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Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation a
Victor I. Danilov & Igor S. Tolokh
a
a
Department of Quantum Biophysics , Institute of Molecular Biology and Genetics Academy of Sciences of the Ukrainian SSR , 150 Zabolotny Street, Kiev-143 , 252143 , USSR Published online: 21 May 2012.
To cite this article: Victor I. Danilov & Igor S. Tolokh (1990) Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation, Journal of Biomolecular Structure and Dynamics, 7:5, 1167-1183, DOI: 10.1080/07391102.1990.10508554 To link to this article: http://dx.doi.org/10.1080/07391102.1990.10508554
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Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 7, Issue Number 5 (1990), "'Adenine Press (1990),
Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation
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Victor I. Danilov and Igor S. Tolokh Department of Quantum Biophysics Institute of Molecular Biology and Genetics Academy of Sciences of the Ukrainian SSR 150 Zabolotny Street, Kiev-143, 252143, USSR Abstract The simulation performed shows that under methylation of uracil and thymine NH-groups the interaction energy between a base and water (Uwb) is increased. It is also detected that the increase in this energy was observed in the 1st and the 3rd sectors. These conclusions do not confirm the assumption made in the literature on the character of an interaction between methylated bases and water. According to this assumption, when the NH-groups are methylated, the energy ofUwb in these sectors decreases as a result of the van der Waals interactions between a methyl group and water, whose energy compensates the increase in the Uwb energy due to the breaking of an H-bond. Regularity of water molecules near a hydrophobic group under the hydration of polar molecules is detected for the first time.
Introduction Methylation of nucleotide bases at certain DNA and RNA sites is a widespread phenomenon in real cellular systems. It changes the character of interactions between bases and their environment, leading for some cases to changes in structural peculiarities of nucleic acid molecules. As a result of creating electronic complementarity or due to direct steric conformity, methylation serves for specific recognition of the base sequences or structural peculiarities of the DNA sites necessary for the functioning of a number of enzymes. Methylation is also essential for the creation of the RNA structures and for their performing different functions. A hydrophobic group is added to the base under methylation. It is known from experimental and theoretical data that water changes its properties near the surface of hydrophobic molecules: rotatory and translation mobilities decrease and the structure of hydrogen bonds (H -bonds) network becomes more ordered. As a result, the entropy of a system decreases strongly while the enthalpy changes insignificantly. The same is also assumed to take place near the hydrophobic groups, making a part of polar molecules. The picture may be considerably changed due to the availability of neighboring hydrophobic groups. At present, direct experimental data on this problem are absent. The information available does not allow us to interpret them unambiguously due to the complexity of the systems under investigation and the experimental methods applied.
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When the bases are methylated, both the structures of their hydration shells and the character of the base - water interaction determining hydration are changed. The study of such systems allows us to understand better the nature of this interaction and to clarify the role of polar (hydrophilic) and non-polar (hydrophobic) groups under hydration. A detailed study of the hydration of base methylderivatives is, therefore, very important. From this point of view, the recent experimental works devoted to a study of hydration of nucleotide bases and their alkylderivatives (1-11) are of certain interest. This problem is most thoroughly studied for Ura, Thy and their alkylderivatives (1,2,4-6,8-11). The results ofthese works indicate, in particular, that under methylation ofUra and Thy in the N-positions the enthalpy of hydration increases. Under methylation in the C5- and C6-positions the enthalpy of hydration decreases appreciably. Proceeding from the results obtained and the theory of solvophobic forces, an attempt was made in the works cited above to estimate the interaction energy between bases and water and its change under methylation. For that purpose, using the theoretical approach to solvation elaborated by Sinanoglu (12-14), the energetic contribution to the energy of the base hydration corresponding to the formation of a cavity in water with the surface area equal to the area of the molecule considered (change in the interaction energy between water molecules) was calculated. As a result, the waterbase interaction energy was calculated as the difference of the energy of hydration and the change in the water- water interaction energy. It was detected (1,4,8,9) that the water- base interaction energy decreased when either the CH- or NH-groups of the bases are methylated; the effect of methylsubstituents in the C5-position was 2 to 3 times larger than that in theN-positions. The authors of (4,8,9) explain this decrease in energy as a consequence of additional van der Waals interactions arising between a methyl group and water. It is assumed that the energy of these additional interactions compensates the energetic loss associated with the breaking of an Hbond between the NH-group and water under methylation in theN-position, i.e., the interaction energy between the CH 3-group and water is lower than that of the NH ...O-bond between a base and water. Method
The purpose of our investigation is a Monte Carlo simulation of the hydration of nucleotide bases and their methylderivatives. As the objects to be studied, we have chosen Ura, m 1Ura, m~·3 , thy, m 1Thy and m~.3Thy, because for these compounds there is a number of experimental data on the hydration of different methyl derivatives (1,2,4-6,8-11). The simulations performed have made it possible to investigate the energetic and structural properties of water near the bases, to consider the hydration of an atomic group and to clarify the influence of methylation upon the structure of water near the bases or the structure of the first water hydration shell. In the present investigation, a computer simulation of the systems was performed using the Metropolis algorithm (15), each system represented a cluster of200 water molecules with one of the bases placed at its center. The simulations were performed at T = 298 K with a cluster approximation as the boundary conditions, i.e., the
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volume the system was placed in was chosen so large that its boundaries would not influence the behavior of the cluster. Interactions between the molecules in each system were taken into account by means of semiempirical atom - atom potential functions: the water- base interaction energy uwb was approximated by the potential(l-6-12)(16,17) and thewater-waterinteraction energyUww bythepotential (l6- exp) (18). In the process of computations, the Markov chains approximately l 600 000 configurations long were generated. To equilibrate the system, 500 000 to 700 000 configurations were used. The average values for the different characteristics of the systems were calculated ranging from 900 000 to 1 100 000 configurations. One of the equilibrium configurations for the system including the base with a smaller degree of methylation was chosen as an initial one. For the system including Ura, one of the equilibrium configurations from the cluster of200 water molecules, in which a few molecules were displaced from the center of the cluster to its surface to create a cavity for the molecule studied, was taken to be initial. To study the hydration of atomic groups of the base, the space around it was divided into six angular sectors (taking into account the structure of pyrimidines), with the boundaries perpendicular to the base plane. Investigations of different energetic and structural characteristics were carried out for each sector.
Results and Discussion A. General Characteristics of the System
The calculation results of the average values of the energy U for the system, the waterwater interaction energy UWW' the water- base interaction energy uwb• the specific number ofH-bonds nHb and the energy ofhydration Uh are given in Table I. In brackets, the experimental values for Uh (4,8,9) are also presented. Applying the same potential functions (18), the value ofUh was calculated from the computed magnitude of the potential energy for the cluster containing 200 water molecules and equal to -7.89 kcal/mol. Table I Energetic and Structural Characteristics of Pyrimidine Base Methylderivatives Hydration in the Cluster of 200 Water Molecules System Ura +water m 1Ura +water 3 mr Ura +water Thy+ water m 1Thy + water mr~hy + water
a
V'
uww
-7.98 -7.98 -8.03 -8.09 -7.99 -8.08
-7.70 -7.72 -7.80 -7.80 -7.73 -7.82
"Kcal/mol water. hKcal/mol system. 'Experimental value of the enthalpy of hydration (4,8,9).
uwh
h
-56.0 -52.1 -46.0 -57.1 -51.8 -51.4
nHh
uh h
1.77 1.79 1.82 1.80 1.75 1.83
-18 (-21.8') -18 (-21.3') -28 (-20.6') -40 (-23.9') -20 (-23.4') -38 (- 23.7')
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Comparison of the theoretical and experimental magnitudes for the energy ofhydration reveals reasonable quantitative agreement between them. The sequence of the Uh values we have calculated reproduces correctly the sequence of the corresponding values observed experimentally when Ura and its N-methylderivatives are methylated in the C5-position. An analogous situation is also observed for Thy and its methylderivatives. For Ura and its derivatives, however, there is no correlation in the sequence of the Uh theoretical and experimental data. It is seen from the data presented that methylation in the Nl- and Nl-, N3-positions increases the uwb energy, i.e., decreases the interaction between a base and water, though form 1Thy and m~· 3Thy these values differ very slightly. This conclusion is in direct contradiction with the results of (4,8,9), in which the combination of the experimental values for the enthalpy of hydration and the theoretical estimates of the change in the water - water interaction energy was used to calculate Uwb· At the same time, methylation in the hydrofhobic C5-position of Ura and its derivatives decreases the Ut,b energy, except m Ura resulting in a slight increase in Uwb (-52.1 kcal/mol form Ura and -51.8 kcal/mol for m 2Thy). Thus, we can conclude about the Uwb energy increase when the H-bond between the NH-group of a base and wateris broken due to methylation. This could be expected, because the breaking of the H-bond 3 to 5 kcal/mol decreases the energy of binding between a base and water, while methyl group can, in principle, increase this energy by 1 to 2 kcal/mol at the expense of the van der Waals interactions. At the same time, this conclusion is not absolutely unambiguous, because generally speaking, methylation can lead to a reorganization of the whole base hydration shell and, hence, to a change in the interaction energy between the nearest water molecules and other hydrophylic groups, decreasing or increasing this energy. The latter is most likely to be observed when m 1Thy is methylated in the N3-position: in this case, the Uwb energy remains unchanged. The energyofUww for the N-methylderivatives ofUra is lower than that for a canonical base, and for a dimethylated base it is lower than for a monomethylated one. Methylation ofUra and its N-methylderivatives in the C5-position also decreases the Uww energy. For the N-methylderivatives of Thy, however, there are not any definite regularities observed when the Uww energy is changed. This energy increases under methylation in the Nl-position, and under further methylation in the N3position it decreases. Such a dependence of the Uww energy upon the degree of methylation may be associated with the fact that this value characterizes the cluster as a whole, including the most different ambiguities at the boundary of the system (density, shape of boundary, orientation of molecules, etc.). Perhaps, owing to this the potential energies of U, the main contribution to which is made by the Uww values and, hence, by the energies of hydration Uh, do not always correlate with the experimental values for the enthalpies of hydration (4,8,9). In addition, it is necessary to remember that the differences between the measured enthalpies ofhydration are within the limits of experimental error.
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Hydration of Uracil and Thymines B. Data for the Subsystems
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To eliminate ambiguities at the boundary of the cluster, let us consider the subsystems situated in a spherical volume of radius R = 7.3 Acounted off from the geometric center of the base. Besides the base, such a volume includes about SO water molecules. The choice of a subsystem size is determined by the fact that the water -base interaction disturbing a solvent does not influence its boundary any longer (the uwb values for the subsystem make up 80 to 90% of the corresponding values for the whole system). Being atthe same time at such a distance from the center, water molecules are not yet subjected to the influence of the changes in the surface layers of the cluster. The values of U', U~, U~b and nHb characterizing the subsystems considered are listed in Table II. Table II Energetic and Structural Characteristics of Pyrimidine Base Mehtylderivatives Hydration in the Cluster of 200 Water Molecules (data are given for the subsystem of radius 7.3 A) Subsystem Ura +water m 1Ura + water m~·\Jra + water Thy+ water m 1Thy + water m~·1'hy + water
U'"
U'wwa
U'wwa
n~h
-9.98 -9.67 -9.76 -9.88 -9.72 -9.82
-9.06 -8.78 -8.93 -8.89 -8.84 -8.91
-47.8 -44.8 -40.5 -50.5 -44.5 -45.6
2.12 2.04 2.07 2.14 2.11 2.19
"Kcal/mol water. bKcal/mol system.
These data indicate that under methylation in the Nl- and Nl-, N3-positions the potential energy ofthe subsystem increases, although this increase is smaller in the latter case. For Thy derivatives, such a qualitative behavior agrees with the experimental data on the enthalpy of hydration (4,8,9). For Ura derivatives, the correlation with the experiment is worse. The energies ofU'ww for the subsystems show that when the bases are methylated in the Nl- and Nl-, N3-positions water becomes less favorable energetically. When the bases are twice methylated in theN-positions, it is, however, a little more favorable than for once methylated bases, and for mi3Thy the given energy is even comparable with Thy. Analysis of the average numbers of the water - water H -bonds per water molecule in the subsystems, n'Hb• shows that their change correlates completely with the change of the U'ww energies. Thus, when Ura and Thy are methylated in the Nlposition, water" deteriorates" both energetically and structurally (in the number of H-bonds per water molecules). When Ura is methylated in the Nl-, N3-positions it also" deteriorates", though to a smaller extent, and for Thy it even "improves" a little. In other words, the availability of three methyl groups in m~· 3 Thy leads to a slight increase in the specific number of H-bonds in its subsystem, as compared to Thy.
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The average number of water molecules in each subsystem correlates with the degree of methylation in theN-positions: a smaller average number of water molecules in the spherical volume of R = 7.3 A corresponds to a greater number of methyl groups. The U~b energies in the subsystems show that methylation ofNH -groups leads to a decrease in the interaction between a base and water (increase in the energy). Methylation of m 1Thy in the N3-position makes an exception: in this case, the subsystem energy of U'wb decreases a little. As was already mentioned above, this is associated with the reorganization of the whole hydration shell, since in this case, too, the interaction energy between a base and the water molecules situated in the sector including N3H-group increases under methylation in the N3-position. As will be shown below, the interaction between water and N3CH 3-group results in an energetic loss of almost 2 kcal/mol, as compared to the interaction between water and N3H-group. C. Sector Distribution Functions
The energies ofUwb and the number of water molecules n in each of the six angular sectors limited by R = 7.3 A are summerized in Table III. Table Ill Angular Distribution of Water Molecules and Their Interaction Energies• with Pyrimidine Base Methylderivatives (data are given for the subsystem of radius 7.3 A) Subsystem
Sector I n
uwh Ura +water m 1Ura + water md":Vra +water Thy+ water m 1Thy + water md"loy'hy + water
-7.08 -4.32 -4.32 -10.33 -4.18 -5.15
Sector 2 n
uwb
8.7 -9.08 7.7 -9.55 8.0 -12.14 9.0 -8.35 8.9 -9.52 9.3 -9.49
8.6 8.5 8.3 9.0 8.9 7.5
Sector 3 n
uwh
-7.82 -6.27 -2.95 -7.87 -5.86 -4.05
8.1 8.3 8.6 8.7 7.7 9.0
Sector4 n
uwh
Sector 5 n
uwh
-13.10 10.3 -6.83 -12.51 8.8 -5.32 -9.08 7.9 -7.18 -13.27 7.9 -5.63 -14.24 9.3 -4.52 -17.31 8.4 -3.53
8.2 6.8 7.2 9.1 8.6 8.3
Sector 6 n
uwb
-3.88 7.9 -6.80 10.1 -4.82 8.8 -5.05 7.5 -6.21 7.4 -6.07 7.7
•KcaVmol system.
These results reveal that methylation of NH-groups both in Nl- and Nl-, N3positions resutls in a 2 to 6 kcal/mol increase in the itneraction energy between a base and water molecules in the sectors of methylation. This testifies directly to the incorrectness of the assumption (4,8,9) suggesting that the decrease in the basewater interaction energy under methylation ofUra and Thy hydrophobic groups is caused by the van der Waals interactions. Comparison of the Uwb energies in the 5th sector ofUra and Thy derivatives show that under methylation in the CS-position the energy ofUwb increases, but not decreases, as could have been expected from (4,8,9) at the expense of the increase in the number of atoms capable of participating in van der Waals interactions. It should be noted that hydrophobic group is not closed. Thus, when the uwb energy of the system decreases
Hydration of Uracil and Thymines
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under methylation ofUra and its N-methylderivatives in the C5-position, this is not associated with its decrease in the 5th sector, as assumed in (4,8,9), but with the reorganization of the whole hydration shell changing the interaction with some, mainly hdyrophobic, groups of the bases. Under methylation in the Nl- and Nl-, N3-positions, the energy ofUwb in the 2nd sector (C20-group) for Ura and Thy derivatives decreases (0.5- 3.1 kcal/mol), in the 4th sector (C40-group) for Thy derivatives it also decreases (1.0- 4.0 kcal/mol), while for Ura derivatives it increases (0.6- 4.0 kcal/mol).lt is to be noted that the increase in the Uwb energy in the 4th sector ofUra derivatives is accompanied by a similar decrease in its value in the 2nd sector (in other words, these effects tend to compensate each other), whereas for Thy derivatives it decreases both in the 2nd and the 4th sectors. A great decrease in the Uwb energy in the 4th sector of m?Thy as compared to Thy and m 1Thy, leads to the fact that despite the increase in the Uwb energy in the 3rd sector 1 when m Thy is methylated, the Uwb energy for the whole system decreases a little. We have already discussed this phenomenon at the end of the previous section. The number ofwater molecules in each sector considered shows that under methylation in the Nl- and then in the N3-positions, a noticeable decrease in the number of water molecules in the 1st and the 3rd sectors is not always observed. Most often, it even increases a little. The increase in the U wb energy in the 4th sector ofUra derivatives is accompanied by a simultaneous decrease in the numberofwater molecules belonging to this sector. As a result, the energy ofUfb per water molecule in this sector (specific energy gwb) does not change at all (form Ura it even decreases a little). Under transition from Thy to 1 m Thy, gwb in the 4th sector does not change at all. But the transition from m 1Thy to m~·:>.rhy is accompanied by a very great decrease in gwb leading in its tum to some decrease in the Uwb energy for the whole subsystem, which was mentioned above. It should be mentioned that the number of water molecules in the 5th sector of Thy
and its derivatives is greater than in the 5th sector ofthe corresponding Ura derivatives, although a methyl group ofThyoccupies a much greater volume than the hydrogen atom in the 5th position ofUra. As was already mentioned, despite this fact the Uwb energy in the 5th sector of Ura derivatives is lower than in the 5th sector of Thy derivatives. It is most likely due to a greater interaction between the water molecules from the 5th sector ofUra and its derivatives, i.e., when methyl group is absent, water molecules in the 5th sector are located in space in such a way that they interact in a stronger way with the C40-group. The obtained angular distribution of the water- water interaction energy by sectors shows directly that the energy ofUww in the 5th sector has lower values for Thy and its derivatives than for Ura and its derivatives. The nub values also testify to a higher regulation in water structure around Thy and its derivatives, which is mainly caused by a spherical layer of water molecules at R = 6.3 - 7.3 A- the one nearest to a methyl group. This proves for the first time that near a hydrophobic group the regulation of water molecules increases even for such polar molecules as the bases are.
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The Uwb energy in the 6th sector has greater values for Ura and its derivatives than 1 for Thy and its derivatives. m Ura is an exception. The sum of the Uwb energies for the 5th and the 6th sectors ofUra and its derivatives is smaller than that of Thy and its derivatives. For Ura and Thy themselves, these values are approximately the same. Thus, the interaction energy between the base and the water molecules situated in the hydrophobic sectors is lower for Ura derivatives than for Thy derivatives. At the same time, the corresponding analysis indicates that the sum of the Uww energies for the 5th and the 6th sectors is a little lower, and the nHb values for the united region of these sectors are a little higher for Thy and its derivatives. This testifies in favor of the fact that the appearance of a hydrophobic surface of a molecule in water leads to a greater regulation of water molecules near this region. Let us consider radial distribution functions of water molecule oxygen atoms & and specific energy gwb in different base angular sectors, depending on the distance from a molecule centre. These functions are ofthe greatest interest for the sectors in which methylation of the bases takes place. Analysis of the & and ~b functions for the 1st sector ofUra shows that the first maximum ofg 0 is at the distance ofR = 4.15Aand is as great as 3.I6(Figure I a). The first maximum of the ~b function almost coincides with it(4.20 A) and amounts to -4.4I kcal/mol. Besides, there are 1.14 water molecules on the average in this sector with R = 4.3 A. Thus, it is seen that both in distance (nitrgoen atoms of uracil ring are at R = 1.0 A from the base center) and energy the water molecule situated in the region of the first maximum of the & function forms and H-bond with the NIH-group of Ura. Consideration of the & and ~b functions for the 1st sector of m 1Ura indicates (Figure I b) that near the base with R = 5.5 A, the density of water molecules does not exceed 1.0 and the maximum interaction energy between them and the base is not more than -2.3 kcal/mol. With the distance of R = 4.3 A, the water molecule forming an H-bond with the base was located at before methylation, there is only average 0.33 water molecule, whose interaction energy is Uwb = -0.4 kcal/mol. All this testifies to the fact that methylation in theN 1-position leads to a breaking of an H -bond and repulsion of the nearest water molecule included in an H-bond. Distribution of the other water molecules in this sector has also changed greatly (Figure 2). The main maximum of g0 lies in the region of R = 6.0 A and amounts to 1.9. Almost analogous changes have taken place in the lst sector of m~· 3Ura (Figure lc). The g0 and gwb functions (Figure ld) characterizing water in the lst sector of Thy show that as forUraeither, the maximum of& is atR = 4.15Aand the maximum of gwb is at R = 4.05 A. Location and intensity of these maxima testify to the fact that the H-bond between water and NIH-group is also formed in the lst sector of Thy. In contrast to Ura, however, for which in the layerofR = 3.8-4.8 A of the 1st sector 1.75
1175
Hydration of Uracil and Thymines ~
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Figure 1: Radial distribution functions of water molecules oxygen atoms&, and specific energy gwh (kcaVmol) for the 1st sector of uracil (a); 1-methyluracil (b); 1,3-dimethyluracil (c); thymine (d); 1-methylthymine (e); 1,3-dimethylthymine (f) depending of the distance from a molecule centre. Figure 1 continued on pages 1176 and 1177.
1176
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1177
Hydration of Uracil and Thymines
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water molecules are located with Uwb = -5.1 kcal/mol, there are 2.77 water molecules with the energy ofUwb = -8.2 kcal/mol at an analogous place of Thy. This makes one assume that water molecules in the 1st sector of Thy form two H -bonds with the base. There are either two bonds including N1 H -group or one of them includes this group and the other the neighboring C20-group. Such an assumption also explains why the Uwb energy is by 3 kcal/mollower in the 1st sector of Thy (with R = 7.3 A) than in the same sector of Ura. Consideration of the distribution functions for the 1st sector of m 1Thy and m~· 3 Thy shows that they differ slightly from the corresponding functions for m 1Ura and m;· 3Ura (Figures le and 1f). In contrast to the latter ones, for Thy derivates there exist rather narrow and high maxima of the~ functions in the region of 3.5 A from the base center. In the 1st sector of m 1Thy and m~· 3 Thy there are 0.97 and 0.82 water molecules, respectively, with R = 4.3 A However, the gwb functions show that the water molecules considered interact with the bases very weakly and, hence, do not form H -bonds with them. So, the U wb energy in the 1st sector of Thy calculated with R = 4.8 A from the base center equals -8.2 kcal/mol, while the analogous energies form 1Thy and m~·3 Thy amount to only -1.2 and -1.7 kcal/mol, respectively. Thus, methylation ofThy in the N1-position leads to a destruction of about two H-bonds between water and the base, and increses the uwb energy approximately by 6 kcal/ mol in the 1st sector. The & and &vb distribution functions for the 3rd sector ofUra show(Figure 2a) thatthe water molecules belonging to this sector form an H-bond with N3H-group. One should note that unlike the 1st Ura sector, the number of water molecules is approximately 2.5 times larger in the area of the first g0 maximum for the 3rd sector (there are 2.6 molecules til14.3 A). Their Uwb energy amounts to -6.46 kcal/mol, which is approximately 1.7 times higher than the corresponding energies in the 1st Ura sector. 1
The maximum of the & function for the 3rd sector of m Ura is 0.4 A shifted from the base, as compared to the corresponding maximum for Ura, and its altitude is smaller (Figure 2b ). In addition, here, with R = 4.3 A there is only 0.96 water molecule with the Uwb energy as great as -1.4 kcal/mol. The maximum of the gwb function, however, situated at 4.1 A and equal to -2.52 kcal/mol indicates that the nearest water molecule can form an H -bond with the base in some configurations. 2.42 water molecules with Uwb = -4.4 kcal/mol are situated in the 3rd sector of m 1Ura with R = 4.8 A. The g0 function for the 3rd sector of m~3 Ura (Figure 2c) looks approximately the same as for the lstsectorofm 1Uraandm/Ura. With R = 4.8Atherisonly0.64water molecule whose energy ofUwb = -0.35 kcal/mol. This points to the fact that like the 1st sector, methylation ofN3H-group increases greatly the interaction energy between the water molecules of the 3rd sector and the base. The energy ofUwb in the 3rd sector of m~· 3 Ura (R = 7.3 A) amounts to -2.95 kcal/mol. An analogous picture is observed when considering the g0 and gwb functions for the 3rd sector of Thy, m 1Thy and m~· 3 Thy (Figures 2d-2f). In these sectors, the water
1179
Hydration of Uracil and Thymines
.,
.,. () •>
(a)
\~
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•~,;t,
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!
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. a,
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Figure 2: Radial distribution functions of water molecules oxygen atoms&, and specific energy &.m (kcaVmol) for the 3rd sector of uracil (a); 1-methyluracil (b); 1,3-dimethyluracil (c); thymine (d); 1-methylthymine (e); 1,3-dimethylthymine (I), depending on the distance from a molecule centre. Figure 2 continued on
pages 1180 and 1181.
Danilov & Tolokh
1180 ~·lura 0 •>
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o~--~-----7;----~~~&c·~~~-----s~·-----&L'-----jL-
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:.s 2.0 1.S , .IJ
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Figure 2 continued
I A
Hydration of Uracil and Thymines
1181
...
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. 0~
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-c.. $.0 2.5 ~.I)
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,
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Figure 2 continued
1182
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molecule nearest to Thy forms an obvious H -bond with the base. The same occurs in the 3rd sector of m 1Thy but the binding energy is a little smaller. The present results on the analysis of the g0 and gwb functions for the 1st and the 3rd sectors, and the data from the analogous analysis performed for the other sectors allow us to estimate the contribution of specific interactions (the interactions between the base and the layer of water moleculesimmediately bordering with it through the H-bonds or by means of electrostatic interaction) to the total Uwb energy. The water molecules responsible for the specific interactions lie in the volume ofR = 5.3 Aand lead to the Uwb energy(in kcal/mol) amounting to -27.9 for Ura, -33.3 for m 1Ura, -25.8 for m;·:rura, -37.8 for Thy, -29.4 form 1Thy and -29.6 for m~·3 Thy. Comparing these values with the results from Table I, it is seen that the contribution indicated amounts to 0.50 for U ra, 0.64 form 1U ra, 0.56 for m;· 3u ra, 0.66 for Thy, 0.57 form 1Thy and 0.58 for m~·3Thy. The data we have obtained show directly that specific interactions make a dominant contribution to the energy of Uwb· Thus, they do not confirm the conclusion of Sukhodub eta/. (2,4,9-11) that the given contribution is small. According to their estimates, it ranges from 0.14 to 0.21 for the compounds considered. The contradiction is easily explained. To estimate this contribution, the authors of (2,4,9-11) used the sum of the base hydration enthalpies in vacuum for the first two water molecules as the enthalpy of specific interactions. They assumed that in solution the water molecules responsible for the specific interactions had the same configurations as in vacuum, and the number of water molecules responsible for these interactions and the interaction energies between them and the bases did not change. Meanwhile, as a result of theoretical analysis and our previous calculations we showed (19,20) that in a large water cluster all the characteristics indicated changed essentially.
Acknowledgments We are deeply indebted to Prof. N.Y. Zheltovsky for creating a good stimulating atmosphere, G.M. Ostrovskaya for technical assistance and E.N. Bugulov for valuable advice and recommendations. References and Footnotes
1. A.B. Tep1itsky, IK Yanson, O.T. G1ukhova,A Zie1enkiewicz, W. Zie1enkiewicz and K.L. Wierzchowski, Biophys. Chern. 11,17-21 (1980). 2. L.F. Sukhodub, O.T. Glukhova, A.B. Tep1itsky, IK Yanson and K.L. Wierzchowski, in Proceedings of the International Symposium of Biochemistry, Tbi1isi, p. 65 (1981 ). 3. O.T. Glukhova, V.D. Kiselev, A.B. Teplitsky, AN. Ustyugov and IK Yanson, Biojizika (USSR) 26, 351-352 (1981). 4. A.B. Tep1itsky, O.T. G1ukhova, L.F. Sukhodub, I.K. Yanson, A. Zie1enkiewicz, W. Zie1enkiewicz, J. Kosinski and KL. Wierzchowski, Biophys. Chern. 15, 139-147 (1982). 5. O.T. G1ukhova, A.B. Tep1itsky, L.F. Sukhodub and K.L. Wierzchowski, in Porceedings of the AllUnion Biophysical Congress, (USSR), Moscow, p. 56 (1982). 6. O.T. G1ukhova, A.B. Tep1itsky, L.F. Sukhodub, A. Zie1enkiewics, W. Zie1enkiewicz and K.L. Wierzchowski, in Proceedings ofthe Third International Conference on Water and Ions in Biological Systems, Bucharest, p. 108 (1984).
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1183
7. A Zielenkiewicz, W. Zielenkiewicz, L.F. Sukhodub, O.T. Glukhova, AB. Teplitsky and KL. Wierzchowski,.J. Solution Chern. 13,757-765 (1984). 8. O.T. Glukhova, Thesis for the Degree of a Candidate of Physical and Mathematical Sciences, Kharkov (1985). 9. L.F. Sukhodub, Synopsis of the Thesis for the Degree ofa Doctor ofPhysical and Mathematical Sciences, Moscow (1985). 10. L.F. Sukhodub, Preprint, 38-87, Kharkov (1987). 11. L.F. Sukhodub, Chern. Rev. 87, 589-606 (1987). 12. 0. Sinanog1u and S. Abdulnur, Fed. Proc. 24, 12-23 (1965). 13. 0. Sinanog1u, in Molecular Associations in Biology, Ed., B. Pullman, Acad. Press, New York, p. 427 (1968). 14. 0. Sinanoglu and S. Abdulnur, Photochem. and Photobiol. 3, 333-342 (1964). 15. N. Metropolis, A W. Rosenbluth, M.N. Rosenbluth, AN. Teller and E. Teller,! Chern. Phys. 21, 10871092 (1953). 16. V.B. Zhurkin, V.I. Poltev and V.L. Florentiev, Mol. Bioi. (USSR) 14, 1116-1130 (1980). 17. V.I. Poltev, V.I. Danilov, M.R Sharafutdinov, AZ. Shvartsman, N.V. Shulyupina and G.G. Ma1enkov, Stud. Biophys. 91,37-43 (1982). 18. L.P. D'yakonova and G.G. Malenkov, Zh. Struk. Khim. (USSR) 20, 854-861 (1979). 19. V.I. Danilov, M.R. Sharafutdinov and I.S. Tolokh, Stud. Biophys. 93, 193-196 (1983). 20. V.I. Danilov, in Steric Aspects ofBiomolecular Interactions, Eds., G. Naray-Szabo and K Simon, CRC Press, Boca Raton, Florida, p. 235 (1987). Date Received: July 15, 1989
Communicated by the Editor Valery I. Ivanov
Journal of Biomolecular Structure and Dynamics Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/tbsd20
Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation a
Victor I. Danilov & Igor S. Tolokh
a
a
Department of Quantum Biophysics , Institute of Molecular Biology and Genetics Academy of Sciences of the Ukrainian SSR , 150 Zabolotny Street, Kiev-143 , 252143 , USSR Published online: 21 May 2012.
To cite this article: Victor I. Danilov & Igor S. Tolokh (1990) Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation, Journal of Biomolecular Structure and Dynamics, 7:5, 1167-1183, DOI: 10.1080/07391102.1990.10508554 To link to this article: http://dx.doi.org/10.1080/07391102.1990.10508554
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Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 7, Issue Number 5 (1990), "'Adenine Press (1990),
Hydration of Uracil and Thymine Methylderivatives: a Monte Carlo Simulation
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Victor I. Danilov and Igor S. Tolokh Department of Quantum Biophysics Institute of Molecular Biology and Genetics Academy of Sciences of the Ukrainian SSR 150 Zabolotny Street, Kiev-143, 252143, USSR Abstract The simulation performed shows that under methylation of uracil and thymine NH-groups the interaction energy between a base and water (Uwb) is increased. It is also detected that the increase in this energy was observed in the 1st and the 3rd sectors. These conclusions do not confirm the assumption made in the literature on the character of an interaction between methylated bases and water. According to this assumption, when the NH-groups are methylated, the energy ofUwb in these sectors decreases as a result of the van der Waals interactions between a methyl group and water, whose energy compensates the increase in the Uwb energy due to the breaking of an H-bond. Regularity of water molecules near a hydrophobic group under the hydration of polar molecules is detected for the first time.
Introduction Methylation of nucleotide bases at certain DNA and RNA sites is a widespread phenomenon in real cellular systems. It changes the character of interactions between bases and their environment, leading for some cases to changes in structural peculiarities of nucleic acid molecules. As a result of creating electronic complementarity or due to direct steric conformity, methylation serves for specific recognition of the base sequences or structural peculiarities of the DNA sites necessary for the functioning of a number of enzymes. Methylation is also essential for the creation of the RNA structures and for their performing different functions. A hydrophobic group is added to the base under methylation. It is known from experimental and theoretical data that water changes its properties near the surface of hydrophobic molecules: rotatory and translation mobilities decrease and the structure of hydrogen bonds (H -bonds) network becomes more ordered. As a result, the entropy of a system decreases strongly while the enthalpy changes insignificantly. The same is also assumed to take place near the hydrophobic groups, making a part of polar molecules. The picture may be considerably changed due to the availability of neighboring hydrophobic groups. At present, direct experimental data on this problem are absent. The information available does not allow us to interpret them unambiguously due to the complexity of the systems under investigation and the experimental methods applied.
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When the bases are methylated, both the structures of their hydration shells and the character of the base - water interaction determining hydration are changed. The study of such systems allows us to understand better the nature of this interaction and to clarify the role of polar (hydrophilic) and non-polar (hydrophobic) groups under hydration. A detailed study of the hydration of base methylderivatives is, therefore, very important. From this point of view, the recent experimental works devoted to a study of hydration of nucleotide bases and their alkylderivatives (1-11) are of certain interest. This problem is most thoroughly studied for Ura, Thy and their alkylderivatives (1,2,4-6,8-11). The results ofthese works indicate, in particular, that under methylation ofUra and Thy in the N-positions the enthalpy of hydration increases. Under methylation in the C5- and C6-positions the enthalpy of hydration decreases appreciably. Proceeding from the results obtained and the theory of solvophobic forces, an attempt was made in the works cited above to estimate the interaction energy between bases and water and its change under methylation. For that purpose, using the theoretical approach to solvation elaborated by Sinanoglu (12-14), the energetic contribution to the energy of the base hydration corresponding to the formation of a cavity in water with the surface area equal to the area of the molecule considered (change in the interaction energy between water molecules) was calculated. As a result, the waterbase interaction energy was calculated as the difference of the energy of hydration and the change in the water- water interaction energy. It was detected (1,4,8,9) that the water- base interaction energy decreased when either the CH- or NH-groups of the bases are methylated; the effect of methylsubstituents in the C5-position was 2 to 3 times larger than that in theN-positions. The authors of (4,8,9) explain this decrease in energy as a consequence of additional van der Waals interactions arising between a methyl group and water. It is assumed that the energy of these additional interactions compensates the energetic loss associated with the breaking of an Hbond between the NH-group and water under methylation in theN-position, i.e., the interaction energy between the CH 3-group and water is lower than that of the NH ...O-bond between a base and water. Method
The purpose of our investigation is a Monte Carlo simulation of the hydration of nucleotide bases and their methylderivatives. As the objects to be studied, we have chosen Ura, m 1Ura, m~·3 , thy, m 1Thy and m~.3Thy, because for these compounds there is a number of experimental data on the hydration of different methyl derivatives (1,2,4-6,8-11). The simulations performed have made it possible to investigate the energetic and structural properties of water near the bases, to consider the hydration of an atomic group and to clarify the influence of methylation upon the structure of water near the bases or the structure of the first water hydration shell. In the present investigation, a computer simulation of the systems was performed using the Metropolis algorithm (15), each system represented a cluster of200 water molecules with one of the bases placed at its center. The simulations were performed at T = 298 K with a cluster approximation as the boundary conditions, i.e., the
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Hydration of Uracil and Thymines
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volume the system was placed in was chosen so large that its boundaries would not influence the behavior of the cluster. Interactions between the molecules in each system were taken into account by means of semiempirical atom - atom potential functions: the water- base interaction energy uwb was approximated by the potential(l-6-12)(16,17) and thewater-waterinteraction energyUww bythepotential (l6- exp) (18). In the process of computations, the Markov chains approximately l 600 000 configurations long were generated. To equilibrate the system, 500 000 to 700 000 configurations were used. The average values for the different characteristics of the systems were calculated ranging from 900 000 to 1 100 000 configurations. One of the equilibrium configurations for the system including the base with a smaller degree of methylation was chosen as an initial one. For the system including Ura, one of the equilibrium configurations from the cluster of200 water molecules, in which a few molecules were displaced from the center of the cluster to its surface to create a cavity for the molecule studied, was taken to be initial. To study the hydration of atomic groups of the base, the space around it was divided into six angular sectors (taking into account the structure of pyrimidines), with the boundaries perpendicular to the base plane. Investigations of different energetic and structural characteristics were carried out for each sector.
Results and Discussion A. General Characteristics of the System
The calculation results of the average values of the energy U for the system, the waterwater interaction energy UWW' the water- base interaction energy uwb• the specific number ofH-bonds nHb and the energy ofhydration Uh are given in Table I. In brackets, the experimental values for Uh (4,8,9) are also presented. Applying the same potential functions (18), the value ofUh was calculated from the computed magnitude of the potential energy for the cluster containing 200 water molecules and equal to -7.89 kcal/mol. Table I Energetic and Structural Characteristics of Pyrimidine Base Methylderivatives Hydration in the Cluster of 200 Water Molecules System Ura +water m 1Ura +water 3 mr Ura +water Thy+ water m 1Thy + water mr~hy + water
a
V'
uww
-7.98 -7.98 -8.03 -8.09 -7.99 -8.08
-7.70 -7.72 -7.80 -7.80 -7.73 -7.82
"Kcal/mol water. hKcal/mol system. 'Experimental value of the enthalpy of hydration (4,8,9).
uwh
h
-56.0 -52.1 -46.0 -57.1 -51.8 -51.4
nHh
uh h
1.77 1.79 1.82 1.80 1.75 1.83
-18 (-21.8') -18 (-21.3') -28 (-20.6') -40 (-23.9') -20 (-23.4') -38 (- 23.7')
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Comparison of the theoretical and experimental magnitudes for the energy ofhydration reveals reasonable quantitative agreement between them. The sequence of the Uh values we have calculated reproduces correctly the sequence of the corresponding values observed experimentally when Ura and its N-methylderivatives are methylated in the C5-position. An analogous situation is also observed for Thy and its methylderivatives. For Ura and its derivatives, however, there is no correlation in the sequence of the Uh theoretical and experimental data. It is seen from the data presented that methylation in the Nl- and Nl-, N3-positions increases the uwb energy, i.e., decreases the interaction between a base and water, though form 1Thy and m~· 3Thy these values differ very slightly. This conclusion is in direct contradiction with the results of (4,8,9), in which the combination of the experimental values for the enthalpy of hydration and the theoretical estimates of the change in the water - water interaction energy was used to calculate Uwb· At the same time, methylation in the hydrofhobic C5-position of Ura and its derivatives decreases the Ut,b energy, except m Ura resulting in a slight increase in Uwb (-52.1 kcal/mol form Ura and -51.8 kcal/mol for m 2Thy). Thus, we can conclude about the Uwb energy increase when the H-bond between the NH-group of a base and wateris broken due to methylation. This could be expected, because the breaking of the H-bond 3 to 5 kcal/mol decreases the energy of binding between a base and water, while methyl group can, in principle, increase this energy by 1 to 2 kcal/mol at the expense of the van der Waals interactions. At the same time, this conclusion is not absolutely unambiguous, because generally speaking, methylation can lead to a reorganization of the whole base hydration shell and, hence, to a change in the interaction energy between the nearest water molecules and other hydrophylic groups, decreasing or increasing this energy. The latter is most likely to be observed when m 1Thy is methylated in the N3-position: in this case, the Uwb energy remains unchanged. The energyofUww for the N-methylderivatives ofUra is lower than that for a canonical base, and for a dimethylated base it is lower than for a monomethylated one. Methylation ofUra and its N-methylderivatives in the C5-position also decreases the Uww energy. For the N-methylderivatives of Thy, however, there are not any definite regularities observed when the Uww energy is changed. This energy increases under methylation in the Nl-position, and under further methylation in the N3position it decreases. Such a dependence of the Uww energy upon the degree of methylation may be associated with the fact that this value characterizes the cluster as a whole, including the most different ambiguities at the boundary of the system (density, shape of boundary, orientation of molecules, etc.). Perhaps, owing to this the potential energies of U, the main contribution to which is made by the Uww values and, hence, by the energies of hydration Uh, do not always correlate with the experimental values for the enthalpies of hydration (4,8,9). In addition, it is necessary to remember that the differences between the measured enthalpies ofhydration are within the limits of experimental error.
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Hydration of Uracil and Thymines B. Data for the Subsystems
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To eliminate ambiguities at the boundary of the cluster, let us consider the subsystems situated in a spherical volume of radius R = 7.3 Acounted off from the geometric center of the base. Besides the base, such a volume includes about SO water molecules. The choice of a subsystem size is determined by the fact that the water -base interaction disturbing a solvent does not influence its boundary any longer (the uwb values for the subsystem make up 80 to 90% of the corresponding values for the whole system). Being atthe same time at such a distance from the center, water molecules are not yet subjected to the influence of the changes in the surface layers of the cluster. The values of U', U~, U~b and nHb characterizing the subsystems considered are listed in Table II. Table II Energetic and Structural Characteristics of Pyrimidine Base Mehtylderivatives Hydration in the Cluster of 200 Water Molecules (data are given for the subsystem of radius 7.3 A) Subsystem Ura +water m 1Ura + water m~·\Jra + water Thy+ water m 1Thy + water m~·1'hy + water
U'"
U'wwa
U'wwa
n~h
-9.98 -9.67 -9.76 -9.88 -9.72 -9.82
-9.06 -8.78 -8.93 -8.89 -8.84 -8.91
-47.8 -44.8 -40.5 -50.5 -44.5 -45.6
2.12 2.04 2.07 2.14 2.11 2.19
"Kcal/mol water. bKcal/mol system.
These data indicate that under methylation in the Nl- and Nl-, N3-positions the potential energy ofthe subsystem increases, although this increase is smaller in the latter case. For Thy derivatives, such a qualitative behavior agrees with the experimental data on the enthalpy of hydration (4,8,9). For Ura derivatives, the correlation with the experiment is worse. The energies ofU'ww for the subsystems show that when the bases are methylated in the Nl- and Nl-, N3-positions water becomes less favorable energetically. When the bases are twice methylated in theN-positions, it is, however, a little more favorable than for once methylated bases, and for mi3Thy the given energy is even comparable with Thy. Analysis of the average numbers of the water - water H -bonds per water molecule in the subsystems, n'Hb• shows that their change correlates completely with the change of the U'ww energies. Thus, when Ura and Thy are methylated in the Nlposition, water" deteriorates" both energetically and structurally (in the number of H-bonds per water molecules). When Ura is methylated in the Nl-, N3-positions it also" deteriorates", though to a smaller extent, and for Thy it even "improves" a little. In other words, the availability of three methyl groups in m~· 3 Thy leads to a slight increase in the specific number of H-bonds in its subsystem, as compared to Thy.
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The average number of water molecules in each subsystem correlates with the degree of methylation in theN-positions: a smaller average number of water molecules in the spherical volume of R = 7.3 A corresponds to a greater number of methyl groups. The U~b energies in the subsystems show that methylation ofNH -groups leads to a decrease in the interaction between a base and water (increase in the energy). Methylation of m 1Thy in the N3-position makes an exception: in this case, the subsystem energy of U'wb decreases a little. As was already mentioned above, this is associated with the reorganization of the whole hydration shell, since in this case, too, the interaction energy between a base and the water molecules situated in the sector including N3H-group increases under methylation in the N3-position. As will be shown below, the interaction between water and N3CH 3-group results in an energetic loss of almost 2 kcal/mol, as compared to the interaction between water and N3H-group. C. Sector Distribution Functions
The energies ofUwb and the number of water molecules n in each of the six angular sectors limited by R = 7.3 A are summerized in Table III. Table Ill Angular Distribution of Water Molecules and Their Interaction Energies• with Pyrimidine Base Methylderivatives (data are given for the subsystem of radius 7.3 A) Subsystem
Sector I n
uwh Ura +water m 1Ura + water md":Vra +water Thy+ water m 1Thy + water md"loy'hy + water
-7.08 -4.32 -4.32 -10.33 -4.18 -5.15
Sector 2 n
uwb
8.7 -9.08 7.7 -9.55 8.0 -12.14 9.0 -8.35 8.9 -9.52 9.3 -9.49
8.6 8.5 8.3 9.0 8.9 7.5
Sector 3 n
uwh
-7.82 -6.27 -2.95 -7.87 -5.86 -4.05
8.1 8.3 8.6 8.7 7.7 9.0
Sector4 n
uwh
Sector 5 n
uwh
-13.10 10.3 -6.83 -12.51 8.8 -5.32 -9.08 7.9 -7.18 -13.27 7.9 -5.63 -14.24 9.3 -4.52 -17.31 8.4 -3.53
8.2 6.8 7.2 9.1 8.6 8.3
Sector 6 n
uwb
-3.88 7.9 -6.80 10.1 -4.82 8.8 -5.05 7.5 -6.21 7.4 -6.07 7.7
•KcaVmol system.
These results reveal that methylation of NH-groups both in Nl- and Nl-, N3positions resutls in a 2 to 6 kcal/mol increase in the itneraction energy between a base and water molecules in the sectors of methylation. This testifies directly to the incorrectness of the assumption (4,8,9) suggesting that the decrease in the basewater interaction energy under methylation ofUra and Thy hydrophobic groups is caused by the van der Waals interactions. Comparison of the Uwb energies in the 5th sector ofUra and Thy derivatives show that under methylation in the CS-position the energy ofUwb increases, but not decreases, as could have been expected from (4,8,9) at the expense of the increase in the number of atoms capable of participating in van der Waals interactions. It should be noted that hydrophobic group is not closed. Thus, when the uwb energy of the system decreases
Hydration of Uracil and Thymines
1173
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under methylation ofUra and its N-methylderivatives in the C5-position, this is not associated with its decrease in the 5th sector, as assumed in (4,8,9), but with the reorganization of the whole hydration shell changing the interaction with some, mainly hdyrophobic, groups of the bases. Under methylation in the Nl- and Nl-, N3-positions, the energy ofUwb in the 2nd sector (C20-group) for Ura and Thy derivatives decreases (0.5- 3.1 kcal/mol), in the 4th sector (C40-group) for Thy derivatives it also decreases (1.0- 4.0 kcal/mol), while for Ura derivatives it increases (0.6- 4.0 kcal/mol).lt is to be noted that the increase in the Uwb energy in the 4th sector ofUra derivatives is accompanied by a similar decrease in its value in the 2nd sector (in other words, these effects tend to compensate each other), whereas for Thy derivatives it decreases both in the 2nd and the 4th sectors. A great decrease in the Uwb energy in the 4th sector of m?Thy as compared to Thy and m 1Thy, leads to the fact that despite the increase in the Uwb energy in the 3rd sector 1 when m Thy is methylated, the Uwb energy for the whole system decreases a little. We have already discussed this phenomenon at the end of the previous section. The number ofwater molecules in each sector considered shows that under methylation in the Nl- and then in the N3-positions, a noticeable decrease in the number of water molecules in the 1st and the 3rd sectors is not always observed. Most often, it even increases a little. The increase in the U wb energy in the 4th sector ofUra derivatives is accompanied by a simultaneous decrease in the numberofwater molecules belonging to this sector. As a result, the energy ofUfb per water molecule in this sector (specific energy gwb) does not change at all (form Ura it even decreases a little). Under transition from Thy to 1 m Thy, gwb in the 4th sector does not change at all. But the transition from m 1Thy to m~·:>.rhy is accompanied by a very great decrease in gwb leading in its tum to some decrease in the Uwb energy for the whole subsystem, which was mentioned above. It should be mentioned that the number of water molecules in the 5th sector of Thy
and its derivatives is greater than in the 5th sector ofthe corresponding Ura derivatives, although a methyl group ofThyoccupies a much greater volume than the hydrogen atom in the 5th position ofUra. As was already mentioned, despite this fact the Uwb energy in the 5th sector of Ura derivatives is lower than in the 5th sector of Thy derivatives. It is most likely due to a greater interaction between the water molecules from the 5th sector ofUra and its derivatives, i.e., when methyl group is absent, water molecules in the 5th sector are located in space in such a way that they interact in a stronger way with the C40-group. The obtained angular distribution of the water- water interaction energy by sectors shows directly that the energy ofUww in the 5th sector has lower values for Thy and its derivatives than for Ura and its derivatives. The nub values also testify to a higher regulation in water structure around Thy and its derivatives, which is mainly caused by a spherical layer of water molecules at R = 6.3 - 7.3 A- the one nearest to a methyl group. This proves for the first time that near a hydrophobic group the regulation of water molecules increases even for such polar molecules as the bases are.
1174
Danilov & Tolokh
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The Uwb energy in the 6th sector has greater values for Ura and its derivatives than 1 for Thy and its derivatives. m Ura is an exception. The sum of the Uwb energies for the 5th and the 6th sectors ofUra and its derivatives is smaller than that of Thy and its derivatives. For Ura and Thy themselves, these values are approximately the same. Thus, the interaction energy between the base and the water molecules situated in the hydrophobic sectors is lower for Ura derivatives than for Thy derivatives. At the same time, the corresponding analysis indicates that the sum of the Uww energies for the 5th and the 6th sectors is a little lower, and the nHb values for the united region of these sectors are a little higher for Thy and its derivatives. This testifies in favor of the fact that the appearance of a hydrophobic surface of a molecule in water leads to a greater regulation of water molecules near this region. Let us consider radial distribution functions of water molecule oxygen atoms & and specific energy gwb in different base angular sectors, depending on the distance from a molecule centre. These functions are ofthe greatest interest for the sectors in which methylation of the bases takes place. Analysis of the & and ~b functions for the 1st sector ofUra shows that the first maximum ofg 0 is at the distance ofR = 4.15Aand is as great as 3.I6(Figure I a). The first maximum of the ~b function almost coincides with it(4.20 A) and amounts to -4.4I kcal/mol. Besides, there are 1.14 water molecules on the average in this sector with R = 4.3 A. Thus, it is seen that both in distance (nitrgoen atoms of uracil ring are at R = 1.0 A from the base center) and energy the water molecule situated in the region of the first maximum of the & function forms and H-bond with the NIH-group of Ura. Consideration of the & and ~b functions for the 1st sector of m 1Ura indicates (Figure I b) that near the base with R = 5.5 A, the density of water molecules does not exceed 1.0 and the maximum interaction energy between them and the base is not more than -2.3 kcal/mol. With the distance of R = 4.3 A, the water molecule forming an H-bond with the base was located at before methylation, there is only average 0.33 water molecule, whose interaction energy is Uwb = -0.4 kcal/mol. All this testifies to the fact that methylation in theN 1-position leads to a breaking of an H -bond and repulsion of the nearest water molecule included in an H-bond. Distribution of the other water molecules in this sector has also changed greatly (Figure 2). The main maximum of g0 lies in the region of R = 6.0 A and amounts to 1.9. Almost analogous changes have taken place in the lst sector of m~· 3Ura (Figure lc). The g0 and gwb functions (Figure ld) characterizing water in the lst sector of Thy show that as forUraeither, the maximum of& is atR = 4.15Aand the maximum of gwb is at R = 4.05 A. Location and intensity of these maxima testify to the fact that the H-bond between water and NIH-group is also formed in the lst sector of Thy. In contrast to Ura, however, for which in the layerofR = 3.8-4.8 A of the 1st sector 1.75
1175
Hydration of Uracil and Thymines ~
5.•"'• 2.
(a)
Ura (1 I)
•"
"',(f
t -~·
, .... (1.~.
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.. '
3
2
0
0
~.s ~
.o
3.5
s.o 2.5 2.0
1.5 1.0
0.5
.. '
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a 111ft ( 1 o)
(b)
1 ••
1. ~ 1.
~
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2
. ._. 2.2 2.0
•••
1.6 1 ... 4,2
1.0 0.1
O.d
rv
0.4
0.2 0
2
5
(\rv
.. '
0
Figure 1: Radial distribution functions of water molecules oxygen atoms&, and specific energy gwh (kcaVmol) for the 1st sector of uracil (a); 1-methyluracil (b); 1,3-dimethyluracil (c); thymine (d); 1-methylthymine (e); 1,3-dimethylthymine (f) depending of the distance from a molecule centre. Figure 1 continued on pages 1176 and 1177.
1176
Danilov & Tolokh fiiJ ( 1 •' !.S
\
~.0
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..
0
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(c)
,,,
5
,
6
D
,_r;-r
•• &
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Figure 1 continued
0 •• &
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1177
Hydration of Uracil and Thymines
..
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(e)
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Figure 1 continued
6
7
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Danilov & Tolokh
1178
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water molecules are located with Uwb = -5.1 kcal/mol, there are 2.77 water molecules with the energy ofUwb = -8.2 kcal/mol at an analogous place of Thy. This makes one assume that water molecules in the 1st sector of Thy form two H -bonds with the base. There are either two bonds including N1 H -group or one of them includes this group and the other the neighboring C20-group. Such an assumption also explains why the Uwb energy is by 3 kcal/mollower in the 1st sector of Thy (with R = 7.3 A) than in the same sector of Ura. Consideration of the distribution functions for the 1st sector of m 1Thy and m~· 3 Thy shows that they differ slightly from the corresponding functions for m 1Ura and m;· 3Ura (Figures le and 1f). In contrast to the latter ones, for Thy derivates there exist rather narrow and high maxima of the~ functions in the region of 3.5 A from the base center. In the 1st sector of m 1Thy and m~· 3 Thy there are 0.97 and 0.82 water molecules, respectively, with R = 4.3 A However, the gwb functions show that the water molecules considered interact with the bases very weakly and, hence, do not form H -bonds with them. So, the U wb energy in the 1st sector of Thy calculated with R = 4.8 A from the base center equals -8.2 kcal/mol, while the analogous energies form 1Thy and m~·3 Thy amount to only -1.2 and -1.7 kcal/mol, respectively. Thus, methylation ofThy in the N1-position leads to a destruction of about two H-bonds between water and the base, and increses the uwb energy approximately by 6 kcal/ mol in the 1st sector. The & and &vb distribution functions for the 3rd sector ofUra show(Figure 2a) thatthe water molecules belonging to this sector form an H-bond with N3H-group. One should note that unlike the 1st Ura sector, the number of water molecules is approximately 2.5 times larger in the area of the first g0 maximum for the 3rd sector (there are 2.6 molecules til14.3 A). Their Uwb energy amounts to -6.46 kcal/mol, which is approximately 1.7 times higher than the corresponding energies in the 1st Ura sector. 1
The maximum of the & function for the 3rd sector of m Ura is 0.4 A shifted from the base, as compared to the corresponding maximum for Ura, and its altitude is smaller (Figure 2b ). In addition, here, with R = 4.3 A there is only 0.96 water molecule with the Uwb energy as great as -1.4 kcal/mol. The maximum of the gwb function, however, situated at 4.1 A and equal to -2.52 kcal/mol indicates that the nearest water molecule can form an H -bond with the base in some configurations. 2.42 water molecules with Uwb = -4.4 kcal/mol are situated in the 3rd sector of m 1Ura with R = 4.8 A. The g0 function for the 3rd sector of m~3 Ura (Figure 2c) looks approximately the same as for the lstsectorofm 1Uraandm/Ura. With R = 4.8Atherisonly0.64water molecule whose energy ofUwb = -0.35 kcal/mol. This points to the fact that like the 1st sector, methylation ofN3H-group increases greatly the interaction energy between the water molecules of the 3rd sector and the base. The energy ofUwb in the 3rd sector of m~· 3 Ura (R = 7.3 A) amounts to -2.95 kcal/mol. An analogous picture is observed when considering the g0 and gwb functions for the 3rd sector of Thy, m 1Thy and m~· 3 Thy (Figures 2d-2f). In these sectors, the water
1179
Hydration of Uracil and Thymines
.,
.,. () •>
(a)
\~
I
4:.:. ~· .r)
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~
I
(1
f..t.S
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•~,;t,
,.5 ~.Q
2.5 2.0 1.5 1.0
o.:: I 0
!.0
I
.
.1v..
!
\~.-
. . . • \,r.,., .. ,/-., ,.J"
s
2
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(b)
a.s t.O 1.5 1.0 0.!1
0
•
I, A 2.!- ....
2.0 1.!1 1.0
o.s 0
2
. a,
•A
Figure 2: Radial distribution functions of water molecules oxygen atoms&, and specific energy &.m (kcaVmol) for the 3rd sector of uracil (a); 1-methyluracil (b); 1,3-dimethyluracil (c); thymine (d); 1-methylthymine (e); 1,3-dimethylthymine (I), depending on the distance from a molecule centre. Figure 2 continued on
pages 1180 and 1181.
Danilov & Tolokh
1180 ~·lura 0 •>
(c)
/'"1
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~.0
1.5
r
1.0
., t
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o~--~-----7;----~~~&c·~~~-----s~·-----&L'-----jL-
1.2
-
.. '
•
...
1.0
o.e 0.6 0 . .&1
0.2
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2
.. '
3
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•>
(d)
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~.0 ~.5
~-0
t.5 2.0
1.5 1.0 0.~
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-
7
•
•.• '
....
3.0
:.s 2.0 1.S , .IJ
O.S 0
7
Figure 2 continued
I A
Hydration of Uracil and Thymines
1181
...
·:·
(e)
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. 0~
1
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-c.. $.0 2.5 ~.I)
1 o5
1.0 Oo5
,
0
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...
:lo:l 2o0
(f)
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1.2 1.0
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{
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1
1
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~
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Figure 2 continued
1182
Danilov & Tolokh
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molecule nearest to Thy forms an obvious H -bond with the base. The same occurs in the 3rd sector of m 1Thy but the binding energy is a little smaller. The present results on the analysis of the g0 and gwb functions for the 1st and the 3rd sectors, and the data from the analogous analysis performed for the other sectors allow us to estimate the contribution of specific interactions (the interactions between the base and the layer of water moleculesimmediately bordering with it through the H-bonds or by means of electrostatic interaction) to the total Uwb energy. The water molecules responsible for the specific interactions lie in the volume ofR = 5.3 Aand lead to the Uwb energy(in kcal/mol) amounting to -27.9 for Ura, -33.3 for m 1Ura, -25.8 for m;·:rura, -37.8 for Thy, -29.4 form 1Thy and -29.6 for m~·3 Thy. Comparing these values with the results from Table I, it is seen that the contribution indicated amounts to 0.50 for U ra, 0.64 form 1U ra, 0.56 for m;· 3u ra, 0.66 for Thy, 0.57 form 1Thy and 0.58 for m~·3Thy. The data we have obtained show directly that specific interactions make a dominant contribution to the energy of Uwb· Thus, they do not confirm the conclusion of Sukhodub eta/. (2,4,9-11) that the given contribution is small. According to their estimates, it ranges from 0.14 to 0.21 for the compounds considered. The contradiction is easily explained. To estimate this contribution, the authors of (2,4,9-11) used the sum of the base hydration enthalpies in vacuum for the first two water molecules as the enthalpy of specific interactions. They assumed that in solution the water molecules responsible for the specific interactions had the same configurations as in vacuum, and the number of water molecules responsible for these interactions and the interaction energies between them and the bases did not change. Meanwhile, as a result of theoretical analysis and our previous calculations we showed (19,20) that in a large water cluster all the characteristics indicated changed essentially.
Acknowledgments We are deeply indebted to Prof. N.Y. Zheltovsky for creating a good stimulating atmosphere, G.M. Ostrovskaya for technical assistance and E.N. Bugulov for valuable advice and recommendations. References and Footnotes
1. A.B. Tep1itsky, IK Yanson, O.T. G1ukhova,A Zie1enkiewicz, W. Zie1enkiewicz and K.L. Wierzchowski, Biophys. Chern. 11,17-21 (1980). 2. L.F. Sukhodub, O.T. Glukhova, A.B. Tep1itsky, IK Yanson and K.L. Wierzchowski, in Proceedings of the International Symposium of Biochemistry, Tbi1isi, p. 65 (1981 ). 3. O.T. Glukhova, V.D. Kiselev, A.B. Teplitsky, AN. Ustyugov and IK Yanson, Biojizika (USSR) 26, 351-352 (1981). 4. A.B. Tep1itsky, O.T. G1ukhova, L.F. Sukhodub, I.K. Yanson, A. Zie1enkiewicz, W. Zie1enkiewicz, J. Kosinski and KL. Wierzchowski, Biophys. Chern. 15, 139-147 (1982). 5. O.T. G1ukhova, A.B. Tep1itsky, L.F. Sukhodub and K.L. Wierzchowski, in Porceedings of the AllUnion Biophysical Congress, (USSR), Moscow, p. 56 (1982). 6. O.T. G1ukhova, A.B. Tep1itsky, L.F. Sukhodub, A. Zie1enkiewics, W. Zie1enkiewicz and K.L. Wierzchowski, in Proceedings ofthe Third International Conference on Water and Ions in Biological Systems, Bucharest, p. 108 (1984).
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Hydration of Uracil and Thymines
1183
7. A Zielenkiewicz, W. Zielenkiewicz, L.F. Sukhodub, O.T. Glukhova, AB. Teplitsky and KL. Wierzchowski,.J. Solution Chern. 13,757-765 (1984). 8. O.T. Glukhova, Thesis for the Degree of a Candidate of Physical and Mathematical Sciences, Kharkov (1985). 9. L.F. Sukhodub, Synopsis of the Thesis for the Degree ofa Doctor ofPhysical and Mathematical Sciences, Moscow (1985). 10. L.F. Sukhodub, Preprint, 38-87, Kharkov (1987). 11. L.F. Sukhodub, Chern. Rev. 87, 589-606 (1987). 12. 0. Sinanog1u and S. Abdulnur, Fed. Proc. 24, 12-23 (1965). 13. 0. Sinanog1u, in Molecular Associations in Biology, Ed., B. Pullman, Acad. Press, New York, p. 427 (1968). 14. 0. Sinanoglu and S. Abdulnur, Photochem. and Photobiol. 3, 333-342 (1964). 15. N. Metropolis, A W. Rosenbluth, M.N. Rosenbluth, AN. Teller and E. Teller,! Chern. Phys. 21, 10871092 (1953). 16. V.B. Zhurkin, V.I. Poltev and V.L. Florentiev, Mol. Bioi. (USSR) 14, 1116-1130 (1980). 17. V.I. Poltev, V.I. Danilov, M.R Sharafutdinov, AZ. Shvartsman, N.V. Shulyupina and G.G. Ma1enkov, Stud. Biophys. 91,37-43 (1982). 18. L.P. D'yakonova and G.G. Malenkov, Zh. Struk. Khim. (USSR) 20, 854-861 (1979). 19. V.I. Danilov, M.R. Sharafutdinov and I.S. Tolokh, Stud. Biophys. 93, 193-196 (1983). 20. V.I. Danilov, in Steric Aspects ofBiomolecular Interactions, Eds., G. Naray-Szabo and K Simon, CRC Press, Boca Raton, Florida, p. 235 (1987). Date Received: July 15, 1989
Communicated by the Editor Valery I. Ivanov
