1

Flexibility of the Flap in the Active Site of BACE1 as Revealed by Crystal Structures and MD simulations

Yechun Xu, Minjun Li, Harry Greenblatt, Wuyan Chen, Aviv Paz, Orly Dym, Yoav Peleg, Tiantian Chen, Xu Shen, Jianhua He, Hualiang Jiang, Israel

Silman, Joel L Sussman

SUPPLEMENTARY MATERIAL

Table S1 PDB code, unit cell parameters, space group, total number of BACE1 monomers in the unit cell (Z), the calculated Matthew coefficient and the

solvent content of the 145 structures of apo BACE1 structures and structures of inhibitor complexes

.

PDB ID

Conformation

number* a b c Space

group Z

Matthew

Coefficient

(A3/D)

Solvent

content

(%)

1ym4(Hanessian et al., 2005) 1,2,3 90.00 100.32 90.00 223.68 107.75 61.47 C121 12 2.82 56

2hm1(Freskos, Fobian, Benson,

Moon et al., 2007)

4

90.00 94.99 90.00 72.99 104.88 50.06 C121 4 2.22 45

2iqg(Maillard et al., 2007) 5 90.00 94.81 90.00 73.09 105.08 50.50 C121 4 2.25 45

2q11(Baxter et al., 2007) 6,7 90.00 102.94 90.00 235.90 108.50 63.10 C121 12 3.05 60

2qu2(Fobare et al., 2007) 8 90.00 95.00 90.00 72.92 104.85 50.48 C121 4 2.24 45

2qu3(Fobare et al., 2007) 9 90.00 95.29 90.00 72.09 103.84 50.02 C121 4 2.17 43

2zdz(Cole et al., 2008) 10 90.00 94.98 90.00 73.31 105.21 51.00 C121 4 2.28 46

2ze1(Cole et al., 2008) 90.00 94.57 90.00 73.03 104.32 50.47 C121 4 2.23 45

2zjk(Yang et al., 2009) 90.00 103.34 90.00 233.15 108.55 64.09 C121 12 3.06 60

3ckp(Park et al., 2008) 11,12,13 90.00 101.47 90.00 224.06 105.65 63.70 C121 12 2.86 57

2

3ckr(Park et al., 2008) 14,15,16 90.00 100.87 90.00 224.46 108.13 61.13 C121 12 2.82 56

3h0b(Stachel et al., 2009) 17,18,19 90.00 99.47 90.00 221.18 107.44 65.08 C121 12 2.96 58

3hvg(Godemann et al., 2009) 20,21,22 90.00 103.73 90.00 232.55 100.13 64.78 C121 12 2.84 57

3hw1(Godemann et al., 2009) 23(A),24(C) 90.00 103.12 90.00 230.62 99.88 62.90 C121 12 2.73 55

3igb(Malamas et al., 2009) 90.00 94.69 90.00 73.14 104.33 49.55 C121 4 2.2 44

3in3(Malamas, Barnes, Johnson

et al., 2010)

25

90.00 94.79 90.00 73.38 104.85 50.53 C121 4 2.25 45

3in4(Malamas, Barnes, Johnson

et al., 2010)

90.00 94.79 90.00 73.38 104.85 50.53 C121 4 2.25 45

3ind(Malamas, Erdei et al., 2010) 26 90.00 94.69 90.00 73.14 104.33 49.55 C121 4 2.2 44

3ine(Malamas, Erdei et al., 2010) 90.00 94.69 90.00 73.14 104.33 49.55 C121 4 2.2 44

3inf(Malamas, Erdei et al., 2010) 90.00 94.69 90.00 73.14 104.33 49.55 C121 4 2.2 44

3inh(Malamas, Erdei et al., 2010) 90.00 94.69 90.00 73.14 104.33 49.55 C121 4 2.2 44

3ivh(Sealy et al., 2009) 27 90.00 95.25 90.00 72.92 105.18 51.03 C121 4 2.27 46

3l38(Malamas, Barnes, Hui et al.,

2010)

90.00 95.04 90.00 72.25 103.69 49.98 C121 4 2.17 43

3l3a(Malamas, Barnes, Hui et al.,

2010)

28

90.00 94.88 90.00 72.23 103.25 49.78 C121 4 2.15 43

3lhg(Zhou et al., 2010) 29 90.00 94.89 90.00 72.91 104.63 50.26 C121 4 2.22 45

3msj(Madden et al., 2010) 30,31,32 90.00 103.36 90.00 229.20 98.83 63.13 C121 12 2.7 54

1tqf(Coburn et al., 2004) 33 90.00 90.00 90.00 104.92 128.18 76.27 C2221 8 2.98 59

2b8l(Stachel et al., 2006) 34 90.00 90.00 90.00 104.68 127.92 76.12 C2221 8 2.96 58

2b8v(Stachel et al., 2006) 35 90.00 90.00 90.00 104.90 127.40 76.40 C2221 8 2.97 59

2irz(Rajapakse et al., 2006) 36 90.00 90.00 90.00 104.53 127.78 76.47 C2221 8 2.97 59

2is0(Rajapakse et al., 2006) 37 90.00 90.00 90.00 104.67 127.91 76.12 C2221 8 2.96 58

2ntr(McGaughey et al., 2007) 38 90.00 90.00 90.00 103.92 128.18 76.46 C2221 8 2.96 58

2oah(Stauffer et al., 2007) 39 90.00 90.00 90.00 104.75 126.99 76.41 C2221 8 2.95 58

3

2p8h(Barrow et al., 2007) 40 90.00 90.00 90.00 104.57 127.29 76.08 C2221 8 2.94 58

2ph6(Lindsley et al., 2007) 41 90.00 90.00 90.00 103.79 127.13 76.21 C2221 8 2.92 58

2ph8(Moore et al., 2007) 42 90.00 90.00 90.00 103.81 128.52 76.28 C2221 8 2.96 58

2qzk(Moore et al., 2007) 43 90.00 90.00 90.00 103.68 127.50 76.41 C2221 8 2.94 58

2qzl(Coburn et al., 2006) 44 90.00 90.00 90.00 104.93 128.15 76.31 C2221 8 2.98 59

2wjo(Nicholls et al., 2010) 45 90.00 90.00 90.00 93.18 126.55 105.80 C2221 8 3.63 66

2zjm(Yang et al., 2009) 46 90.00 90.00 90.00 103.64 127.84 76.56 C2221 8 2.95 58

3exo(Steele et al., 2009) 47 90.00 90.00 90.00 104.43 127.92 76.67 C2221 8 2.98 59

3fkt(Barrow et al., 2008) 48 90.00 90.00 90.00 103.74 128.04 76.77 C2221 8 2.96 59

1fkn(Hong et al., 2000) 49,50 90.00 101.36 90.00 53.65 85.85 109.24 P1211 4 2.87 57

1sgz(Hong & Tang, 2004) 51,52,53,54 90.00 97.27 90.00 86.16 130.81 88.65 P1211 8 2.88 57

1xn2(Turner et al., 2005) 55,56,57,58 90.00 97.71 90.00 86.22 130.78 88.74 P1211 8 2.88 57

1xn3(Turner et al., 2005) 59,60,61,62 90.00 97.27 90.00 86.16 130.87 88.57 P1211 8 2.88 57

1ym2(Hanessian et al., 2005) 63,64,65 90.00 104.12 90.00 82.26 103.26 100.62 P1211 6 3.21 62

2f3e(Hanessian et al., 2006) 66,67,68 90.00 103.04 90.00 82.24 103.78 100.96 P1211 6 3.25 62

2f3f(Hanessian et al., 2006) 69,70,71 90.00 103.03 90.00 82.25 103.20 101.00 P1211 6 3.24 62

2fdp(Yang et al., 2006) 72,73,74 90.00 103.21 90.00 81.19 102.19 99.53 P1211 6 3.12 61

2g94(Ghosh et al., 2006) 75,76,77,78 90.00 97.39 90.00 86.63 131.02 88.24 P1211 8 2.89 57

2hiz(Freskos, Fobian, Benson,

Bienkowski et al., 2007)

79,80,81

90.00 103.46 90.00 82.24 104.09 100.95 P1211 6 3.26 62

2p4j(Ghosh et al., 2007) 82,83,84,85 90.00 97.48 90.00 86.93 129.97 87.48 P1211 8 2.85 57

2p83(Kortum et al., 2007) 86,87,88 90.00 104.12 90.00 81.96 103.35 101.01 P1211 6 3.22 62

2vkm(Ghosh et al., 2008) 89,90,91,92 90.00 97.41 90.00 86.70 130.31 87.71 P1211 8 2.86 57

3dm6(Back et al., 2008) 93,94,95 90.00 103.50 90.00 83.43 103.02 103.11 P1211 6 3.34 63

3duy(Machauer, Veenstra et al.,

2009)

96,97,98

90.00 103.64 90.00 82.54 103.06 100.60 P1211 6 3.22 62

3dv1(Machauer, Laumen et al., 99,100,101 90.00 103.66 90.00 82.03 102.94 99.92 P1211 6 3.18 61

4

2009)

3dv5(Machauer, Laumen et al.,

2009)

102,103,104

90.00 103.72 90.00 81.66 103.35 99.47 P1211 6 3.16 61

3i25(Bjorklund, Adolfsson et al.,

2010)

105,106,107

90.00 103.53 90.00 81.42 102.48 100.19 P1211 6 3.15 61

3ivi(Sealy et al., 2009) 108,109,110 90.00 104.83 90.00 82.71 104.48 100.62 P1211 6 3.26 62

3ixj(Bjorklund, Oscarson et al.,

2010)

111,112,113

90.00 103.42 90.00 81.91 102.71 100.42 P1211 6 3.19 61

3ixk(Wangsell et al., 2010) 114,115,116 90.00 103.32 90.00 81.84 103.07 100.50 P1211 6 3.2 62

3k5c(Lerchner et al., 2010) 117,118,119 90.00 104.44 90.00 81.75 103.19 100.14 P1211 6 3.17 61

3k5d(Hanessian et al., 2010) 120,121,122 90.00 104.16 90.00 82.55 101.30 102.22 P1211 6 3.21 62

3k5f(Hanessian et al., 2010) 123,124,125 90.00 102.53 90.00 82.65 103.71 101.82 P1211 6 3.3 63

3k5g(Hanessian et al., 2010) 126,127,128 90.00 103.94 90.00 81.40 103.41 99.81 P1211 6 3.16 62

3kyr(Wangsell et al., 2011) 129,130,131 90.00 102.90 90.00 81.76 102.77 101.43 P1211 6 3.22 62

3n4l(Truong et al., 2010) 132,133,134 90.00 104.63 90.00 83.05 105.58 101.57 P1211 6 3.34 63

3nsh(Probst et al., 2010) 135,136,137 90.00 104.50 90.00 82.15 104.59 100.15 P1211 6 3.23 62

1m4h(Hong et al., 2002) 138,139 90.00 90.00 90.00 86.45 88.79 130.95 P212121 8 2.92 58

2qk5(Iserloh, Wu et al., 2008) 140,141 90.00 90.00 90.00 86.49 89.20 131.15 P212121 8 2.94 58

2qmd(Iserloh, Wu et al., 2008) 142,143 90.00 90.00 90.00 86.45 89.21 131.05 P212121 8 2.94 58

2qmf(Iserloh, Wu et al., 2008) 144,145 90.00 90.00 90.00 86.65 89.24 130.96 P212121 8 2.94 58

2qmg(Iserloh, Pan et al., 2008) 146,147 90.00 90.00 90.00 86.55 89.29 130.75 P212121 8 2.94 58

2qp8(Iserloh, Wu et al., 2008) 148,149 90.00 90.00 90.00 86.45 89.08 131.03 P212121 8 2.93 58

2vie(Clarke et al., 2008b) 150 90.00 90.00 90.00 47.92 75.85 104.53 P212121 4 2.21 44

2vij(Beswick et al., 2008) 151 90.00 90.00 90.00 47.95 76.73 105.29 P212121 4 2.25 45

2viy(Clarke et al., 2008a) 152 90.00 90.00 90.00 48.80 76.86 104.01 P212121 4 2.27 46

2viz(Clarke et al., 2008a) 153 90.00 90.00 90.00 48.74 76.97 104.22 P212121 4 2.27 46

2vj6(Clarke et al., 2008b) 154 90.00 90.00 90.00 48.48 76.76 104.89 P212121 4 2.27 46

5

2vj7(Clarke et al., 2008b) 155 90.00 90.00 90.00 48.33 77.21 103.93 P212121 4 2.25 45

2vj9(Clarke et al., 2008b) 156 90.00 90.00 90.00 49.04 77.23 104.82 P212121 4 2.31 46

2vnm(Charrier et al., 2008) 157 90.00 90.00 90.00 47.95 76.22 104.49 P212121 4 2.22 45

2vnn(Charrier et al., 2008) 158 90.00 90.00 90.00 48.47 76.70 104.17 P212121 4 2.25 45

2wez(Charrier, Clarke et al.,

2009a)

159

90.00 90.00 90.00 48.53 76.76 104.43 P212121 4 2.26 46

2wf0(Charrier, Clarke et al.,

2009a)

160

90.00 90.00 90.00 48.37 76.71 104.18 P212121 4 2.25 45

2wf1(Charrier, Clarke, Demont et

al., 2009)

161

90.00 90.00 90.00 48.18 77.00 104.24 P212121 4 2.25 45

2wf2(Charrier, Clarke, Demont et

al., 2009)

162

90.00 90.00 90.00 48.69 75.92 104.63 P212121 4 2.25 45

2wf3(Charrier, Clarke, Demont et

al., 2009)

163

90.00 90.00 90.00 48.45 76.87 104.48 P212121 4 2.26 46

2wf4(Charrier, Clarke et al.,

2009b)

164

90.00 90.00 90.00 48.52 76.63 104.74 P212121 4 2.26 46

2xfi(Clarke et al., 2010) 165 90.00 90.00 90.00 48.33 76.95 104.69 P212121 4 2.26 46

2xfj(Clarke et al., 2010) 166 90.00 90.00 90.00 48.48 76.76 104.89 P212121 4 2.27 46

2xfk(Clarke et al., 2010) 167 90.00 90.00 90.00 47.86 76.85 104.47 P212121 4 2.23 45

2zhr(Shimizu et al., 2008) 168,169 90.00 90.00 90.00 86.33 89.91 130.79 P212121 8 2.95 58

2zjj(Yang et al., 2009) 90.00 90.00 90.00 47.21 93.29 100.33 P212121 4 2.57 52

3cib(Cumming et al., 2008) 170,171 90.00 90.00 90.00 86.68 89.43 131.45 P212121 8 2.96 58

3cic(Cumming et al., 2008) 172,173 90.00 90.00 90.00 86.40 89.04 130.70 P212121 8 2.92 58

3cid(Cumming et al., 2008) 174,175 90.00 90.00 90.00 86.30 89.13 130.59 P212121 8 2.92 58

3kmx(Wang et al., 2010) 176,177 90.00 90.00 90.00 86.39 89.33 131.22 P212121 8 2.94 58

3kmy(Wang et al., 2010) 178,179 90.00 90.00 90.00 86.40 89.29 131.07 P212121 8 2.94 58

3kn0(Wang et al., 2010) 180(B) 90.00 90.00 90.00 86.45 89.74 131.26 P212121 8 2.96 58

6

3l58(Zhu et al., 2010) 181,182 90.00 90.00 90.00 86.46 89.34 131.17 P212121 8 2.95 58

3l59(Zhu et al., 2010) 183,184 90.00 90.00 90.00 86.30 89.22 131.01 P212121 8 2.93 58

3l5b(Zhu et al., 2010) 90.00 90.00 90.00 86.17 89.43 130.95 P212121 8 2.93 58

3l5c(Zhu et al., 2010) 90.00 90.00 90.00 86.26 89.33 130.84 P212121 8 2.93 58

3l5d(Zhu et al., 2010) 185(B) 90.00 90.00 90.00 86.23 89.22 130.60 P212121 8 2.92 58

3l5e(Zhu et al., 2010) 186(A) 90.00 90.00 90.00 86.48 89.47 130.65 P212121 8 2.94 58

3l5f(Zhu et al., 2010) 187,188 90.00 90.00 90.00 86.31 89.03 130.78 P212121 8 2.92 58

3lnk(Cumming et al., 2010) 90.00 90.00 90.00 86.36 89.37 131.51 P212121 8 2.95 58

3lpi(Cumming et al., 2010) 189,190 90.00 90.00 90.00 86.43 89.45 131.35 P212121 8 2.95 58

3lpj(Cumming et al., 2010) 191,192 90.00 90.00 90.00 86.33 89.05 130.89 P212121 8 2.93 58

3lpk(Cumming et al., 2010) 193,194 90.00 90.00 90.00 86.51 89.93 131.15 P212121 8 2.97 59

1w50(Patel et al., 2004) 195 90.00 90.00 120.00 103.24 103.24 169.11 P6122 12 3.03 59

1w51(Patel et al., 2004) 196 90.00 90.00 120.00 102.35 102.35 168.00 P6122 12 2.95 58

2of0(Murray et al., 2007) 197 90.00 90.00 120.00 102.41 102.41 169.24 P6122 12 2.98 59

2ohk(Murray et al., 2007) 198 90.00 90.00 120.00 102.89 102.89 168.31 P6122 12 2.99 59

2ohl(Murray et al., 2007) 199 90.00 90.00 120.00 102.83 102.83 168.85 P6122 12 3 59

2ohm(Murray et al., 2007) 200 90.00 90.00 120.00 101.17 101.17 170.92 P6122 12 2.94 58

2ohn(Murray et al., 2007) 201 90.00 90.00 120.00 102.39 102.39 170.23 P6122 12 3 59

2ohp(Congreve et al., 2007) 202 90.00 90.00 120.00 102.54 102.54 169.06 P6122 12 2.98 59

2ohq(Congreve et al., 2007) 203 90.00 90.00 120.00 102.69 102.69 169.06 P6122 12 2.99 59

2ohr(Congreve et al., 2007) 204 90.00 90.00 120.00 101.03 101.03 172.33 P6122 12 2.95 58

2ohs(Congreve et al., 2007) 205 90.00 90.00 120.00 101.30 101.30 170.35 P6122 12 2.93 58

2oht(Congreve et al., 2007) 206 90.00 90.00 120.00 103.19 103.19 169.05 P6122 12 3.02 59

2ohu(Congreve et al., 2007) 207 90.00 90.00 120.00 102.16 102.16 168.38 P6122 12 2.95 58

2q15(Baxter et al., 2007) 208 90.00 90.00 120.00 102.35 102.35 169.71 P6122 12 2.98 59

2va5(Edwards et al., 2007) 209 90.00 90.00 120.00 102.14 102.14 168.26 P6122 12 2.95 58

2va6(Edwards et al., 2007) 210 90.00 90.00 120.00 102.97 102.97 167.28 P6122 12 2.98 59

7

2va7(Edwards et al., 2007) 211 90.00 90.00 120.00 102.69 102.69 168.34 P6122 12 2.98 59

2zhs(Shimizu et al., 2008) 212 90.00 90.00 120.00 103.00 103.00 170.63 P6122 12 3.04 60

2zht(Shimizu et al., 2008) 213 90.00 90.00 120.00 102.59 102.59 171.16 P6122 12 3.02 59

2zhu(Shimizu et al., 2008) 214 90.00 90.00 120.00 102.93 102.93 172.29 P6122 12 3.06 60

2zhv(Shimizu et al., 2008) 215 90.00 90.00 120.00 102.33 102.33 170.52 P6122 12 3 59

2zjh(Yang et al., 2009) 90.00 90.00 120.00 103.60 103.60 168.74 P6122 12 3.04 60

2zji(Yang et al., 2009) 90.00 90.00 120.00 103.31 103.31 168.01 P6122 12 3.01 59

2zjl(Yang et al., 2009) 90.00 90.00 120.00 104.09 104.09 167.98 P6122 12 3.05 60

2zjn(Yang et al., 2009) 90.00 90.00 120.00 103.99 103.99 167.08 P6122 12 3.03 59

3bra(Kuglstatter et al., 2008) 216 90.00 90.00 120.00 102.97 102.97 170.49 P6122 12 3.03 59

3buf(Kuglstatter et al., 2008) 217 90.00 90.00 120.00 102.84 102.84 169.27 P6122 12 3 59

3bug(Kuglstatter et al., 2008) 218 90.00 90.00 120.00 103.50 103.50 167.62 P6122 12 3.01 59

3buh(Kuglstatter et al., 2008) 219 90.00 90.00 120.00 102.49 102.49 170.06 P6122 12 3 59

3msk(Madden et al., 2010) 220 90.00 90.00 120.00 102.51 102.51 170.53 P6122 12 3.01 59

3msl(Madden et al., 2010) 221 90.00 90.00 120.00 100.19 100.19 172.84 P6122 12 2.91 58

3s2o(Madden et al., 2010) 222 90.00 90.00 120.00 101.88 101.88 170.18 P6122 12 2.91 58

*The number of the conformation used in Figure 4. The letter inside the () refers to a chain label in each pdb code.

8

Figure S1 LIGPLOT representations of the interactions of the inhibitor with the enzyme in the previously deposited structure of the complex obtained

by soaking the ligand BSIIV into BACE1 (pdb code 2b8l), space group C2221. H-bonds are shown as dashed lines, and hydrophobic interactions are

denoted by eyelashes.

9

Figure S2 1/2 plot for Y71. The data plotted were obtained from 222 BACE1 conformations extracted from 145 depositions in the PDB. Each

triangle represents one conformation.

10

Figure S3 Molecular representation of the interface near the flap in structures 3msj (A), 2b8l (B), 1fkn (C), 3duy (D, E, and F), 2g94 (G and H), 2qp8

(I), and 1w50 (J). The flap (residues 67-75) is colored red. The area of each interface and the two monomers which contribute to the interface are

displayed. The orientation at which maximal visibility of the flap is achieved has been selected for each representation.

A (719.8 A2)

chains B and C

B (512.9 A2)

chain A and copy (-x+1/2,-y+1/2,z-1/2)

C (222.6 A2)

chain A and copy (-x+1,y-1/2,-z)

D (430.2 A2)

E (400.2 A2)

F (334.6 A2)

11

chains B and A chain C and copy (-x,y-1/2,-z) chain C and copy (-x+1,y-1/2,-z+1 )

G(407.4 A2)

chain B and copy (-x+1,y-1/2,-z+1)

H (216.8 A2)

chain A and copy (-x+1,y-1/2,-z+1)

I (188.1 A2)

chains B and A

J (1690.6 A2)

chain A and copy (x,x-y,-z+1/6)

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12

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