Conformation of ATP and ADP Molecules in AqueousSolutions Determined by High-Energy X-ray Diffraction

Takuya Miyazaki • Yasuo Kameda • Yasuhiro Umebayashi •

Hiroyuki Doi • Yuko Amo • Takeshi Usuki

Received: 27 November 2013 / Accepted: 28 December 2013� Springer Science+Business Media New York 2014

Abstract High-energy X-ray diffraction measurements were carried out at 26 �C for

aqueous 1.0, 2.0 and 2.05 mol% disodium adenosine 50-triphosphate (ATP) and 2.0 and

2.05 mol% disodium adenosine 50-diphosphate (ADP) solutions in order to obtain direct

experimental information on the intramolecular conformations of ATP and ADP molecules

in aqueous solutions. Observed interference terms were analyzed in terms of the

intramolecular geometry of the ATP and ADP molecules. Dihedral angles between adenine

and the ribose group (t1), ribose-ring and methylene group of ribose (t2), and the methylene

group of ribose and triphosphate (or diphosphate) group (t3), were determined through the

least-squares fitting procedure of the observed interference term.

Keywords ATP � ADP � Intramolecular structure � Conformation � X-ray

diffraction

1 Introduction

Adenosine 50-triphosphate (ATP) is one of the most important biomolecules in the energy

metabolism in the living cell. The energetics of ATP is promoted by the hydrolysis of the

terminal P–O bond in the triphosphate group to form the adenosine 50-diphosphate (ADP)

molecule. The conformation of the ATP molecule plays an important role in determining

the amount energy stored. In crystalline ATP disodium salt, the triphosphate group of ATP

is folded back towards the adenine base [1–3]. This bent conformation is stabilized by the

sodium ions that form a bridge between the phosphate chain and nitrogen (N7) atom in the

T. Miyazaki � Y. Kameda (&) � Y. Amo � T. UsukiDepartment of Material and Biological Chemistry, Faculty of Science, Yamagata University,Yamagata, Yamagata 990-8560, Japane-mail: SC025@kdw.kj.yamagata-u.ac.jp

Y. Umebayashi � H. DoiGraduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan

123

J Solution ChemDOI 10.1007/s10953-014-0153-8

adenosine residue. The conformation of the ATP molecule in the isolated state obtained

from ab initio calculations is characterized by intramolecular hydrogen bonds within the

triphosphate group [4, 5]. In aqueous solution, the triphosphate, ribose and adenine groups

of the ATP molecule should form intermolecular hydrogen bonds with neighboring water

molecules. According to a 1H NMR study, the phosphate groups of ATP and ADP mol-

ecules in aqueous solutions have an unfolded conformation [6].

In principle, information concerning the intramolecular structure (conformation) of ATP

can be determined by diffraction experiments; however, direct determination of the

intramolecular conformation of the ATP molecule has not yet been reported. It is in general

difficult to separate the intra- and intermolecular contributions in the interference term

observed from a single diffraction experiment because of considerable overlap of intra- and

intermolecular distances for relatively large molecule such as ATP. Even if the

intramolecular interference term of ATP could successfully be extracted, it may not be

possible to evaluate the large number of independent intramolecular parameters to be

determined from the least-squares fitting analysis. Since the local structural parameters for

adenine and the ribose ring within the ATP molecule are considered to remain almost

constant for any conformation of the molecule in aqueous solution, the intramolecular

interference term can be evaluated approximately by using the small number of dihedral

angles between local atomic groups within the ATP molecule. The intermolecular con-

tributions such as intermolecular hydrogen bonds between the ATP and neighboring water

molecules should be involved in the observed total interference term. If we assume fixed

values of the dihedral angles between the functional groups of the ATP molecule, then it is

possible to evaluate short-range intermolecular ATP–water, Na?–water, and water–water

interactions and the long-range random contribution through the least-squares fitting

procedure. The optimized set of values for dihedral angles within the ATP molecule can be

determined by searching the minimum of the residual sum-of-squares determined from the

least-squares fit for observed total interference term. In order to carry out the above

structural analysis, scattering data of wide Q-range with high statistical accuracy are

required.

In the present paper, we describe results of high-energy X-ray diffraction measurements

on aqueous disodium ATP and disodium ADP solutions. Observed X-ray interference

terms were analyzed by a least-squares fitting procedure to obtain the dihedral angles

between functional groups within the ATP and ADP molecules.

2 Experimental

2.1 Materials

Weighed amounts of adenosine 50-triphosphate disodium salt (ATP-Na2, 99.8 % in

chemical purity, Wako Pure Chemical Industries, Ltd.) and adenosine 50-diphosphate

disodium salt (ADP-Na2, 96.7 % in chemical purity, Wako Pure Chemical Industries, Ltd.)

were dissolved into distilled water to prepare aqueous 1.0, 2.0 and 2.05 mol% ATP-Na2

and 2.0 and 2.05 mol% ADP-Na2 solutions, respectively. The pH value measured for the

1.0, 2.0 and 2.05 mol% ATP solutions is 2.7. The value pH = 5.1 was obtained for the 2.0

and 2.05 mol% ADP solutions. The sample solution was sealed in a flat plate cell with

thickness of 2 mm, which had X-ray transmission windows made of Kapton� film with

thickness of 25 lm.

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2.2 High-Energy X-ray Diffraction Measurements

Synchrotron X-ray diffraction measurements in the transmission geometry were carried out

at 26 ± 2 �C on the horizontal two-axis diffractometer [7, 8] installed at the beamline

BL04B2 [9] of the SPring-8 synchrotron facility, Hyogo, Japan. An incident X-ray

wavelength k = 0.2009 A was employed. Scattered X-ray photons were collected by a

liquid N2 cooled Ge solid-state detector over an angular range of 0.3 B 2h B 42.08(0.16 B Q B 22.4 A-1, Q = 4p sinh/k) for aqueous 2.05 mol% ATP and ADP solutions,

which was carried out in 2011. Measurements for 1.0 and 2.0 mol% ATP and 2.0 mol%

ADP solutions were made in 2012 in the angular range of 0.3 B 2h B 48.08(0.16 B Q B 25.4 A-1). The total exposure time was ca. 6.1 h for aqueous 2.05 mol%

ATP and ADP solutions and ca. 4.3 h for 2.0 and 1.0 mol% ATP and 2.0 mol% ADP

solutions, respectively.

2.3 Data Reduction

Observed scattering intensities from the sample were normalized by monitor counts from

an incident ionization chamber. Normalized intensities were corrected for instrumental

background, polarization and absorption within the sample and cell [10]. Absorption

coefficients for constituent atoms were taken from those tabulated by Sasaki [11]. Ana-

lytical expressions of the atomic scattering factor and incoherent scattering intensities were

used from the paper by Hajdu [12] and from the International Tables for Crystallography

[13]. The data normalization procedure was carried out by using a least-squares fit by the

high-angle method modified by Habenschuss and Spedding [14].

The observed total interference term, i(Q), is given by

i Qð Þ ¼ Ieu Qð Þ�\f 2 [� �

=\f [ 2; ð1Þ

where

\f 2 [ ¼X

cif2i Qð Þ;

and

\f 2 [ ¼X

cifi Qð Þh i2

;

Ieu(Q) denotes the normalized coherent scattering intensity in electron units, ci corre-

sponds to the number of i-th atom in the stoichiometric unit, (Z)x(H2O)1-x (Z = ATP or

ADP), and fi(Q) is the atomic scattering factor of the i-th atom.

The observed total interference term can be divided into intra- and intermolecular

contributions,

i Qð Þ ¼ iintra Qð Þ þ iinter Qð Þ; ð2ÞThe intramolecular interference term is written as the sum of contributions from ATP

(or ADP) and water molecules.

iintra Qð Þ ¼ xiintraZ Qð Þ þ 1� xð Þiintra

H2O Qð Þ; Z ¼ ATP or ADPð Þ ð3Þ

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where

iintraZ Qð Þ ¼

XX

i 6¼j

fi Qð Þfj Qð Þexp �l2ijQ

2=2� �

sin Qrij

� �= Qrij

� �; Z ¼ ATP or ADPð Þ ð4Þ

iintraH2O Qð Þ ¼ 4fO Qð ÞfH Qð Þexp �l2

OHQ2=2� �

sin QrOHð Þ= QrOHð Þ ð5Þ

þ2f 2H Qð Þexp �l2

HHQ2=2� �

sin QrHHð Þ= QrHHð Þ:

The intermolecular interference term, iinter(Q), can be expressed as the sum of contri-

butions from short-range intermolecular interactions and long-range random distribution of

atoms as follows [15–17]:

iinter Qð Þ ¼2cinij

Xfi Qð Þfj Qð Þexp �l2

ijQ2=2

� �sin Qrij

� �= Qrij

� �

þ 4pqexp �l20Q2=2

� �Qr0cos Qr0ð Þ�sin Qr0ð Þ½ �Q�3:

ð6Þ

where q is the number density of the stoichiometric unit. The long-range parameter, r0,

denotes the distance beyond which a continuous distribution of atoms can be assumed. The

parameter, l0, describes the sharpness of the boundary at r0.

Since the amplitude of the intermolecular interference term is known to diminish much

faster than that for the intramolecular one with increasing Q-value, interference features

observed in the high-Q region are, in general, regarded as the intramolecular interference

term [18]. However, in the present analysis, it is difficult to divide the intra- and inter-

molecular interference contributions because of their considerable overlap. Then, the

dihedral angles that determine the conformation of ATP and ADP molecules were deter-

mined by the following procedure.

(a) The intramolecular interference term for the water molecule, iintraH2O Qð Þ; was evaluated

using parameters rOH = 0.98 A, rHH = 1.55 A, lOH = 0.06 A, and lHH = 0.12 A

[19, 20] and then subtracted from the observed total interference term for the sample

solution to obtain the observed interference term, iobs Qð Þ ¼ i Qð Þ � 1� xð ÞiintraH2O Qð Þ.

This procedure is effectively removes the low-frequency systematic error involved in

the observed interference term.

(b) The intramolecular interference term for an ATP (or ADP) molecule, iATPintra(Q) (or

iADPintra (Q)), was estimated for fixed dihedral angles, t1 (between the plane involving

C8(adenine)-N9(adenine)-C10(ribose) atoms and the plane involving atoms N9(ade-

nine)-C10(ribose)-O(ribose)), t2 (between the plane involving O(ribose)-C40(ribose)-

C50(ribose) atoms and the plane involving atoms C40(ribose)-C50(ribose)-O(phos-

phate)), and t3 (between the plane involving C40(ribose)-C50(ribose)-O(phosphate)

and the plane involving atoms C50(ribose)-O(phosphate)-Pa(phosphate)) as indicated

in Fig. 1. Intramolecular bond distances, rij, within the adenine, ribose and

triphosphate groups were fixed at values determined for the crystalline ATP salt [1].

The conformation of the phosphate group within ATP (or ADP) was assumed to

take a linear form in the present analysis which was suggested from previous NMR

[6] and DFT calculation [21] studies; dihedral angle between the plane involving

C50(ribose)-O(phosphate)-Pa(phosphate) and the plane involving Oa-Pa-Oab atoms is

1808 (where Oij denotes an oxygen atom binding with both Pi and Pj atoms), the

dihedral angle between the plane involving Oa-Pa-Oab atoms and the plane

involving Pa-Oab-Pb atoms is 08, dihedral angle between the plane involving atoms

Pa-Oab-Pb and the plane involving Oab-Pb-Obc is 1808, the dihedral angle between

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the plane involving atoms Oab-Pb-Obc and the plane involving Pb-Obc-Pc is 1808,and the dihedral angle between the plane involving atoms Pb-Obc-Pc and the plane

involving atoms Obc-Pc-Oc is 08. The root-mean-square amplitudes, lij, for the

intramolecular interactions within the ATP (or ADP) molecules were evaluated by

the following equation;

lij ¼ l� � rij=r�� �1=2

: ð7Þ

In the present analysis, the parameter l* was treated as an independent parameter while the

value of r* was fixed to 1.50 A.

(c) The intermolecular interference term was evaluated using assumptions described

below. The contribution from the nearest neighbor Na?���H2O interaction was

involved in the theoretical function with fixed values, rNaþ���H2O = 2.40 A,

lNaþ���H2O = 0.20 A and nNaþ���H2O = 5 [22]. The structural parameters concerning

the first and second neighbor hydrogen-bonded H2O���H2O interactions,

H2O���H2O(I) and H2O���H2O(II), were treated as independent parameters. Intermo-

lecular hydrogen-bonded N(adenine)���H2O, O(ribose)���H2O and O(phosphate)���H2O

interactions and the other short-range non-bonded intermolecular interactions are also

involved in the above H2O���H2O(I) and H2O���H2O(II) interactions.

Fig. 1 Molecular structure of ATP and dihedral angles, t1, t2 and t3

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(d) Parameters for the long-range random distribution of atoms, r0 and l0, in Eq. 6 were

allowed to vary independently.

(e) The least-squares fitting analysis was carried out for the observed interference term,

iobs(Q), in the range of 1.0 B Q B 22.0 A-1 for 2.05 mol% ATP and ADP solutions,

and 1.0 B Q B 25.0 A-1 for 2.0 and 1.0 mol% ATP and 2.0 mol% ADP solutions

using the SALS program [23]. The model function, imodel(Q), was evaluated by the

following equation,

imodel Qð Þ ¼ iintraZ Qð Þ þ iinter Qð Þ; Z ¼ ATP or ADPð Þ: ð8Þ

The R-factor defined below, was then determined for the best-fit result with fixed dihedral

angles of t1, t2 and t3:

Rt1;t2;t3 ¼X

iobs Qð Þ�imodel Qð Þ� �2

=X

iobs Qð Þ� �2�100 ð9Þ

(f) Rt1;t2;t3 was obtained for the fixed angles t1, t2 and t3 in the range of 0�–3608 with

angular interval of 308. Least-squares refinements were carried out for

12 9 12 9 12 = 1,728 times to obtain the values of Rt1;t2;t3 : The set of angles t1, t2and t3 which gives the minimum value of Rt1;t2;t3 corresponds to the possible

conformer of the ATP (or ADP) molecule.

The total distribution function, g(r), was evaluated by the Fourier transform of the

observed iobs(Q),

g rð Þ ¼ 1þ ð2p2qrÞ�1

ZQmax

0

Qobsi Qð Þsin Qrð Þ dQ; ð10Þ

The upper limit of the integral, Qmax = 20 A-1, was employed in the present study.

3 Results and Discussion

The observed interference terms for aqueous 1.0, 2.0, and 2.05 mol% ATP, and 2.0 and

2.05 mol% ADP solutions are shown in Fig. 2. The observed interference terms for all

sample solutions are characterized by double peaks at around Q = 2 A-1 followed by

interference features extending to the high-Q region. The calculated interference term for

each sample solution successfully reproduces the observed interference term. The observed

distribution functions, g(r), for the investigated sample solutions are shown in Fig. 3. A

dominant peak at r = 1.5 A appearing for all samples is assigned to the contribution

mainly from intramolecular P–O bonds within the ATP and ADP molecules. Contributions

from intramolecular C–C, C–O, and C–N bonds within the adenine and ribose groups of

ATP and ADP molecules are also involved in this peak. The peak located at r = 2.8 A in

the observed g(r) mainly involves contributions from intermolecular hydrogen-bonded

O(H2O)���O(H2O) interactions among solvent water molecules. This peak also includes

intermolecular hydrogen-bonded O(phosphate)���O(H2O), O(ribose)���O(H2O) and N(ade-

nine)���O(H2O) interactions.

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Fig. 2 Interference term,observed for aqueous ATP andADP solutions (dots), and thebest-fit results of least-squaresfitting analysis (solid line). Theresidual functions d(Q) areshown below

Fig. 3 Distribution function,g(r), observed for aqueous ATPand ADP solutions (black dots)and the Fourier transform of thebest-fit to the observedinterference term (green).Contributions fromintramolecular ATP and ADP(red), intermolecular Na?���H2O(orange), H2O���H2O(I) (pink),H2O���H2O(I) (blue), and long-range interaction (gray)

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Structural features observed in the experimental g(r) in each solution are well repro-

duced by the calculated distribution function derived from the least-squares fitting pro-

cedure. In order to obtain information on the conformation of the ATP and ADP molecules,

the least-squares fitting procedure was carried out with fixed dihedral angles t1, t2 and t3 to

obtain the residual sum of squares, Rt1;t2;t3 , which is represented in Fig. 4. This reveals that

values of Rt1;t2;t3 plotted against the dihedral angles t1, t2 and t3 are not randomly dis-

tributed, implying that the ATP and ADP molecules have a tendency to take on a certain

conformation in aqueous solution. The smallest Rt1;t2;t3 value was obtained at dihedral

Fig. 4 Distribution of the residual sum-of-squares (R-factor) for three dihedral angles t1, t2 and t3 (indegrees), obtained from the least-squares fit of the observed interference term, and the smallest value of theR-factor is indicated by a red circle. For the ADP molecule, the second smallest value is also shown by ablue circle

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angles of t1 = 240�–3008, t2 = 60�–908, and t3 = 120�–2408 for the ATP molecule. These

dihedral angles correspond to an unfolded conformation of the ATP molecule. All inde-

pendent parameters determined from the least-squares fit in the condition of fixed dihedral

angles t1, t2 and t3, which gives the smallest value of the R-factor, are summarized in

Table 1. The value of residual sum-of-squares (R-factor) for each solution ranges from

0.54 to 1.51 %, indicating that the least-squares fitting procedure was adequately per-

formed and assumptions applied in evaluating the theoretical interference term are valid.

The plot of Rt1;t2;t3 for the 2.05 and 2.0 mol% ATP solutions (Fig. 4a, b) indicates that

possible conformation are distributed around t1 = 240�–300� and 0�–908, which implies

that a broadened distribution of the t1 value occurs in these concentrated solutions. On the

other hand, the minimum Rt1;t2;t3 distribution seems more localized in the case of the

1.0 mol% ATP solution. The solute–solute (ATP���ATP and/or ATP���Na?) interactions

become more significant in concentrated solutions. This may cause the difference in the

minimum Rt1;t2;t3 distribution between the 2 and 1 mol% ATP solutions. The conformation

of the ATP molecules for dihedral angles t1 = 2408, t2 = 608, and t3 = 2408 show an

L-shape for the ATP molecule as seen in Fig. 5.

The distribution of the smallest Rt1;t2;t3 value for the ADP molecule in aqueous 2.05 and

2.0 mol% solutions was obtained at the dihedral angles of t1 = 120�–1508, t2 = 2708, and

t3 = 120�–2108 (see Table 1). The conformation of the ADP molecule for dihedral angles

Table 1 Results of the least-squares refinements for the observed interference term, iobs(Q)

Parameters 2.05 mol%ATP

2.0 mol%ATP

1.0 mol% ATP 2.05 mol%ADP

2.0 mol%ADP

Dihedral angle t1/8 240 300 240 120 150

t2/8 60 90 60 270 270

t3/8 240 120 210 120 210

R.M.S. parametera l*/A 0.059(1) 0.066(1) 0.063(1) 0.056(1) 0.065(1)

H2O���H2O(I)b rij/A 2.89(1) 2.87(1) 2.90(1) 2.88(1) 2.88(1)

lij/A 0.20(1) 0.20(1) 0.25(1) 0.19(1) 0.19(1)

nij 2.32(1) 2.22(1) 3.05(1) 2.66(5) 2.06(1)

H2O���H2O(II)c rij/A 3.88(1) 3.93(1) 4.14(1) 4.12(1) 3.80(1)

lij/A 0.74(1) 0.75(1) 0.76(1) 0.87(1) 0.75(1)

nij 14.8(1) 19.1(2) 18.2(1) 26.5(1) 14.4(1)

Long-range r0/A 4.55(1) 4.78(1) 5.06(1) 5.21(1) 4.60(1)

l0/A 0.96(1) 0.73(1) 0.67(1) 0.64(1) 0.94(1)

R-factor Rt1 ;t2 ;t3 0.54 1.51 1.43 0.61 1.00

Fitting Q-range Qmin/A-1 1.0 1.0 1 1 1

Qmax/A-1 22.0 25.0 25.0 22.0 25.0

Estimated standard deviations are given in parenthesesa Intramolecular root-mean-square amplitude parameter for the ATP/ADP moleculeb Involving the nearest neighbor hydrogen-bonded O(phosphate, ribose)���H2O, N(adenine)���H2Ointeractionsc Involving intermolecular interactions among all constituent species

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of t1 = 1208, t2 = 2708, and t3 = 1208 shows a bent (U-shape) of the ADP molecule (see

Fig. 5). Another conformer corresponding to t1 = 08, t2 = 908, t3 = 1508 is found to exist

at the second smallest value of the R-factor for the ADP molecule (indicated by blue circles

in Fig. 4d, e), which exhibits the unfolded form of the ADP molecule (Fig. 5). In aqueous

solutions these two conformers of ADP may coexist.

According to a previous 1H NMR study, the N1 atom of the adenine ring (see Fig. 1) is

protonated to form the cationic form, N1?-H, and interacts with the negatively charged

phosphate group in the pH range above 4.43 for ATP and above 4.19 for ADP [6]. In the

pH range below these values, protonation of the phosphate group is considered to occur

and the interaction between the adenine ring and phosphate group will be reduced due to

the neutralization of the negatively charged phosphate group [6]. In the present experi-

mental condition, the ionization state of the phosphate group of ATP is protonated

(pH = 2.7), suggesting weaker interaction between the adenine ring and phosphate group.

On the other hand, the protonation of the phosphate group does not occur for the ADP

molecule in the present experimental condition (pH = 5.1). This may cause stronger

interaction between the adenine and phosphate groups within the ADP molecule. The

difference in the stable conformations for ATP and ADP molecules obtained from the

present X-ray study is considered to reflect the difference in interaction between the

adenine and phosphate groups within these molecules. To obtain more detailed information

on the conformation of ATP and ADP molecules in aqueous solutions, further systematic

Fig. 5 Possible conformers of ATP and ADP molecules in aqueous solution derived from X-ray diffraction

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studies on the pH and concentration dependences of the intramolecular structures of these

molecules will be necessary.

In order to obtain more detailed information on the molecular geometry of ATP and

ADP molecules and hydration structure of these molecules in aqueous solutions, the use of

neutron diffraction with 14N/15N and H/D isotopic substitution techniques [24–26] can be

an effective experimental method to distinguish intramolecular interactions relating to N

and H atoms within the adenine and ribose groups. This will be a future research project.

Acknowledgments The authors would like to thank Dr. Shinji Kohara (Japan Synchrotron ResearchInstitute) for his help during X-ray diffraction measurements. The synchrotron radiation experiments wereperformed with the approval of JASRI (Proposal Nos. 2011A1368 and 2012B1509).

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