential path thatsuggests an ensemble of barriers, and from its analysis it wasconcluded (6–9) that the protein, like glasses and spin glasses,assumes a large number of slightly differing conformational sub-states. At ambient temperature, these substates rapidly equilibrateto produce a thermally averaged homogeneous state, but at cryo-genic temperatures they are distinct and noninterconvertible. Moredirect methods, such as x-ray scattering (7) and Mossbauer spec-troscopy (for review, see ref. 1) and spectroscopic and kinetic holeburning (10–12), have indeed detected such populations of slightlydiffering conformations.

Conformational heterogeneity will result in nonconventional,distributed kinetics. A multibarrier ‘‘energy landscape’’ must bea property of all proteins (1–3), but its consequences for enzymekinetics at cryogenic temperatures are difficult to explore with-out the technical advantages of the photodissociation and re-binding of the CO–myoglobin complex, and a few other suchreactions (for reviews, see ref. 1) that can be initiated byillumination in the frozen state. The photocycle of bacteriorho-dopsin, a proton pump (for reviews, see refs. 13–15), is also alight-driven reaction. It is described by the sequence, BR–h�3K 7 L 7 M1 7 M2 7 M�2 7 N 7 N� 7 O 3 BR, containingthe various spectrally identified configurational transitions of thephotoisomerized 13-cis,15-anti-retinal chromophore and the

protein that recover the initial state, in �10 ms. Bacteriorho-dopsin would be another obvious candidate for such studies.

There are several reports of the bacteriorhodopsin photocycleat cryogenic temperatures, which contain clues for the existenceof conformational substates. Spectral and kinetic anomalies near100 K had suggested the existence of multiple K photoproducts(16, 17), which come to a steady-state mixture only at temper-atures above 200 K (16), in a suggested analogy with myoglobin.Similar findings were reported for the low-temperature batho-product of 13-cis bacteriorhodopsin (17). In a different ap-proach, optical hole burning (18) indicated the existence ofvibrational substates that give rise to inhomogeneous bandbroadening in this protein.

We report here real-time FTIR monitoring of the K3L reactionat cryogenic temperatures. In this reaction, the initially twistedphotoisomerized 13-cis,15-anti-retinal of the primary photoproductrelaxes and the protonated Schiff base regains its hydrogen bond toAsp-85 that was transiently lost in K (19–22). In the temperaturerange examined, there is also a shunt from the L state to the BRstate that bypasses the normal photocycle (23), not observable atambient temperature. Analysis of the observed kinetics accordingto conventional concepts, such as equilibration, branching, andparallel reactions, leads to unresolvable contradictions. Instead, theobservations can be well accounted for with distributed kinetics, inwhich between 125 and 195 K an apparently increasing fraction ofthe protein undergoes reaction at increasing temperatures, reflect-ing the heterogeneous barriers of microscopic conformationalsubstates.

ResultsBlue-light (500 � 20 nm) illumination of bacteriorhodopsin filmsat temperatures below 155 K produces photostationary statesthat contain mostly the K intermediate because any L generatedfrom K by a thermal reaction will be reconverted to the BR stateby the blue light (24), and the temperature is too low for theL3M reaction (16, 25). Once the actinic light is off, the L stateis built up from K through a thermal reaction. The differenceFTIR spectra in Fig. 1 were measured during illumination (inred) and after 200 min (in blue) at the indicated temperatures.Fig. 1 illustrates that after blue-light illumination, virtually noK3 L reaction is observable within 200 min at 125 K (Fig. 1a),but a partial transformation of K to L is evident at 155 K (Fig.1b). The derived spectra of K and L shown in Fig. 2 agree withearlier published spectra for L (e.g., refs. 26 and 27) and K whenmeasured at these temperatures (28). The characteristic changes(20, 26) are (i) in the CAO stretch region where the overlappingnegative CAO stretch bands of the protonated Asp-96 andAsp-115 at �1,740 cm�1 are shifted in L to higher and lower

Author contributions: A.K.D. and J.K.L. designed research; A.K.D. performed research;A.K.D. analyzed data; and A.K.D. and J.K.L. wrote the paper.

The authors declare no conflict of interest.

*To whom correspondence should be addressed. E-mail: [email protected].

© 2007 by The National Academy of Sciences of the USA

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frequencies, respectively; (ii) at the Schiff base CAN stretchband, which is at 1,609 cm�1 in K but shifts to a higher frequencyin L similar to that in the BR state; (iii) in the ethylenic stretchregion, where the 1,514 cm�1 band of K is up-shifted andbecomes partly hidden under the amide band at �1,555 cm�1 inL; (iv) in the fingerprint region where the �1,194 cm�1 COCstretch band decreases in amplitude in L; and (v) in the HOOP(hydrogen-out-of-plane) region (900–1,000 cm�1). Fig. 2a alsoshows that in the temperature range examined, two K statesexist. One, measured at 100 K (Fig. 2a, red) contains the wellknown FTIR features of ‘‘low-temperature’’ K (20, 27, 28), withlarge HOOP bands at 956 and 974 cm�1. At higher temperatures,in accord with previously published data (28–30), we findmixtures of this KLT state and another K with a characteristicHOOP band at 987 cm�1 in Fig. 1 a (red and blue) and b (red).However, at �135 K, the low-temperature K decays to the nextK much more rapidly than the K 3 L transition, and itscontribution need not be considered in the analysis of the latterkinetics.

The time course of the K 3 L reaction can be tracked mostreadily with the amplitudes of the positive 1,514 cm�1 ethylenicstretch band for K and the negative CAO stretch band at 1,740cm�1 for L. Fig. 3a shows the decay of K after the illuminationat various temperatures between 135 and 155 K. Although notshown, the rise of L follows the same time course as the decayof K. The K3 L conversion under such conditions occurs nearlyquantitatively. Although the apparent amplitude of the ethylenicstretch band at 1,528 cm�1, which reflects BR depletion in Fig.1b, changes somewhat, most of this change is caused by thedecrease in the overlapping (positive) ethylenic stretch band ofK at 1,514 cm�1. When decomposed (data not shown), theamplitude of the depletion at 1,528 cm�1 is constant within 5%,in accord with the previously proposed (31) lack of significantshunt of K to BR. Unexpectedly, the decay of K is not describedby a single exponential. The K and L states appear to approachlimiting mixtures that contain less K at increasing temperatures

(Fig. 3a). An alternative plot of the same data, with bothamplitude and time on logarithmic scales, is shown in Fig. 3b.The lack of breaks or inflections agues against multiexponentialkinetics as in the case of the myoglobin reaction in the sametemperature range (3, 6, 9). Further, global multiexponential fits

Fig. 3. Time course of IR features from K (ethylenic stretch band), shown on alogarithmic scale vs. linear time (a) and vs. logarithmic time (b) at various tem-peratures, after a photostationary state containing predominantly K was createdat the same temperature with blue light. (a) Fitted curves are to multicomponentexponentials. (b) For clarity, only every third data point is displayed. Fitted curvesare to the empirical equation, rate � (1� t/to)�n (6).

Fig. 1. FTIR difference spectra of bacteriorhodopsin films at different tem-peratures, during and after illumination. Spectra during illumination areshown in red, spectra after 200 min of subsequent thermal reaction are in blue.(a) Spectra at 125 K (blue-light illumination). (b) Spectra at 155 K (blue-lightillumination). (c) Spectra at 195 K (red-light illumination).

Fig. 2. FTIR difference spectra. (a) KLT was measured at 100 K; spectrum isshown in red. Calculated K is shown in blue. (b) Calculated L. The latter twospectra were calculated from data as in Fig. 1b measured at 135, 145, and 155K. At each temperature, a spectrum under illumination (e.g., Fig. 1b, red) wassubtracted from the spectrum at �200 min (e.g., Fig. 1b) to eliminate K-specific(26) spectral features. The resulting pure but unscaled spectrum for L wassubtracted from the spectrum under illumination to eliminate L-specific spec-tral features (26), producing a pure but unscaled K spectrum. The coefficientsof these two subtractions were used for scaling K and L at 135, 145, and 155K, which were then averaged.

9622 � www.pnas.org�cgi�doi�10.1073�pnas.0703859104 Dioumaev and Lanyi

with increasing numbers of exponentials did not yield additionalcomponents with different spectra. Thus, we must consider thepossibility of distributed kinetics.

Illumination with red light (�640 nm) traps a nearly pure Lstate in the photostationary mixtures because the primaryphotoproduct K is efficiently reconverted to BR by the red light(23, 32), whereas the L state accumulates slowly by the compet-ing K3 L thermal reaction, during the illumination. Up to 165K, the L state appears stable within 3 h (data not shown). Attemperatures between 165 and 195 K, the L state decays directlyto the BR state instead of M (see Fig. 1c), as reported earlier(23). Fig. 4a contains the time course of changes in the amount of the L state after red illumination at various temperatures. As

for the K3 L reaction (Fig. 3a), the time course deviates froma single exponential, and the extent of the decay seems to reachlimiting values that increase with increasing temperatures.Again, the alternative plots, with logarithmic scales for bothamplitude and time, are shown in Fig. 4b. As in Fig. 3b, theirshapes suggest distributed kinetics. A minor amount of M mightbe present at higher temperatures (e.g., at 195 K in Fig. 1c), butthe spectra in Fig. 1c before and after incubation are fullyscalable, indicating a decay of L back to BR rather than anL-to-M redistribution.

In conventional kinetics (Fig. 3a), it appears that the K 3 Lreaction proceeds to limiting mixtures that contain more productat higher temperatures, and the same is true for the L 3 BRreaction (Fig. 4a). In Fig. 5, the apparent final amounts of the Land BR states, extrapolated from the first 200 min after illumi-nation, are shown as functions of temperature. In both cases, theassumption of conventional kinetics with distinct kinetic com-ponents yields accumulations of the product of the thermalreaction that are strongly temperature-dependent, with mid-points of 143 and 195 K for the K 3 L and L 3 BR reactions,respectively.

The reversibility of the K3 L reaction was tested in two ways.First, the thermal reaction after blue-light illumination, as in Fig.3, was allowed to proceed to near apparent completion, and thetemperature was then either raised or lowered. Fig. 6 a and bshows, respectively, incubation at 135 K followed by a shift to 155K and in another experiment, illumination and incubation at 155K followed by a shift to 135 K. If K and L were in a thermallycontrolled equilibrium, the two experiments should yield mix-tures that depend solely on the final temperature. However, the

Fig. 4. Time course of the decay of IR features from L (CAO stretch band),illustrating the decay of L to BR (Fig. 1c) at various temperatures, after aphotostationary state containing virtually only L was created at the sametemperature with red light. The data and the fitted curves are as in Fig. 3 a andb. (b) For clarity, only every third data point is displayed.

Fig. 5. Limiting amounts of the L state formed from K (open circles) and therecovered BR state from L (closed circles) that accumulate after prolongedincubation at various temperatures, as in Figs. 3 and 4. At temperatures above165 K, the decay of the L state to BR (Fig. 4) would interfere with furthermonitoring of the K3 L reaction. Likewise, the recovery of the BR state fromL could not be determined at above 195 K because of interference by the L3Mreaction. Therefore, the sigmoidal curves were calculated only from datapoints below 165 and 195 K for the two curves, respectively, but for clarity thelines are drawn as if at higher temperatures the L3BR and L3M reactions didnot interfere.

Fig. 6. Tests of the reversibility of the K3 L reaction. Filled circles representthe time course when the K state was created by blue illumination and itsdecay was followed at either 135 or 155 K (as in Fig. 3a). Open circles are datafrom separate experiments, with K created and its dynamics monitored for thefirst 180 min at 135 K, followed by shift of the temperature to 155 K (a) orcreated and monitored for the first 140 min at155 K, and then the temperaturewas shifted to 135 K (b). In both cases, the time course of the temperature-induced changes was monitored after the temperature jump, but no datawere collected during the reequilibration of the temperature, for periods of130 min (a) and 40 min (b). (a) The dashed line is the estimate of the furtherprogress of the K3 L reaction at the higher temperature. (b) The dashed lineillustrates what would be expected (approximately) if the L3K back-reactionoccurred.

Dioumaev and Lanyi PNAS � June 5, 2007 � vol. 104 � no. 23 � 9623

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up-shift and down-shift of the temperature yield different re-sults. The amount of the K state decreases further when thetemperature is raised from 135 to 155 K, to the level reachedwhen both illumination and incubation are at 155 K. Importantly,however, the amount of K does not increase when the temper-ature is shifted from 155 to 135 K, even though the test is carriedout as long as the reaction requires at 135 K. Second, the timecourses of thermal reactions at 155–165 K are different afterblue-light and red-light illumination. If the mixture produced bythe illumination contains mainly K, the K3 L thermal reactionis observable (Figs. 1b and 3), but if the mixture contains mainlyL, the reverse L 3 K reaction is absent (Figs. 1c and 4). Thus,both sets of experiments demonstrate that L is produced from Kby an irreversible reaction.

The L3 BR thermal reaction is obviously irreversible, but achange in the yield of the BR state was determined in atemperature up-shift experiment as in Fig. 6a (data not shown).At 175 K, the limiting extent of conversion of L to the BR stateis �8%, but raising the temperature to 195 K produces furtherconversion, to a total of �43%, consistent with the limiting yieldsof BR at these temperatures in Fig. 4a.

For distributed kinetics, it is possible to calculate theactivation energy spectrum (6) from the fits in Fig. 3b. Thedata for the L3 BR reaction (Fig. 4b) was not suited for sucha plot because we are restricted to a narrow temperature rangewhere it can be examined without interference (see legend toFig. 5). By using the approach to this calculation in ref. 6, Fig.7a shows a plot of RT�ln(n/to) vs. temperature for the K 3 Lreaction, where n and to are parameters in the fits to thekinetics (see legend to Fig. 3b). It is linear, as expected (6). Theintercept on the ordinate gives the activation enthalpy at thepeak of the distribution curve, and it is 41 kJ/mol, in accordwith the Eyring activation enthalpy, 41 � 1 kJ/mol, at ambienttemperatures (33). Fig. 7b shows the energy spectrum, calcu-lated as in ref. 6. The curves from the fits at differenttemperatures are nearly superimposable (data not shown), andin Fig. 7b we give their average. The distribution spectrumindicates that the deviations from a single exponential in Fig.3a are accounted for by a spread of �7 kJ/mol (full-width at

half-maximum in Fig. 7b) around the mean activation energy,a value comparable with that for myoglobin (6).

DiscussionThe need to postulate conformational substates for myoglobinarose from the nonexponential time course of the geminaterebinding that follows photodissociation of its CO complex (1, 6,9). Unlike this reaction, the bacteriorhodopsin photocycle is acascade of numerous consecutive reactions, which severely limitsthe temperature range in which individual reactions can beexamined. With many intermediate states, it is particularlydifficult to distinguish between conventional but multiexponen-tial kinetics and distributed kinetics.

In conventional kinetics, the thermal reaction after blue-lightillumination (Fig. 3a) is a reequilibration of mixtures thatcontain initially mostly K to produce mixtures that contain muchincreased amounts of L. For example, at 155 K, the initialmixture (at the end of the illumination) contains �93% K and�7% L, and extrapolation to infinite time yields a mixturecontaining �23% K and �77% L. This treatment of the data atdifferent temperatures between 135 K and 155 K produces a setof extrapolated mixtures of K and L, in which the higher thetemperature, the more L is found in the final mixture (Figs. 3aand 5). The simplest explanation would be a reversible K 7 Lreaction with a temperature-dependent K/L equilibrium.

To distinguish between a complex kinetic scheme with mul-tiple, distinct, but closely lying time constants and a simple K3Lreaction with a continuous distribution of time constants, weused perturbation experiments. When the dynamics is probed inthis way, the scheme BR -hv 3 K 7 L and its simple variants,as suggested for ambient temperatures (34–37), lead to incon-sistencies. When the reaction is allowed to come to a steady stateat 135 K (Fig. 6a) and the temperature is increased to 155 K, theamount of L increases, and the composition of the sample shiftsto what would be reached when illuminated and allowed to reactthermally further at the higher temperature. On the other hand,when the initial equilibration is at 155 K, decreasing the tem-perature to 135 K does not result in a decrease in the amount ofL (Fig. 6b). Similarly, two different illumination regimes at asingle fixed temperature produce seemingly inconsistent results:illumination with blue light, which produces mostly K, leads toa thermal reaction producing L, but illumination with red light,which produces mostly L, is not followed by a thermal reactionleading back to K. Thus, the limiting mixtures K and L thatdevelop at these temperatures are not temperature-dependentequilibria because they can be shifted from K toward L but notfrom L toward K, and all models that include a back-reactionfrom L to K are excluded.

Kinetic schemes alternative to those with reversible reac-tions, as have been proposed and long argued over for theambient-temperature photocycle (for review, see 14), containeither parallel reaction sequences from several alternativeinitial BR states, or branching. The reason for heterogeneityor branching would be, for example, partial protonation statesof critical residues depending on the pH (38), nonequivalenceof the monomers in the bacteriorhodopsin trimer (39), or aneighbor/cooperativity effect of photocycling molecules onone another in the membrane (40, 41). However, the temper-ature up-shift experiment (Fig. 6a) rules out both parallel andbranching cycles, as a group. Without a reversible step, all suchmodels lead to end-state mixtures of K and L (of necessity,multiple K and/or L states), whose compositions are fullydetermined by (i) the initial heterogeneity of the sample in allmodels with parallel photocycles, and (ii) the ratio of rates atthe branching point in all branching models. Without an L3 Kback-reaction (and it is excluded), once the final compositionsare reached in these models, there is no possibility of furtherchange. Yet the amount of L in the final mixtures is not fixed

Fig. 7. Calculation of activation energy spectra for the K3 L reaction fromthe fits in Fig. 3b, as described in ref. 6 and the text. (a) Test of theapplicability of the method in ref. 6 and estimation of the activation energyat the peak of the distribution curve and the preexponential factor. Themean activation enthalpy is 41 kJ/mol, and the preexponential factor, A, is�10�11 s�1. (b) Calculated energy spectrum. The spectrum in bold is theaverage of the curves calculated at 135, 140, 145, and 155 K; the shadedarea corresponds to �1 SD. The full-width at half-maximum of the distri-bution function is �7 kJ/mol.

9624 � www.pnas.org�cgi�doi�10.1073�pnas.0703859104 Dioumaev and Lanyi

but can be increased by increasing the temperature (Fig. 6a).We conclude that the limiting K plus L mixtures are neitherthermal equilibria nor true end states, even though the con-version is partial and depends on temperature. The samearguments apply to the L 3 BR reaction.

Conventional kinetic analyses thus lead to irresolvable contra-dictions, but the results are consistent with kinetics determined bymicroscopic conformational substates (Figs. 3b and 4b). In this kindof a model, the time course of the thermal reactions reflects thesampling of numerous separate substates, frozen and not intercon-vertible at cryogenic temperatures (1). The observed time progres-sion of the conversion of distinct protein substates is in the order oftheir increasing barrier size. In this case, the apparent rate constantis time variable, and extrapolation to infinite time is in principle notpossible. The suggested empirical equation (6) for distributedkinetics fits the data well, as shown on double-logarithmic plots(Figs. 3b and 4b). With distributed kinetics, what appears to be afinal fraction of reaction product will be the population withimpediments to the reaction too high to overcome with a reasonableprobability on the time scale of the experiment. Depending on thedistribution of barrier magnitudes in the energy landscape of theprotein, the fraction of the readily reactive population may besteeply dependent on temperature, as found (Fig. 5). The temper-ature dependence of the yields of the product is then not from theenthalpy change in the overall reaction. Rather, it gives an indirectdescription of the distribution of the barriers. The result of theexplicit calculation of the barrier distribution according to ref. 6. isgiven in Fig. 7b.

This interpretation of the reaction at cryogenic tempera-tures precludes conventional kinetic and thermodynamic anal-yses, but some concepts remain valid. The barriers to theback-reaction from L, however numerous, must be higher thanfor the forward reaction, i.e., the K 3 L reaction will beirreversible under these conditions because the tests of thereversibility were on the same time scale as the rise of L anddid not produce K from L (Fig. 6b). The L 3 BR reaction isinherently irreversible because otherwise it would be possibleto enter the photocycle without illumination. Further, if basednot on kinetic but other spectral evidence, alternative sub-states for the intermediates cannot be excluded. Indeed, for K,we detect some of the differing HOOP bands reported earlier(28). Although not immediately evident, the possibility ofalternative L substates remains.

The results raise a number of questions. Might ambient-temperature kinetics reflect heterogeneous barriers from confor-mational substates also? There is evidence from neutron scatteringthat the average internal motion in bacteriorhodopsin begins toincrease sharply at a critical temperature between 150 and 200 K(42, 43), as in other proteins, although the retinal region is morerigid than the rest of the protein (44). The results suggest that rapidprotein motions, allowing thermal averaging of substates on thetime scale of the photocycle reactions, do become possible atambient temperature, and one would predict therefore conven-tional kinetics. Attempts have been made to account for experi-mental discrepancies from simple models with distributed kinetics(45, 46); however, although they gave better fits, the validity of thisapproach (vs. more complex conventional kinetic schemes) remainsan open question.

Apart from the presence of distinct substates, the low-temperature photocycle differs from the ambient-temperaturecycle in at least two respects. First, the K 3 L reaction thatleads to a transient mixture of K and L during the photocycleand had suggested K 7 L equilibration at ambient tempera-ture (34–37) is unidirectional at low temperatures. Second, theL 3 BR shunt reaction (23), which we confirm here, is notevident at ambient temperature. The difference between alow-temperature and a high-temperature L state noted earlierby FTIR spectroscopy (27, 47), perhaps from greater recovery

of the changed geometry around the retinal (21) to give a moreBR-like structure in L at low temperatures than at ambienttemperature, would account for both of these differences.However, the L intermediate produced at low temperature iscapable of entering the next photocycle step. Warming ofilluminated bacteriorhodopsin that contains the trapped Lstate, from �170 K to above 200 K, yields the M state (16, 23,48), as it would in the normal photocycle sequence. On theother hand, a shunt reaction had been suggested to uncoupletransport from the photochemical cycle when the pump gen-erates excessive proton gradient across the membrane andtherefore increased proton back-pressure (49, 50). Thus, analternative explanation for the L 3 BR shunt, at least, wouldbe that it occurs in the ambient-temperature photocycle also,under some conditions. This possibility remains open becausethe photocycle has been studied mostly in the absence ofcontrol by the proton potential it produces.

Materials and MethodsPurple membrane containing wild-type bacteriorhodopsin wasisolated according to a standard procedure (51). The membraneswere washed with 0.5–1 mM [bis(2-hydroxyethyl)amino]tris(hy-droxymethyl)methane buffer, pH 7.0, and deposited on a 13-mmCaF2 IR window (Harrick, Ossining, NY) followed by dryingunder mild vacuum and rehumidification for �3 weeks at 100%humidity. The films were covered by a second CaF2 window(separated from the first by a 0.8-mm Teflon spacer) and sealedwith vacuum grease. The films had optical densities of �0.5 at570 nm. After humidification, the samples developed a �0.64OD absorption in the water band at �3,300 cm�1. This proce-dure produced samples capable of a normal photocycle.

The sample holder was placed in an Optistat DM cryostat,equipped with an ITC 601 temperature controller (both by OxfordInstruments, Abingdon, U.K.) that provided temperature stabilitywithin 0.1 K. A heavy (�100 g) homemade cold block for holdingthe sample was mounted on the tip of the standard sample holder.Temperature was monitored with a K-type thermocouple and anHH 81 digital thermometer (both by Omega Engineering, Stam-ford, CT), attached directly to the cold block. An equilibration timeof �60 min was allowed for each temperature change.

The IR measurements were performed with a Bruker IFS-66/s FTIR spectrometer, equipped with a photovoltaic MCTdetector (model KMPV11-1-LJ2/239; Kolmar Technologies,Congers, GA), at 2 cm�1 resolution. Data were collected forthe 0–5,250 cm�1 range in the rapid-scan mode with averagingon a quasi-logarithmic time scale (33 points per decade).Preillumination spectra (6,196 scans) were always collected atthe same temperature, before the time-resolved measure-ments. The sample chamber was separated from the rest of thespectrometer with two germanium cut-off filters with antire-f lection coating, which provided transmission in the range of830–3,900 cm�1 (Janos Technology, Keene, NH), but blockedstray visible light, including that of the IR globar and thespectrometer He-Ne laser. The germanium filter closer to thedetector was tilted by 45° and used also as a mirror forillumination with the excitation visible light along the geo-metric axis of the measurement.

Excitation light was provided by a 175-W Cermax xenon lamp(ILC Technology, Sunnyvale, CA) through a 5-mm diameter liquidlight guide and either a 500 � 20-nm interference filter (blue light,�30 mW/cm2 for 480–520 nm) or a high-pass filter �640 nm (redlight, �60 mW/cm2 for 640–680 nm). The samples were routinelylight-adapted at 280 K with blue light for 10 min before cooling thesample to the desired temperature.

We thank H. Frauenfelder for valuable discussions. This work was sup-ported in part by National Institutes of Health Grant R01-GM29498 andDepartment of Energy Grant DEFG03-86ER13525 (to J.K.L.).

Dioumaev and Lanyi PNAS � June 5, 2007 � vol. 104 � no. 23 � 9625

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9626 � www.pnas.org�cgi�doi�10.1073�pnas.0703859104 Dioumaev and Lanyi