Proc. Natl. Acad. Sci. USAVol. 90, pp. 2920-2924, April 1993Biochemistry

Experimental resolution of the free energies of aqueous solvationcontributions to ligand-protein binding: Quinone-QA siteinteractions in the photosynthetic reaction center protein

(hydrophobicity/solvent transfer/partition coefficient/cofactor)

KURT WARNCKE* AND P. LESLIE DUTTONJohnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104

Communicated by William P. Jencks, November 19, 1992 (received for review March 4, 1992)

ABSTRACT Equilibrium binding free energies of 14benzo-, naphtho-, and anthraquinone cofactors have beendetermined at the QA redox catalytic site of the purifiedphotosynthetic reaction center protein from Rhodobactersphaeroides solubilized in water (AGB,w), in hexane solutioncontaining 30 mM water (AGTB,hh), and after partial dehydra-tion (AGTB,dh) with magnesium sulfate. Our aim is to resolve thecontributions of aqueous bulk phase solvation and proteinhydration contributions to binding in order to characterize indetail the direct interactions between the ligands and protein atthe QA site. This is accomplished by comparing the differencesbetween AGB,W and AGB,hh (or AGB,dh) with the water to hexanesolvent transfer free energies of the quinones (AGt,Q). Valuesof AGtF,Q are determined separately in binary solution andrange from 0.65 to -5.69 kcal/mol (1 cal = 4.184 J). Theresults are interpreted in terms of a thermodynamic cycle thatlinks the species involved in the binding and solvent transferequilibria. Values of AGB,hh - AGB,W are linearly correlatedwith -AG'F,Q (slope, 0.78 ± 0.04; ordinate intercept, -0.13 ±0.12 kcal/mol). The deviation of the experimental slopes fromthe predicted value of unity is attributed in part to a systematicdecrease of quinone thermodynamic activity in the aqueousbinding medium relative to the aqueous phase in the binarypartitioning solvent system. The difference between the qui-none-QA site binding free energies measured in hydratedhexane and water is therefore related only to the difference inbulk phase quinone solvation, as given by 0.78 AG',Q. Thelinear relation obtained using AGTB,dh - AG9B,W has the sameslope, but the intercept is decreased to -1.48 ± 0.19 kcal/mol,indicating that quinone binding strengths in the hexane systemare uniformly enhanced after partial dehydration. This sug-gests that the quinones encounter a common opposition tointeraction with the site in the hydrated, relative to the partiallydehydrated, state. The further utility of the method to directlyassess ligand-site binding free energies is demonstrated withexamples that address the contributions of molecular size anddipolar or hydrogen bond interactions to the binding of qui-nones at the QA site.

Solvent water can exert a powerful influence on the mech-anisms of molecular recognition that are central to protein-ligand binding and catalytic processes conducted in aqueoussolution (1-4). A small organic molecule, whether a cofactor,substrate, or inhibitor, gains a strong favorable contributionfrom the hydrophobic effect (5-7) and encounters unfavor-able contributions from loss of dipolar and hydrogen bond (2,4) contacts with the solvent upon transfer from the bulkaqueous phase into the protein interior binding site. Uponentry to the site, the molecule fits into the contours andestablishes new interactions, the description of which is

essential to understanding molecular recognition and catal-ysis. Moreover, the ligand may again encounter water thatmay require relocation before the binding is complete (8-12).The important contribution of protein hydration water to thethermodynamics and specificity ofligand-protein binding hasbeen discussed (e.g., see refs. 3 and 4) and investigated bycomputational methods (13). Quantitative descriptions of therole of water based on experimental approaches, however,remain a challenge.

In this report, we address the free energies of aqueoussolvation contributions to ligand-protein affinities by com-paring binding free energies determined in water with thosedetermined in hexane solution. The reaction center (RC)protein from Rhodobacter sphaeroides (14, 15) is well-suitedfor this type of analysis, because it can be solubiized inwater, hexane, and partially dehydrated hexane solutions(16-18). We focus on the equilibrium binding interactionbetween the QA redox catalytic site of the RC protein and aseries of 14 replacement quinone cofactors and 8 selectedstructural analogues. Binding constants are measured by asensitive photochemical assay that addresses functional qui-none occupancy on a nanosecond time scale. Thus, themethod obviates interference from diffusional encounter andallows measurements at very low protein concentrations (19,20). In addition to these features, the x-ray crystallographicstructures of the RC proteins from Rb. sphaeroides (21, 22)and Rhodopseudomonas viridis (23) allows correlation of thebinding free energy results with protein structural features.

SOLVATION ANALYSISThe binding free energy of the protein site for the same ligandhas been measured separately in water (AGB,W) and in awater-saturated (hydrated) hexane solvent (AGB,hh). Thethermodynamic cycle presented in Fig. 1 can be used toderive an expression that allows the difference betweenAGB,hh and AGB,W for quinone binding at the RC protein QAsite to be quantitatively specified in terms of the water-to-hexane solvent transfer free energies (AGtr,i) of the ithequilibrating species:

AGB,hh-AGB,W

= -AGt,Q + [m + n]AGtr H20 + AGtr - . [1]

Contributions of direct ligand interactions within the proteinbinding site, as well as losses of ligand translational androtational free solution entropy associated with binding (1,24), are effectively canceled in the subtraction of the AGB

Abbreviations: RC, reaction center; NQ, 1,4-naphthoquinone; AQ,9,10-anthraquinone; LDAO, lauryldimethylamine-N-oxide.*Present address: Department of Chemistry, Michigan State Uni-versity, East Lansing, MI 48824.

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The publication costs of this article were defrayed in part by page chargepayment. This article must therefore be hereby marked "advertisement"in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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1I (m+n)AGotrH20

(H20)m'Q + (H20)neP " QeP + (m+n)H20

AG0B,w

FIG. 1. Thermodynamic cycle that links ligand-protein bindingequilibria in water and hydrated hexane systems through the waterto hexane solvent transfer equilibria for the participants. Q and P,quinone ligand and RC protein, respectively. AG',hh, binding freeenergy measured in hydrated hexane solution; AGBW, binding freeenergy measured in water; AG'j, water-to-hexane solvent transferfree energies of quinone (i = Q), quinone-free RC protein (i = P),quinone-bound RC protein (i = Q P), and water (i = H20).

terms on the left hand side of Eq. 1. Thus, the right hand sideof Eq. 1 gives the contribution of the solvation differencesbetween water and hexane to [AGB,hh - AGB,W], with theassumption that direct quinone-protein interactions in thesite are independent of the supporting solvent. The termAG'r,Q represents the aqueous contribution due to bulk de-solvation of the quinone. This includes the hydrophobiceffect (5-7) as well as losses of hydrogen bond and dipolarcontacts with the aqueous solvent (2, 4) that are absent in thehexane phase. The term [m + n]AGtr,H2O represents thecontribution of n water molecules ejected from the site intothe bulk phase and m water molecules released from themolecule upon entry into the site. When the hydrocarbonphase is water saturated, as is the case in the hydrated hexanesystem examined here, AGtr,H2O is equal to zero. The term[AGtr,Q-p - AGtr,p] represents the contribution of ligandbinding-induced alterations in the interior or surface solva-tion properties of the protein-for instance, through anallosteric change.

Eq. 1 predicts that a plot of [AGB,hh - AG,BW] versus-AGr,Q determined for different quinone ligands will yield a

linear relation with unit slope and an ordinate intercept ofvalue AGtr,Q_p - AGtr,p. The influence of the protein hydra-tion state on the binding equilibrium is addressed by studyingthe effect of partial dehydration of the protein-containingorganic phase on the binding free energy by replacing AGB,hhin Eq. 1 with AG0B,dh, the binding free energy measured afterpartial drying.

MATERIALS AND METHODS

Preparations. RC protein was purified from Rb. sphae-roides strain R26 (25). The native ubiquinone 10 cofactor wasremoved from the QA and QB sites as described (26), withmodifications (27).The procedure followed for preparation of RC protein in

hexane was essentially as described by Schonfeld et al. (18),with the following exceptions: (i) the buffer was 10 mMTris-HCl (pH 8.0), (ii) soybean phospholipid (AssociatedConcentrates, Woodside, NY) was used, and (iii) after ex-traction, the system was allowed to stand for 30 min toachieve separation of the hexane phase. The optical spec-troscopic properties and kinetics of QA site-mediated elec-tron transfer reactions are comparable with those of RCprotein solubilized in aqueous detergent solution, as demon-strated (18). The concentration of water in the hydratedhexane system was 300 mM, as assayed by infrared spec-troscopy (28). After dilution with dry hexane in the bindingassay, the water concentration was lowered to 30 mM, a level

that is still 5.6-fold greater than the reported concentration inwater-saturated hexane (29).

Partial dehydration of the hexane solution of RC proteinwas performed by incubation for 6-8 hr with 25 mg ofmagnesium sulfate per ml after 1:10 dilution of the originalpreparation volume with dry hexane. The dried hexanesolution was separated from drying agent by a 1-min centrif-ugation at 3000 x g. The yield of total RC protein from thatpresent prior to magnesium sulfate treatment was 50-60%o.Measurement of the water content in the dried hexane

system is precluded at present due to the prohibitively largeamounts of RC protein required. A rough upper limit of 10,uM in the partially dehydrated hexane system as preparedwas estimated from the failure to detect water in a 10-foldconcentrated preparation using the infrared spectroscopicassay.RC protein in the partially dehydrated hexane system

exhibits significant differences from RC protein in the aque-ous (20) and hydrated hexane (18) systems. These are (i) thewavelength of the 860-nm absorption band of the primarydonor, the bacteriochlorophyll dimer (BChl2), undergoes an-16-nm hypsochromic shift, (ii) the quantum yield for flash-induced formation of the oxidized BChl2 and reduced QA sitequinone state (BChl QA) is diminished to -0.50, (iii) rateconstants for direct charge recombination between QA andBChl+ are increased by 2- to 3-fold, and (iv) the time requiredto achieve binding equilibrium between the QA site andquinone compounds is slowed to several minutes. Propertiesi-iii have been previously noted in air- and vacuum-driedfilms of the native RC protein (30). The change in the yield ofBChlQA formation does not interfere with determination ofproper equilibrium dissociation constants, since only theamplitude, but not the midpoint, ofthe binding titration curveis altered. The kinetic and spectroscopic properties of thehydrated hexane system can be regenerated by addition of asmall amount of water to the dried preparation.Quinone and analog compounds used in these studies were

obtained from commercial sources and were recrystallizedbefore use, with the exception of the liquids, 1-methyl- and1,4-dimethylnaphthalene, which were used without furtherpurification. The compounds were added to the bindingsystems by using dimethyl sulfoxide (aqueous system, <5%of total assay volume) or hexane (hexane system) as carriersolvents. No carrier solvent effects on the measurementswere observed.

Binding Data Acquisition and Analysis. Dissociation con-stants of quinones for the QA site of the RC protein dilutedfrom the preparations to assay concentrations of 0.05-0.2,uM in the hexane and aqueous systems were determinedfrom functional QA site occupancy versus concentration ofadded quinone (T = 295 ± 2 K) (19, 20). The standard freeenergy of binding (molar standard state) was obtained fromthe measured Kd by AGB = RTlnKd. The Kd values of thenonfunctional compounds were determined by competitionwith an active quinone (19).Measurement of Partition Coefficients. Partition coeffi-

cients of the quinones [P = concentration (M) in hexane/concentration (M) in water] were determined at 295 ± 2 K bythe shake-flask method (31), and transfer free energies werecalculated by AGtr,Q = -RTlnP. For compounds with P >1000, values cannot be determined accurately by this method,and values previously determined by a quinone-calibrated,reversed-phase HPLC technique were used (32).

RESULTS AND DISCUSSIONComparison of Quinone-QA Site Binding Free Energies

Determined in Aqueous and Hexane Systems. Table 1 listsvalues for AGB,W, AGGB,hh, AGB,&, and AGOr,Q. Fig. 2 shows

I the values of AGB,W and AGB,hh plotted as a function of

HydAtied Haxan

AGOBh(H20)m'Q + (H20)n.P (* Q*P + (m+n)H20

AG0t,Q AGopGtPT AGot,Q-P Ti

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Table 1. Aqueous and hexane system quinone-QA site dissociation constants and binding free energies and quinone water to hexanepartition coefficients and solvent transfer free energies

Log Kd,w,* &GB,W Log Kd,hh,* AGB,hh, Log Kd,dh,* AG,dh, AGtor,Quinone M kcal/mol M kcal/mol M kcal/mol Log P* kcal/mol

BenzoquinoneUnsubstituted -2.53 ± 0.18 -3.44 -2.90 ± 0.33 -3.94 -4.18 ± 0.32 -5.68 -0.51 ± 0.16 0.69Methyl -2.85 ± 0.26 -3.88 -2.77 ± 0.04 -3.77 -3.67 ± 0.11 -5.00 0.28 ± 0.01 -0.382,5-Dimethyl -3.56 ± 0.10 -4.84 -3.23 ± 0.04 -4.39 -4.26 ± 0.06 -5.79 1.11 ± 0.03 -1.50Tetramethyl -6.41 ± 0.17 -8.72 -4.36 ± 0.13 -5.92 -5.34 ± 0.38 -7.26 2.59 ± 0.07 -3.52

NaphthoquinoneUnsubstituted -5.20 ± 0.06 -7.07 -4.30 ± 0.18 -5.84 -5.48 ± 0.42 -7.45 1.29 ± 0.10 -1.752-Methyl -6.34 ± 0.05 -8.62 -5.05 ± 0.43 -6.86 -5.82 ± 0.24 -7.91 1.76 ± 0.17 -2.395-Methyl -5.42 ± 0.01 -7.37 -3.77 ± 0.19 -5.12 -4.68 ± 0.33 -6.37 1.78 ± 0.11 -2.426-Methyl -6.39 ± 0.02 -8.69 -5.00 ± 0.22 -6.79 -5.90 ± 0.10 -8.02 1.77 ± 0.08 -2.402-Methoxy -6.34 ± 0.01 -8.62 -5.86 ± 0.05 -7.97 -6.82 ± 0.10 -9.28 0.81t -1.10

AnthraquinoneUnsubstituted -6.85 ± 0.16 -9.31 -4.92 ± 0.16 -6.69 -5.83 ± 0.18 -7.93 2.86t -3.881-Methyl -6.85 ± 0.24 -9.31 -4.00 ± 0.12 -5.44 -t - 3.66t -4.982-Methyl -7.02 ± 0.47 -9.55 -4.40 ± 0.13 -5.99 -i - 3.5Ot -4.751-Chloro -7.20 ± 0.24 -9.79 -4.73 ± 0.10 -6.43 -5.73 ± 0.10 -7.79 3.25t -4.432-Chloro -7.08 ± 0.10 -9.63 -3.96 ± 0.14 -5.38 -5.34 ± 0.10 -7.26 4.19t -5.69

*Values refer to molar standard state. SDs are derived from results of at least three binding titration measurements, performed using at leasttwo separate RC protein preparations or at least three partition coefficient measurements.tValues were obtained by a calibrated reversed-phase HPLC method (32). SD for values determined by this technique is <0.10 kcal/mol.tKd values could not be accurately determined because the lifetime of the BChl'QA state for these compounds in the dehydrated hexane systemis comparable with the width of the xenon flash.

-AGtr,Q. Common patterns of binding strength changes,introduced by the variation in quinone structure, are evidentin water and hexane. This close correlation strongly com-plements the finding that the two preparations share commonspectroscopic properties and electron transfer rates. Theseobservations therefore support the requirement of Eq. 1 thatthe quinone ligands bind in a comparable manner to a QA sitebinding domain that maintains the same structure in eachbinding system. Furthermore, the patterns of quinone struc-

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0 0

6N<3 6 <

BQ NQ

0 12

0AQ

HydratedHexane

ture-dependent changes in the partially dehydrated hexanesystem (Table 1), which are not included in Fig. 2 for clarity,are comparable. This provides evidence that the integrity ofthe QA site also remains intact after partial dehydration of theRC protein.

Fig. 2 also reveals a general trend of increased magnitudeof the free energy difference between AGB,hh and AGB,W withincreasing values of -AGtr,Q. This is shown more clearly inFig. 3, where the data are plotted following the form of Eq.

5 HydratedHexane-Water

5 ,/14

3-

0)

/0)

18 '--

-1 0 1 2 3 4 5 6

-1 0 1 2 3 4 5 6 7

-AG%Q (kcal/mole)

FIG. 2. Binding free energies of quinones at the QA site of the RCprotein solubilized in aqueous and hydrated hexane solutions. Forclarity, error bars are not shown; see Table 1 for details. Structuresof quinones examined and substituent positions are illustrated. Me,methyl; Mx, methoxy group substituents. BQ, 1,4-benzoquinone.

-AGO Q (kcal/mole)

FIG. 3. Difference between quinone binding free energy at the QAsite determined in hexane and in water as a function of the corre-sponding quinone solvent transfer free energy, -AG'r,Q. For soliddata points, ordinate axis represents the difference AGB,hh - AGI,W.For open data points, ordinate axis represents the difference AGB,dh- AGB,W. Solid lines represent the best linear least-squares fit to thedata.

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Proc. Natl. Acad. Sci. USA 90 (1993) 2923

1. As predicted by Eq. 1, the correlation is linear (R2 =

0.973). The ordinate intercept is -0.13 ± 0.12 kcal/mol (1 cal= 4.184 J). However, in contrast with the prediction of Eq.1, the slope of0.78 ± 0.04 is less than unity. Fig. 3 also showsthe result of replacing the values of AGB,hh in Eq. 1 with thecorresponding values of AGB,dh. A linear relation is againobtained (R2 = 0.933), with a slope (0.76 ± 0.07) that isidentical within experimental error to that obtained with thehydrated hexane data. However, the ordinate intercept isnow lowered to -1.48 ± 0.19 kcal/mol.

Possible Origins of the Less-Than-Unit Slope. The failure ofthe relations in Fig. 3 to achieve the unit slopes was unex-pected and the reasons for this are not completely under-stood. The discrepancy does not appear to be linked todifferences in the solvation of the quinones between thehexane phase in the binding experiments and the hexanephase in the partition coefficient measurements, for thefollowing reasons: (i) QA site affinities in the hydrated systemare independent of protein and water concentration (ranges,0.02-0.20 ,uM and 6-60 mM, respectively), and (ii) reductionof water and free phospholipid and detergent by pelleting andresuspension of RC protein in hydrated hexane (18) do notalter the affinities. The effect also does not appear to besimply related to quinone size or aqueous phase bindingstrength, as shown in Fig. 3 by the data for 2-methoxy1,4-naphthoquinone (NQ). This compound displays a muchstronger QA site affinity and a lower -AG6r,Q value relative tomethyl-substituted quinones ofcomparable bulk, yet the datapoint adheres to the linear relation.On the other hand, we have confirmed earlier observations

made in this laboratory (M. R. Gunner and P.L.D., unpub-lished data) that, in the presence of increasing concentrationsofadded detergent that are still well below the critical micelleconcentration, the aqueous phase QA site affinities of hydro-phobic quinones are diminished. This suggests that a contri-bution to the discrepancy may arise from a difference in thesolvation of the quinones between the aqueous phase in thebinding measurements, which includes 10-20 ,uM lauryldi-methylamine-N-oxide (LDAO) detergent, and the aqueousphase in the partition coefficient measurements. Indeed,addition of0.001% LDAO detergent to the binary partitioningsolvent system resulted in reduction of the solvent transferfree energies of hydrophobic quinones (present at soluteconcentrations corresponding to those used in the aqueousphase binding titrations) by factors of 0.85-0.90 relative tothe values of -AGtr,Q reported in Table 1. Therefore, weconsider that the less-than-unit slope may result, at least inpart, from an interaction of quinone with the subcriticalmicellar concentrations of LDAO detergent in the aqueousbinding medium that in effect lowers the activity of the addedquinone.

Interpretation of the Value of the Ordinate Intercept. Thezero ordinate intercept of the [AGB,hh - AGB,Wl versus-AG'r,Q relation indicates that the value of the term AGtr,Q-p- AGtr,p is equal to zero within experimental error. Ittherefore appears unlikely that there are thermodynamicallysignificant differences in the solvation of the free and qui-none-bound RC protein. This agrees with the lack of evidencefor long-range protein conformational changes associatedwith quinone binding at the QA site and the location of thebinding cavity =10 A within the surface of the protein(21-23).

After partial dehydration of the hexane system, the bindingaffinities of the quinones at the QA site are uniformly en-hanced, as indicated in Fig. 3 by the ordinate intercept of-1.5 kcal/mol. Substantial dehydration of the RC protein isindicated by the electron transfer and spectroscopic proper-ties (see Materials and Methods). In addition, the timerequired to achieve equilibrium occupancy of the QA site wason the order of minutes after drying, in contrast with the <5-s

equilibration times in the assays performed in the aqueousand hydrated hexane systems. Therefore, we attribute thechange in affinity to the removal of protein-bound water that,in the hydrated state of the protein, is involved in the bindingprocess. The results are consistent with findings that dehy-dration ofproteins restricts dynamic fluctuations (33, 34) thatmay, in our case, be required for binding. However, thisinfluence of dehydration would oppose the tighter equilib-rium binding that is observed, suggesting that the rate ofdissociation of quinone from the site is decreased by an evengreater proportion. The uniform decrease in AG°B,dh relativeto AGB,hh that is observed for all quinones suggests that,whatever the mechanism, it acts in common on all of thecompounds equally.On the basis of the thermodynamic information, we can

only speculate on the mechanistic basis of the dehydrationeffect. A reasonable explanation is that drying reduces theoccupancy of specific water molecules bound within or in theimmediate vicinity of the quinone-free QA site that arecompetitively displaced or undergo energetically unfavor-able, intraprotein rearrangements upon quinone binding tothe hydrated RC protein in the aqueous and hydrated hexanesystems. The QA site quinone binding domain that is visual-ized in the Rb. sphaeroides RC protein structure (21, 22)presents a substantial cavity (volume of 200-300 A3 versus-24 A3 for a water molecule) that is flanked with severalhydrogen bond donor and acceptor groups. It would thus besurprising to find no water occupancy in this domain. In fact,two protein-interior water molecules are observed 2-3 A fromone side of the native quinone-occupied QA site bindingcavity in the 2.2 A resolution structure of the Rp. viridis RCprotein (23). Further high-resolution x-ray crystallographicstructures of RC protein with an empty QA site could clarifythe possible involvement of these and other bound watermolecules in quinone binding.

Empirical Relation Between Quinone-QA Site Binding inHexane and Water. The results demonstrate that the differ-ence between quinone-QA site binding free energies in thehydrated hexane and aqueous systems is given, to an accu-racy of <0.3 kcal/mol, by the following empirical expression:

AGB,hh -AGB,W = a(-AGt,Q). [2]

The coefficient a gives the ratio of quinone activities in thehexane and aqueous phases for the binding relative to thepartitioning systems and has a value of 0.78 for the measure-ments reported here. Substitution ofAGB,dh for AGB,hh in Eq.2, and addition of a term of -1.5 kcal/mol to the right handside, yields the corresponding expression relating the differ-ence in quinone-QA site binding free energies between par-tially dehydrated hexane and water.

Eq. 2 also shows that affinities of quinones for the QA siteofthe RC protein in hydrated hexane solution can be obtainedeither by direct measurement of AGB,hh or by subtraction of0.78 AG,r,Q from a measured AGB,W value. This unprece-dented versatility allows us to obtain values of AGB,hh orAGB,W for a variety of compounds with widely divergentsolubility properties.

Application to the Resolution of Direct, in Situ InteractionsBetween the Quinone and Protein at the QA Site. Informationabout the structural and free energetic contributions to sub-strate or ligand binding within a protein site is commonlyderived from comparisons of the affinities among a series ofstructurally related compounds (1, 3). For example, in orderto directly assess the presence and strengths of dipolar orhydrogen bond interactions between the quinone carbonylgroups and protein at the QA site, the AGB,hh values of9,10-anthraquinone (AQ) and the near-isosteric analogue,9-anthrone, which lacks one carbonyl oxygen atom, can becompared. Choice of the three-ring compounds is made

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Table 2. Hydrated hexane system QA site dissociation constantsand binding free energies for quinone analog compounds

Log Kd,hh, AG%,hh,Compound M kcal/mol

9,10-AQ -4.92 ± 0.16 -6.699-Anthrone -4.80 ± 0.40 -6.531,4-NQ -4.30 ± 0.18 -5.841,4-Dimethylnaphthalene -1.63 ± 0.52 -2.221-Methylnaphthalene -2.35 ± 0.22 -3.201-Fluoronaphthalene - 1.62* -2.201-Nitronaphthalene -3.03 ± 0.26 -4.121-Cyanonaphthalene -3.19 ± 0.28 -4.341-Aminonaphthalene -3.27* -4.451-Hydroxynaphthalene -3.79 ± 0.34 -5.45

*Value is from a single binding measurement.

because in the two-ring system, the single carbonyl groupanalogue of NQ, 1-tetralone, deviates strongly from planar-ity. As shown in Table 2, the AGB,hh values for AQ and9-anthrone are the same within experimental error. Thus, theloss of a quinone oxygen atom does not significantly influ-ence the strength of interaction with the site.To determine the interaction strength of both carbonyl

groups with the QA site, the roughly isosteric two-ringcompounds, 1,4-NQ and 1,4-dimethylnaphthalene, can becompared. The three-ring compounds cannot be used be-cause 9,10-dimethylanthracene is not sufficiently soluble inwater or hexane to allow detection of binding to the QA site.Table 2 shows that replacement of both carbonyl oxygenatoms with methyl groups leads to a loss in binding strengthof 3.6 kcal/mol. Thus, it would appear, applying the simplestinterpretation, that -3.6 kcal/mol is provided by one of thecarbonyl oxygen atoms. However, it is worth noting that the1 kcal/mol binding increment encountered upon removingone methyl group from 1,4-dimethylnaphthalene leaves openthe possibility for a weak hydrogen bonding interaction oftheother carbonyl group of about -1 kcal/mol.The finding of a dominant carbonyl in the quinone-QA site

interaction is consistent with x-ray crystallographic studies(21-23), which indicate that only one carbonyl oxygen atomis sufficiently near a polypeptide heteroatom to form ahydrogen bond of significant strength.The six 1-substituted naphthalene compounds included in

Table 2 were used to assess the binding specificity of the QAsite. For these types of compounds, working in the hexanesystem is essential for measuring in situ interactions becausethe aqueous phase solubility is either too low (methyl-,fluoro-, nitro-, cyano-) or too high (amino-, hydroxy-) toallow detection of binding in water. Table 2 shows that theheteroatom-substituted naphthalenes all bind significantlymore strongly than 1-methylnaphthalene, suggesting thatthey are capable of dipolar or hydrogen bond interaction withthe protein in the site. Indeed, when compared to thecarbonyl substituent, the contributions to the binding freeenergy from the various heteroatoms reveal a rather modestrole for the carbonyls in establishing specificity of the QA sitebinding for the native ubiquinone.

The authors thank M. R. Gunner, J. Higgins, J. S. Leigh, andC. C. Moser for helpful discussions and the laboratories of D. C.Rees, G. Feher, and J. P. Allen for early communication of the Rb.

sphaeroides RC protein atomic coordinates. This work was sup-ported by grants from the U.S. Public Health Service (GM27309) andthe National Science Foundation (DMB 88-17240).

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