Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides

Chemical Physics Letters 547 (2012) 89–96

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Chemical Physics Letters journal homepage: www.elsevier.com/locate/cplett

Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides Kazuya Nomura a, Akisumi Okamoto a, Atsushi Yano a, Shin’ichi Higai b, Takashi Kondo b, Seiji Kamba b, Noriyuki Kurita a,⇑ a b

Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan Murata Manufacturing Co., Ltd., 1-10-1 Higashikohtari, Nagaokakyo, Kyoto 617-8555, Japan

a r t i c l e

i n f o

Article history: Received 8 June 2012 In final form 3 August 2012 Available online 10 August 2012

a b s t r a c t Aggregation of amyloid b (Ab) peptides, which is a key pathogenetic event in Alzheimer’s disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Ab with some types of monosaccharides using molecular simulations based on protein–ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Ab and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Ab and inhibit the Ab aggregation. Ó 2012 Elsevier B.V. All rights reserved.

1. Introduction The cause and progression of Alzheimer’s disease (AD) is considered to be associated with the aggregation of amyloid b (Ab) peptides, which are 40–42 amino acid fragments of the b-amyloid precursor protein (APP) produced in nerve cells of the brain. Due to strong cohesive forces between the Ab peptides, they are easily aggregated into a fibriform neuritic plaque, which is considered to cause neuronal cell death, leading to an onset of AD. Accordingly, characterization of the Ab aggregation behavior is one of the critical issues in understanding the role of Ab in the pathogenetic process of AD. Recently, cell-surface saccharides were found to be involved in the aggregation of Ab peptides [1]. Experimental studies reported that the interactions of Ab with ganglioside (GM1) [2] and glycosaminoglycan [3] cause the Ab aggregation, resulting in a neuritic plaque. To predict the interaction between Ab and these complicated saccharides, the interactions of Ab with several monosaccharide arrays were investigated by electro-chemical experiments [4,5], indicating that Ab interacts with these monosaccharides to change its conformation into a b-sheet. In particular, the acidic saccharides having 6-sulfo-GlcNAc or sialic acid were found to interact strongly with Ab. Therefore, it seems likely that Ab shows conformation transition into a b-sheet on the saccharide-immobilization substrate, and that the aggregation of Ab peptides is induced by some specific saccharides. Cell-surface saccharides also play many important roles as a signal molecule within living organisms. Their binding to the lectin ⇑ Corresponding author. Fax: +81 532 44 6875. E-mail address: [email protected] (N. Kurita). 0009-2614/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.cplett.2012.08.010

protein is related to various vital phenomena such as adhesion and molecular recognition of cells, transmission of infectious agent, immunity and flare. It is thus possible to detect infectious agents by using the interactions of saccharides with the proteins related to the agents. The interactions depend remarkably on the chemical structure and conformation of saccharide as well as the structure of the recognition site of the target protein. To elucidate what kinds of saccharides prefer to bind to Ab, the binding affinity between Ab and various monosaccharides was investigated by the experiment [6,7], indicating that the sugar I shown in Figure 1 has the highest binding affinity to Ab, while the sugar II has the lowest affinity. As shown in Figure 1, the chemical structures of these two sugars are very similar to each other. It is thus difficult to explain the reason for this remarkable difference in binding affinity by only the difference in the chemical structures of these sugars. In the present study, to elucidate the reason for this difference, we searched stable structures for the solvated complex of Ab with sugar by molecular simulations based on protein–ligand docking and classical molecular mechanics (MM) methods. For the most stable structure determined by ab initio fragment molecular orbital (FMO) calculations, the specific interactions between Ab and the sugar were investigated at an electronic level. Based on the results, we attempted to elucidate (1) which amino acid residues of Ab are important for the binding between Ab and the sugar, (2) which parts of the sugar contribute to the binding, and (3) which types of the sugar can bind strongly to Ab. The present results may be useful in developing novel saccharides for inhibiting the Ab aggregation. These saccharides are also applicable as detecting materials of the sensor for the Ab aggregation.

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S Na+ (a) Sugar I + Na+

(b) Sugar II + Na+

(c) Sugar III + Na+

(d) Sugar IV + Na+

(e) Sugar V + Na+ Figure 1. Structures of (a) Sugar I + Na+, (b) Sugar II + Na+, (c) Sugar III + Na+, (d) Sugar IV + Na+ and (e) Sugar V + Na+ optimized by MP2/6-31G⁄⁄ in vacuum.

2. Details of calculations 2.1. Optimization of solvated structures of Ab-sugar complexes We first optimized the structures of the sugars I and II shown in Figure 1 in vacuum by using ab initio MO calculations. The MP2/631G(d,p) method implemented in the ab initio MO program package GAUSSIAN03 (G03) [8] was used. Counter ion (Na+) was added to each SO3 part of the optimized structure, and the structure of sugar + Na+ was fully optimized by the MP2/6-31G(d,p) method. The optimized structures of the sugar I and II are shown in Figure 1a and b, respectively. The sugar I has the highest binding affinity to Ab, while the sugar II has the lowest affinity [6]. This difference in binding affinity is expected to be related with the number of the polar parts SO3 . The sugar I and II have one or two SO3 part, respectively. We thus proposed novel sugars shown in Figure 1c, d and e and investigated their specific interactions to Ab. The sugar III and IV have two SO3 parts, while the sugar V has three SO3 parts. Their structures optimized in vacuum are shown in Figure 1. In the structure optimizations for the Ab-sugar complexes, we employed the classical MM method based on the AMBER99 [9] force fields. Since the AMBER99 force fields for the novel sugars are not

prepared, we analyzed charge distributions for the sugars by using the restrained electrostatic potential (RESP) method [10] in G03 [8] and prepared the atomic charge parameters in the AMBER99 force fields for the sugars. The MP2/6-31G(d,p) method in G03 was used for the RESP calculations. Other parameters in the AMBER99 force fields such as van der Waals interaction, bond length, bond angle and dihedral angle for the sugars were converted from those for molecules having similar structures. Ab is intrinsically unstructured and does not acquire a compact tertiary fold but rather populates a set of structures in solution. Since Ab cannot be crystallized easily, most of structural knowledge on Ab were obtained by NMR experiments or classical molecular dynamics (MD) simulations. The NMR-derived models for a 26-residues polypeptide Ab(10–35) show a collapsed coil structure devoid of significant secondary structure content [11]. Replica exchange MD (REMD) studies based on Amber FF99SB force field and implicit solvation model suggested that Ab(1–42) and Ab(1–40) can indeed populate multiple discrete structural states [12], whereas more recent REMD studies for Ab(1–42), in which the FF99SB force field, explicit solvation model and larger number of replicas were used, identified a multiplicity of discrete conformational clusters by statistical analysis [13]. In addition, the NMR-guided MD simulations [14] elucidated that Ab(1–40) and

K. Nomura et al. / Chemical Physics Letters 547 (2012) 89–96

Ab(1–42) seem to feature highly different conformational states, with the C-terminus of Ab(1–42) being more structured than that of Ab(1–40). It is noted that the results obtained by classical MD simulations are significantly dependent upon force fields and solvation model emplyed in the simulation. In the present study, to elucidate how the specific interactions between Ab and sugar are changed depending on the Ab structure, we first considered two types of model structures for Ab(1–42), each of which is mainly composed with a-helix or b-sheet secondary structure. The initial structure of the a-helix Ab was constructed based on the NMR structure (PDB ID: 1IYT [15]). On the other hand, as for the b-sheet Ab structure, there is an NMR structure for only the short Ab(17–42) peptide (PDB ID: 2BEG [16]). We thus modeled the structure of the 1–16 peptide by using homology modeling program MODELLER [17] and connected the modeled structure to the experimentally obtained Ab(17–42) structure. By using the above procedure, we constructed the two model structures of Ab(1–42), both of which are similar to the NMR structures [15,16]. We added solvating water molecules with a 8 Å layer around the modeled Ab structure and optimized the solvated structure by the classical MM/MD calculation program AMBER9 [18]. In the AMBER9 optimization, the AMBER99 [9] and TIP3P [19] force fields were assigned for Ab and water molecules, respectively. The threshold value of the energy-gradient for the convergence in the AMBER9 optimization was set as 0.001 kcal/mol/Å. In order to confirm the accuracy of the AMBER99 force filed, we compared the a-helix and the b-sheet Ab structures obtained by our simulations with those obtained by the previous experiments [15,16]. The root mean square deviation (RMSD) values between the optimized and the experimental structures of Ca atoms of Ab are 1.0 Å (a-Ab) and 1.2 Å (b-Ab), respectively, indicating the accuracy of AMBER99 force field for obtaining the stable structures of Ab. Since the original PDB structures [15,16] of Ab have no information about hydrogen atoms, hydrogen atoms should be added to the PDB structure in an appropriate manner. In particular, it is not unique to determine the positions of hydrogen atoms for His amino acid, because His has some different protonated structures depending on the pKa value around the His. We here evaluated the pKa values of His residues contained in Ab by using PROPKA Web Interface 2.0 [20] and determined the His protonation based on the pKa values. His amino acid has three types of protonated structures: Hid has a hydrogen atom at the d-site of its imidazole ring, Hie has a hydrogen atom at the e-site of the imidazole ring, and positively charged Hip has hydrogen atoms at both the dand e-sites. His residues with pKa value larger than 6 have the Hip protonation, while those with pKa value smaller than 6 have the Hid or Hie protonation. The Ab contains three His residues, and all of them were found to have Hip protonation. As for the other ionizable amino acid residues contained in Ab, the ionized state was used. To obtain candidate structures for the complex of Ab with sugar, we docked sugar to a variety of sites around Ab using the automated protein–ligand docking program AUTODOCK 4.2 [21]. In the docking procedure, the grid box was set as the 37.50  24.75  47.25 Å3 centered on the gravity center of the a-helix Ab, and the spacing between the nearest neighboring grid points was set to 0.375 Å, which is the default value of AUTODOCK 4.2. On the other hand, for the b-sheet Ab, the grid box was set as the 54.9  26.2  41.0 Å3 centered on the gravity center of Ab, and the spacing between the nearest neighboring grid points was set to 0.436 Å. The structures of Ab and sugar were fixed, and a rigid docking approach was employed to search stable configurations of sugar docked to Ab. The RESP charges obtained by the MP2/631G(d,p) calculation were assigned to each atom of sugar. We here created 1000 candidate structures by using the genetic algorithm

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of AUTODOCK 4.2. They were classified into some clusters according to the RMSD value (10 Å) between each of the structures created. The representative structures of all clusters were fully optimized by the AMBER9-MM method. To consider the solvation effect on the Ab-sugar complex properly, we added water molecules with a 8 Å layer around the complex and optimized the solvated structure by using AMBER9 [18], in which the AMBER99 [9] and TIP3P [19] force fields were assigned for the complex and water molecules, respectively. The threshold value of the energy-gradient for the convergence in the AMBER9 optimization was set as 0.001 kcal/ mol/Å. Finally, total energies of these optimized structures were calculated accurately by the ab initio MP2/6-31G method in FMO [22–28], and the most stable structure of the solvated Ab-sugar complex was determined. 2.2. Ab initio FMO calculations for solvated Ab-sugar complexes In the present study, we considered solvating water molecules explicitly, because these water molecules are capable of making hydrogen bonds bridging between amino acid residues of Ab and sugar, and because these hydrogen bonds are indispensable for analyzing the specific interactions between Ab and sugar. The implicit and continuum solvent model cannot consider these hydrogen bonds. In the explicit solvent model, since the electronic properties of solvated systems are sensitive to the configurations of solvating water molecules, the statistical analysis averaging over a variety of water configurations should be done in principle. However, the analysis using the ab initio FMO method is not practical at present. We considered that the existing probability of water molecules is the highest at the optimized position, although they can change their positions around the optimized position. And we analyzed the electronic properties for the optimized structure of the solvated Ab-sugar complexes, as a first step of our investigation. The electronic properties for the most stable structure of the solvated Ab-sugar complex were investigated by the ab initio FMO calculations [22–28], to elucidate which amino acid residues in Ab are important for the specific interactions between Ab and sugar. The FMO program ABINIT-MP Ver.4.3 [27,28] was used, in which the target molecule is divided into units called fragment, and the electronic properties of the target molecule are estimated from the electronic properties of the monomers and dimers of the fragments. Since the electronic properties of the dimers are calculated in FMO, we can obtain the interaction energies between specific fragments with considering the effect from the other fragments. We here performed the FMO calculations for both the a-helix and the b-sheet Ab structures combined with sugar, in order to elucidate the influence of the Ab structure on the specific interactions between Ab and sugar. From the results obtained, it can be predicted what types of sugar can detect the change in Ab structure. To investigate the relative stability among the Ab-sugar complexes and the binding energy between Ab and sugar, the number of solvating water molecules was reduced to be 664 for all the Absugar complexes, keeping the water molecules within a 8 Å from the surface of the complex. It is thus possible to determine the most stable structure among the candidate structures of the complex from the total energies evaluated by the ab initio FMO calculations. In this way, we contained the solvation effect consistently. Each amino acid residue of Ab, sugar, Na+ ion and each water molecule were assigned as a fragment, because this fragmentation enables us to evaluate the interaction energies between the amino acid residue of Ab, sugar and solvating water molecules. From the comparison of the interaction energies, it is possible to propose which amino acid residues of Ab have large contribution to the specific interactions between Ab and sugar. In the FMO calculation, ab initio MP2/6-31G(d,p) method was employed to investigate

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accurately the p–p stacking, NH–p and CH–p interactions between the amino acid residues of Ab and sugar. In addition, by considering water molecules explicitly, we attempted to elucidate the influence of solvating water molecules on the specific interactions.

Table 1 Total energies (T.E.) (kcal/mol) for the a-helix Ab + sugar complexes optimized in water by classical MM method based on AMBER99 and TIP3P force fields. The energies obtained by AMBER9 and ab initio ABINIT MP4.3 methods are compared for (a) Ab + sugar I, (b) Ab + sugar II, (c) Ab + sugar III, (d) Ab + sugar IV and (e) Ab + sugar V complexes. Cluster

T.E.

3. Results and discussion 3.1. Stable structures of the solvated Ab-sugar complexes Structures of five types of sugars + Na+ optimized by MP2/631G(d,p) are shown in Figure 1. In an initial structure of the sugar + Na+, we put Na+ at the position of equal distance from the three oxygen atoms of the SO3 part of sugar. By the full structure optimization, Na+ moves significantly to be stabilized at the different position near the other oxygen atoms of the sugar. The main reason of this change in the Na+ position seems to be related to the electrostatic attraction between Na+ and the oxygen atoms of sugar. In the sugars II, IV and V, which have two or three SO3 parts, Na+ is stabilized between the two SO3 parts, as shown in Figure 1b, d and e. To check the accuracy of the AMBER99 force field for the sugar + Na+ complexes, we optimized the structures of the complexes by AMBER99 and confirmed that the optimized structures are similar to those optimized by MP2/6-31G(d,p). The RMSD values between them are in the range between 0.1 and 0.8 Å. Structures of two types of Abs with a-helix or b-sheet secondary structure optimized by the MM method in solvating water molecules are shown in Figure S1. In the a-helix Ab, the hydrogen bonds between the CO and the NH groups of the Ab backbone stabilize the a-helix structure. On the other hand, b-sheet Ab has no hydrogen bond between the backbone, although the side chains of Lys28 and Asp23 are hydrogen bonded. As a consequence, b-sheet Ab has a bended structure shown in Figure S1b. To elucidate the difference in hydration between the a-helix and the b-sheet Abs, we analyzed the number of water molecules directly hydrogen-bonded to Ab. The number is 59 (a-helix Ab) and 109 (b-sheet Ab), respectively, indicating that hydrating state is significantly affected by the change in the Ab structure. We first docked five types of sugars to the a-helix Ab and optimized the complexes in solvating water molecules by the AMBER9MM method. In addition, their total energies were calculated by using the classical AMBER9 and the ab initio ABINIT MP programs to determine the most stable structure. Table 1 indicates that the most stable structures determined by the both programs are the same for the five complexes of the a-helix Ab with sugar. These structures are shown in Figure S2. To elucidate the specific interactions between Ab and sugar, we analyzed the amino acid residues of Ab existing within a 3 Å distance from sugar in the optimized structures. As listed in Table 2a, sugars II and IV bind to the positively charged Hip14 residue of the a-helix Ab, while the other sugars do not exist near Hip14. To investigate the effect of structural change of Ab on the specific interactions, the five sugars were docked to the b-sheet Ab (Figure S1b), and the solvated structures of Ab + sugar complexes were fully optimized by the AMBER9-MM method. Their total energies are listed in Table 3. As for the b-sheet Ab + sugar III and the b-sheet Ab + sugar V complexes, the most stable structures determined by the AMBER9-MM and the FMO methods are not identical. For these complexes, we employed the most stable structure determined by the FMO method. This result indicates that classical AMBER9-MM method, which has been widely used for determining the stable structures of biomolecules such as proteins and DNA, is sometimes insufficient for investigating the relative stability among the optimized structures of biomolecules, although their stable structures are obtained accurately by AMBER9-MM method. In particular, if there is charge transfer between Ab and sugar,

AMBER 9

ABINIT MP 4.3

DT.E.

T.E.

DT.E.

(a) Ab + sugar I 1 2 3 4 5

9599 9601 9629 9607 9597

30 28 0 22 32

42630545.3 42630520.8 42630612.2 42630591.4 42630594.9

66.9 91.4 0.0 20.8 17.3

(b) Ab + sugar II 1 2 3 4 5 6 7

10142 10073 10076 10096 10139 10101 10085

0 69 66 46 3 41 57

43026666.7 43026538.0 43026466.5 43026632.4 43026578.0 43026588.2 43026494.4

0.0 128.7 200.2 34.3 88.7 78.5 172.3

(c) Ab + sugar III 1 2 3 4

10041 10021 10103 10029

62 82 0 74

43816446.8 43816392.3 43816516.2 43816381.1

69.4 123.9 0.0 135.1

(d) Ab + sugar IV 1 10051 2 9998 3 10018 4 9998 5 10015

0 53 33 53 36

43864331.8 43864244.1 43864255.2 43864228.2 43864273.9

0.0 87.7 76.6 103.6 57.9

82 98 0 92 106 136 91

45050041.2 45050075.2 45050203.2 45050046.2 45050073.2 45050005.2 45050113.2

162 127.3 0.0 156.3 130.2 197.5 90.1

(e) Ab + sugar V 1 2 3 4 5 6 7

10453 10437 10535 10443 10429 10399 10444

Table 2 Amino acid residues of Ab existing within a 3 Å from the sugar + Na+ ion in the Ab + sugar complexes optimized in water by AMBER9. The values in parentheses are the shortest distance (Å) between sugar and each amino acid residue of Ab. Complex

Residues of Ab

(a) a-Helix Ab + Sugar Ab + Sugar Ab + Sugar Ab + Sugar

Ab + sugar I Gly33(1.6), Hip13(1.9), Leu34(2.2) II Ala42(1.6), Tyr10(1.7), Hip14(1.9), Ile41(2.5) III Leu17 (1.6), Ala 21(2.1), Val18 (2.4), Phe20 (2.4), Phe19 (3.0) IV Hip14 (1.8), Tyr10 (2.0), Ala42 (2.0), Hip13 (2.2), Ile41 (2.5), Leu34 (3.0) Ab + Sugar V Gln15 (1.9), Val18 (2.1), Phe19 (2.2) (b) b-Sheet Ab + sugar Ab + Sugar I Gln15(1.7), Asp1(1.8), Lys16(2.0), Val18(2.0), Phe19(2.0), Phe20(2.2), Hip6(2.4) Ab + Sugar II Asp23(1.6), Met35(2.0), Gly37(2.1), Leu34(2.3), Val36(2.4) Ab + Sugar III Hip13(1.8), Hip14(1.8), Leu17(2.5), Val40(2.6) Ab + Sugar IV Tyr10(1.8), Arg5(1.9), Val12(1.9), Hip14(1.9) Ab + Sugar V Tyr10(1.8), Hip14(1.8), Arg5(2.0), Val12(2.0), Gln15(2.2)

classical MM force fields cannot take it into account, and ab initio MO calculations such as FMO are indispensable for obtaining the total energy of the complex accurately. The most stable structures of the complexes with the b-sheet Ab and sugar determined by the FMO calculations are shown in Figure S3. Compared with the structures of the a-helix Ab + sugar complexes, the binding site of sugar on the b-sheet Ab varies significantly depending on the type of sugar. As listed in Table 2b, sugars III, IV and V are stabilized near the positively

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K. Nomura et al. / Chemical Physics Letters 547 (2012) 89–96 Table 3 Total energies (T.E.) (kcal/mol) for the b-sheet Ab + sugar complexes optimized in water by classical MM method based on AMBER99 and TIP3P force fields. The energies obtained by AMBER9 and ab initio ABINIT MP4.3 methods are compared for (a) Ab + sugar I, (b) Ab + sugar II, (c) Ab + sugar III, (d) Ab + sugar IV and (e) Ab + sugar V complexes. Cluster

AMBER 9 T.E.

ABINIT

DT.E.

MP

4.3

T.E.

DT.E.

(a) Ab + sugar I 1 2 3 4 5 6 7 8 9

9453 9508 9470 9522 9502 9518 9549 9450 9472

96 41 79 27 47 31 0 99 77

42630399.1 42630472.0 42630378.0 42630497.7 42630412.3 42630408.5 42630529.0 42630348.2 42630349.2

129.9 57 151 31.2 116.7 120.5 0.0 180.7 179.7

(b) Ab + sugar II 1 2 3 4 5 6 7 8

9696 9683 9660 9689 9702 9639 9628 9620

6 20 43 13 0 64 75 82

43026698.0 43026718.0 43026674.0 43026714.4 43026814.4 43026698.5 43026612.5 43026604.7

116.4 96.3 140.4 100 0.0 115.9 201.9 209.7

(c) Ab + sugar III 1 2 3 4 5 6 7 8 9

9736 9743 9790 9729 9729 9730 9777 9794 9725

58 51 4 65 66 64 17 0 69

43099534.9 43099502.8 43099593.1 43099608.8 43099595.3 43099570.0 43099653.2 43099622.5 43099531.6

118.3 150.5 60.1 44.4 57.9 83.3 0.0 30.8 121.6

(d) Ab + sugar IV 1 2 3 4 5 6 7

9713 9685 9702 9654 9690 9744 9693

31 60 42 90 55 0 52

43099623.9 43099504.6 43099570.9 43099496.9 43099554.5 43099626.8 43099525.8

3.0 122.2 55.9 130 72.4 0.0 101.0

(e) Ab + sugar V 1 2 3 4 5 6 7 8

9978 9943 9932 9989 9980 9947 9936 9872

10 46 57 0 9 41 53 117

43568771.6 43568736.8 43568684.5 43568814.8 43568848.9 43568775.2 43568748.9 43568662.4

77.3 112.1 164.4 34.1 0.0 73.7 100 186.4

charged Hip14 residue, as in the complex with the a-helix Ab and sugars II and IV. On the other hand, sugar I is stabilized near the other positively charged residues Lys16 and Hip6, and sugar II is stabilized near the negatively charged Asp23 residue. The reason for these specific interactions will be explained in the next subsection based on the electronic states of these complexes. From the comparison of the optimized structures of two Abs, it is elucidated that the b-sheet Ab is more extended than the a-helix Ab, and that each side chain of the b-sheet Ab has a free space around it. It is thus expected that sugar can bind to more variety of sites on the b-sheet Ab compared with the a-helix Ab. 3.2. Electronic properties of solvated Ab-sugar complexes calculated by FMO To elucidate the binding affinity between Ab and sugar, we evaluated the binding energy between Ab and sugar for the most stable structures determined by the FMO calculations. Table 4 lists the total energies for the solvated Ab + sugar complexes, solvated Ab, solvated sugars and solvating water molecules, and the binding energies (B.E.) estimated from these total energies. The previous experiment [6] indicated that the sugar I has the highest binding affinity to Ab, while the sugar II has the lowest affinity. The present results (Table 4a) calculated for the a-helix Ab + sugar complexes indicate that the B.E. of sugar I is smaller than that of sugar II, being not consistent with the experimental results which indicate higher binding affinity of sugar I to Ab compared with sugar II. In contrast, the results (Table 4b) for the b-sheet Ab + sugar complexes indicate that the B.E. between Ab and sugar I is 19 kcal/mol larger than that between Ab and sugar II. This result is comparable with the experimental results. In addition, the comparison between Table 4a and b elucidates that the B.E. between Ab and sugar for the b-sheet structure is larger than that for the a-helix structure, indicating that the b-sheet Ab can bind sugar more strongly. To elucidate the specific interactions between Ab and sugar, we moreover investigated the interaction energies (I.E.) between each amino acid residue of Ab and sugar for the most stable structures of the complexes with the a-helix Ab and sugar by the ab initio FMO method. As shown in Figure 2a, in the a-helix Ab + sugar I complex, Hip13 and Leu34 interact strongly with sugar I. These residues are hydrogen bonded to the SO3 or OH group of sugar I, as shown in Figure S4a. In the a-helix Ab + sugar II complex (Figure 2b), the positively charged Hip14 has large attractive interaction, while the negatively charged Glu11 has large repulsive interaction. Figure S4b indicates that the side chain of Hip14 and the NHSO3 group of sugar II are hydrogen bonded, and that the COO group of Glu11 and the SO3 group of sugar II are located near each other.

Table 4 Total energies (T.E.)(kcal/mol) for solvated Ab + sugar complexes, solvated Ab, solvated sugar and solvating water molecules, and estimated binding energies (B.E.) (kcal/mol) between Ab and sugar obtained by FMO calculations. Complex

T.E Complex + water

B.E. AB + water

Sugar + water

Water

(a) a-Helix Ab + sugar Ab + sugar I Ab + sugar II Ab + sugar III Ab + sugar IV Ab + sugar V

42630612.2 43026666.7 43099648.1 43099634.4 43568682.5

41626464.6 41626196.4 41626253.2 41626199.4 41626116.5

32728457.3 33124518.5 33197483.7 33197509.0 33666506.0

31724357.4 31724106.3 31724152.1 31724119.1 31723985.1

47.7 58.1 63.3 45.1 45

(b) b-Sheet Ab + sugar Ab + sugar I Ab + sugar II Ab + sugar III Ab + sugar IV Ab + sugar V

42630529.0 43026814.4 43099653.2 43099626.8 43568848.9

41626384.6 41626375.1 41626306.0 41626258.8 41626232.8

32727678.5 33123993.1 33196772.9 33196648.7 33665891.4

31723613.6 31723614.2 31723502.1 31723349.8 31723421.4

79.4 60.4 76.4 69.1 146

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K. Nomura et al. / Chemical Physics Letters 547 (2012) 89–96

40

(a) 20 0 -20

Leu34 -40

Hip13

-60

40

(b)

Glu11 20 0

Interaction energy [kcal/mol]

-20 -40

Hip14 -60

10

(c)

0 -10

Ala21

-20 -30 -40

Val18

-50 10

(d)

0 -10 -20 -30

Hip14

Ala42

-40 -50

10

(e)

0 -10 -20

Gln15

Phe19

-30 -40 -50 0

6

12

18

24

30

36

42

Amino acid residues Figure 2. Interaction energies between sugar and each amino acid residue of ahelix Ab; (a) Sugar I, (b) Sugar II, (c) Sugar III, (d) Sugar IV and (e) Sugar V.

In a similar way, sugar IV interacts specifically to Hip14, as shown in Figure 2d. In addition, the sugar IV interacts attractively with the COO terminal of Ala42. This strong interaction comes from the negative charge of COO terminal, because Ala42 is not hydrogen bonded to sugar IV, as shown in Figure S4d. Therefore, we eliminate Ala42 from the important residues for the sugar IV binding.

As shown in Figure 2c, the specific interactions between the ahelix Ab and sugar III are remarkably different from the other sugars. Sugar III interacts strongly with the non-charged Val18 residue of Ab. The OH group of sugar III makes a hydrogen-bond with the oxygen atom of the Val18 backbone, as shown in Figure S4c. In addition, the NH group of the Ala21 backbone has a hydrogen bond with the SO3 group of sugar III. In this way, non-charged Val18 and Ala21 residues of Ab can contribute to the specific interactions with sugar III. As for the sugar V, Figure 2e indicates the strong attractive interactions between sugar V and non-charged residues Gln15 and Phe19 of Ab. Figure S4e shows that the NH2 group of Gln15 and the SO3 group of sugar V are hydrogen bonded, and that the side chain of Phe19 is stacked to sugar V. This stacking structure seems to create the attractive interaction between Phe19 and sugar V. As described above, in the complexes with a-helix Ab and five types of sugars, sugars I, II and IV interact mainly with the charged residues of Ab, while sugars III and V have attractive interactions with non-charged residues. This difference is likely to be related with the positions of the SO3 groups of sugar. In general, the binding affinity between Ab and sugar becomes higher, as the SO3 group of sugar comes closer to the positively charged residues of Ab. However, the side chains of the a-helix Ab are so crowded that the bulky SO3 group of sugar cannot easily come closer to the positively charged parts of Ab. In particular, the sugar V composed of three SO3 groups is stabilized near the non-charged residues as listed in Table 2a. To elucidate how is the specific interactions between Ab and sugar affected by the change in Ab structure, we investigated the interaction energies between the b-sheet Ab and the five types of sugars. As shown in Figure 3, the specific interactions depend more significantly on the types of sugars compared with the a-helix Ab + sugar complexes. It seems that this dependence comes from the more extended structure of the b-sheet Ab, which has more sites acceptable for sugar binding. As shown in Figure 3c, d and e, the specific interactions between the b-sheet Ab and the sugar III, IV and V are similar to each other. These sugars interact strongly with the positively charged residues Hip13 or Hip14. In addition, the sugars IV and V have strong attractive interaction with Try10, as shown in Figure 3d and e. The sugar V particularly has large (100 kcal/mol) attractive interaction with Try10. To elucidate the reason of this strong interaction, we analyzed the structure around the sugar V. As shown in Figure 4, the two SO3 groups of sugar V are both located near the side chain of Tyr10, and one of the SO3 groups makes a hydrogen bond with the OH group of the Tyr10 side chain. In addition, Na+ ion bridges between the SO3 groups and the OH group of Tyr10 to enhance the attractive interaction between sugar V and Tyr10. It is thus expected that Na+ ion may contribute significantly to the binding between Ab and sugar. In contrast, sugar I is hydrogen bonded with the oxygen atom of Lys16 backbone, the side chain of Hip6 and the NH3+ terminal of Asp1, as shown in Figure S5a. These residues of the b-sheet Ab have strong attractive interactions to sugar I, as indicated in Figure 3a. Figure 3b elucidates that sugar II interacts to the different residues from the other sugars. Non-charged Met35 and Val36 residues of Ab contribute to the specific interactions between the b-sheet Ab and sugar II. As shown in Figure S5b, sugar II is hydrogen bonded with the Met35 side chain and the oxygen atom of Val36 backbone. As described above, the binding affinity as well as the specific interactions between Ab and sugar is significantly affected by the change in Ab structure. In particular, as listed in Table 4, the B.E. between the b-sheet Ab and sugar V is about three time as large as that between the a-helix Ab and sugar V. Accordingly, sugar V can be used as a detecting material of the sensor for the conformational change of Ab. In the b-sheet Ab + sugar V complex shown in

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10

(a)

Tyr10

0

1.8Å 2.5

-20 -30 -40

Hip14

3.6

-10

Asp1 Hip6

2.5 2.3

Lys16 1.8

-50

Sugar V

10

(b)

0 -10 -20

Met35 Val36

Interaction energy [kcal/mol]

-30 -40 -50

10

(c)

0

Figure 4. Interacting structure between sugar V and Tyr10 and Hip14 residues of the b-sheet Ab. Green dot-lines indicate hydrogen bonds, while purple dot-lines indicate the interactions between Tyr10 side chain and the SO3 parts of sugar V bridged by Na+ ion.

SO3 group of sugar cannot come closer to Ab, because of the steric hindrance between the SO3 group and the side chain. This structural difference of Abs is expected to cause the significant difference in the binding affinity and specific interactions between Ab and sugar.

-10

4. Conclusions

-20 -30

Hip13

-40

Hip14

-50 10

(d)

0 -10 -20

Tyr10

-30

Hip14

-40 -50

20

(e)

0

We here investigated the specific interactions between Ab (1– 42) and sugar for the two types of Ab structures as well as the five kinds of sugars (Figure 1) by ab initio molecular simulations, in which protein–ligand docking, classical molecular mechanics and ab initio fragment molecular orbital methods were used. The results elucidate the following points. (1) Specific interactions between Ab and the sugars are significantly dependent on the Ab structure. (2) The b-sheet Ab binds sugars more strongly than the a-helix Ab, because the b-sheet Ab has an extended structure to make it easy for the SO3 groups of sugar to come closer to the positively charged residues of Ab. (3) The sugar V (Figure 1e) composed of three SO3 groups binds most strongly to the b-sheet Ab through the specific interactions shown in Figure 4. (4) Among the 42 amino acid residues of Ab, the positively charged residue Hip14 is important for the binding between Ab and many kinds of sugars.

-20

Hip14

-40 -60 -80

Tyr10

-100 0

6

12

18

24

30

36

42

Amino acid residues Figure 3. Interaction energies between sugar and each amino acid residue of bsheet Ab; (a) Sugar I, (b) Sugar II, (c) Sugar III, (d) Sugar IV and (e) Sugar V.

It is noted that the present results were obtained for only the two types of Ab structures, each of which was constructed based on the experimental structures [15,16] and composed mainly of a-helix or b-sheet secondary structure. Since Ab is very flexible to have a variety of structures, classical molecular dynamics simulations combined with replica exchange method are underway now to search the stable structures of Ab more widely. For the several stable Ab structures obtained by the simulations, the specific interactions between Ab and sugars will be investigated. The results will be useful for proposing novel compounds inhibiting the Ab aggregation. Acknowledgments

Figure 4, all of three SO3 groups contribute to the interactions to the b-sheet Ab, because the extended structure of the b-sheet Ab makes it possible for the bulky SO3 groups to be located near Ab. On the other hand, in the a-helix Ab + sugar complexes, the Ab side chains are located near each other, so that the bulky

We would like to thank Prof. Y. Miura for very useful discussion about the binding affinity between Ab and various monosaccharides. The present work was supported by JSPS Grant-in-Aid for Challenging Exploratory Research (No. 22 650 061), the grants from the

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Murata Science Foundation, the Iketani Science and Technology Foundation, the Tatematsu Foundation and the CASIO Science Promotion Foundation. Appendix A. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.cplett.2012.08. 010. References [1] Y. Miura, K. Yasuda, K. Yamamoto, M. Koike, Y. Nishida, K. Kobayashi, Biomacromolecules 8 (2007) 2129. [2] A. Kakio, S.I. Nishimoto, K. Yanagisawa, Y. Kozutsumi, K. Matsuzaki, Biochemistry 41 (2002) 7385. [3] J. McLaurin, T. Franklin, X. Zhang, J. Deng, P.E. Fraser, Eur. J. Biochem. 266 (1999) 1101. [4] J. McLaurin, P.E. Fraser, Eur. J. Biochem. 267 (2000) 6353. [5] Y. Miura, T. Yamauchi, H. Sato, T. Fukuda, Thin Solid Films 516 (2008) 2443. [6] E. Matsumoto, T. Yamauchi, T. Fukuda, Y. Miura, Sci. Technol. Adv. Mater. 10 (2009) 034605. [7] Y. Miura, M. Koike, Y. Nishida, PCT/JP2006/302281, 2006. [8] M.J. Frisch, et al., GAUSSIAN 03 (Revision D.01), GAUSSIAN Inc., Pittsburgh, USA (2003). [9] W. Cornell, P. Cieplak, C. Bayly, I. Gould, K. Merz, D. Ferguson, D. Spellmeyer, T. Fox, J. Caldwell, P.A. Kollman, J. Am. Chem. Soc. 117 (1995) 5179. [10] B. Besler, K. Merz, P. Kollman, J. Comput. Chem. 11 (1990) 431. [11] S. Zhang, K. Iwata, M.J. Lachenmann, J.W. Peng, S. Li, E.R. Stimson, Y. Lu, A.M. Felix, J.E. Maggio, J.P. Lee, J. Struct. Biol. 130 (2000) 130.

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