The effect of curcumin on the stability of Aβ. dimers

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1 The effect of curcumin on the stability of Aβ dimers Li Na Zhao, See-Wing Chiu, Jérôme Benoit, Lock Yue Chew,, and Yuguang Mu, School of Physical and Mathematical Sciences, Nanyang Technological University, Beckman Institute, University of Illinois, Urbana, Illinois, and School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore To whom correspondence should be addressed Nanyang Technological University University of Illinois Nanyang Technological University S1

2 Figure S1: The snapshot of the dimer at the end of the set 2 simulation. The dimer was represented as cartoon (β-sheet: yellow; helix: purple; for the others from peptide A: tv_green; for the others from pepitde B: tv_blue). S2

3 Figure S2: The initial M0-10 models. The secondary structure of dimer was represented as transparent cartoon (β -sheet: yellow; α-helix: purple; others for peptide A: tv_blue; others for peptide B: tv_green). The curcumin was shown as stick and colored by element (C: yellow; H: grey; O: red). For the residues from peptide A involved in the contacts with curcumin was represented as stick and colored by element (C: marine; N: blue; H: grey; O: red). For the residues from peptide B involved in the direct contact with curcumin was also represented as stick and colored by the similar element except C atom was colore as green to distinguish from peptide A. Please note for those Cα atom exits in the β -sheet part was colored as yellow, and purple for the Cα atom in α-helix part. S3

4 Figure S3: The initial M11-20 models. The secondary structure of dimer was represented as transparent cartoon (β -sheet: yellow; α-helix: purple; others for peptide A: tv_blue; others for peptide B: tv_green). The curcumin was shown as stick and colored by element (C: yellow; H: grey; O: red). For the residues from peptide A involved in the contacts with curcumin was represented as stick and colored by element (C: marine; N: blue; H: grey; O: red). For the residues from peptide B involved in the direct contact with curcumin was also represented as stick and colored by the similar element except C atom was colore as green to distinguish from peptide A. Please note for those Cα atom exits in the β -sheet part was colored as yellow, and purple for the Cα atom in α-helix part. S4

5 Table S1: Calculated pka value for titratable residues. Residues pka values N-terminus 7.9 AspNT 2.4 Glu Arg His Asp Tyr Glu His His Lys Glu Asp Lys C-terminus 4.4 S5

6 Figure S4: Evolution of the secondary structure of protein in the presence of keto-enol conformers and the controlled group M0. S6

7 Table S2: Simulation System β-diketone tautomers keto-enol tautomers Binding Energy Binding Energy Model ID Potential binding sites Rank Water molecules Model ID Potential binding sites Rank Water molecules kcal/mol kcal/mol M1 M2 A: LEU-34 A: LEU-34, ILE M11 B :HIS-14 α, PHE-19 β B: HIS-14 α A: VAL-12 B: ILE M12 β, LEU-34 B: ARG-5, ALA-21 β MET-35 β M3 A: PHE-20, VAL M13 M A: LEU-17, PHE-19 β VAL-39 B: ARG-5, ALA-21 β M14 B: GLY-38, VAL-40 β GLY-38 β, VAL-40 M5 B: HIS-14 α, LEU-17 B: GLU-3, HIS M15 PHE-19 SER-8 B: ILE-32 β, LEU-34 B: ILE-32 β, LEU-34 M M16 MET-35 β MET-35 β A: HIS-14 α, LEU-17 M7 A: LEU-17, PHE-19 β M17 PHE-19 β, ALA-21 α M8 A: ARG-5, VAL M18 A: TYR-10, VAL-12 B: GLU-3 A: ALA-2 β, PHE-4 M9 B: ARG M19 ARG-5, HIS-16 M10 A: HIS-14, LEU-17 A: ASP M20 PHE-19 B: GLY-25 β M indicates NULL. α indicates residue sites on α-helix. β indicates residue sites on β-sheet S7

Figure S5: Time evolution of the number of residues in β-structure (β-sheet and β-bridge) of peptide A (black line) and B (colored by red) and the contact numbers

8 Figure S5: Time evolution of the number of residues in β-structure (β-sheet and β-bridge) of peptide A (black line) and B (colored by red) and the contact numbers between peptide A and B (colored by magenta). The data were extracted from each 11 model trajectories and averaged per 4 ns. The contact number were divided by 100. S8

9 Figure S6: The secondary structure propensity of Aβ residues in the presence and absence of curcumin. S9

10 Figure S7: The π-π stacking propensity of Aβ residues His, Tyr and Phe with curcumin R1 and R2 respectively. S10

11 Table S3: The occurence of dehydron. The occurence of dehydron pairs occurence B: (24V, 27N) 292 A: (24V, 27N) 222 B: (11E, 15Q) 157 B: (34L, 41I) 150 (A: 40V, B: 28K) 133 A:(30A, 37G) 124 A:(11E, 15Q) 110 B:(12V, 16K) 98 A:(22E, 29G) 89 A:(12V, 16K) 53 B:(22E, 29G) 52 A:(6H, 12V) 51 (A:38G, B:41I) 49 A:(23D, 27N) 45 A:(23D, 28K) 44 A:(5R, 9D) 42 (A:36V, B:39V) 37 B:(1D, 15Q) 35 A:(22E, 27N) 35 (A:3E, B:24V) 34 (A:41I, B:28K) 33 (A:1D, B:26S) 32 (A:1D, B:27N) 31 A:(7D, 10Y) 31 A:(28K, 35G) < 30 S11

12 [ moleculetype ] ; Name nrexcl CUR 3 Table S4: The curcumin topology [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 CUR C OA 1 CUR O C 1 CUR C CR1 1 CUR C HC 1 CUR H C 1 CUR C OA 1 CUR O H 1 CUR H CR1 1 CUR C HC 1 CUR H CR1 1 CUR C HC 1 CUR H C 1 CUR C C 1 CUR C C 1 CUR C C 1 CUR C OA 1 CUR O H 1 CUR H C 1 CUR C C 1 CUR C O 1 CUR O C 1 CUR C C 1 CUR C C 1 CUR C CR1 1 CUR C HC 1 CUR H CR1 1 CUR C HC 1 CUR H CR1 1 CUR C HC 1 CUR H C 1 CUR C OA 1 CUR O H 1 CUR H C 1 CUR C OA 1 CUR O CH3 1 CUR C [ bonds ] ; ai aj fu c0, c1, ; O4 C ; C19 O ; C19 C ; C19 C ; C20 H ; C15 C ; C18 O ; C18 C ; O5 H ; C17 H ; C17 C ; C16 H ; C15 C ; C15 C ; C14 C ; C12 C ; C12 O ; C12 C ; O3 H ; C10 C ; C10 O ; C10 C ; C9 C ; C4 C ; C4 C ; C4 C ; C3 H31 S12

13 ; C2 C ; C5 H ; C5 C ; C6 H ; C7 C ; C7 O ; C7 C ; O2 H ; C2 O ; O1 C1 [ pairs ] ; ai aj fu c0, c1, ; C21 C ; C21 C ; O4 H ; O4 O ; O4 C ; O4 C ; C19 H ; C19 H ; C19 C ; C19 C ; C20 O ; C20 C ; C20 H ; C20 C ; H20 C ; H20 C ; H20 C ; C18 H ; C18 C ; O5 H ; O5 C ; H52 C ; C17 C ; H17 H ; H17 C ; C16 C ; H16 C ; C15 C ; C14 O ; C14 C ; C13 H ; C13 C ; C12 O ; C12 C ; O3 C ; H32 C ; C11 C ; C10 C ; O6 C ; C9 C ; C9 C ; C8 H ; C8 H ; C8 C ; C8 C ; C4 H ; C4 C ; C4 O ; C3 H ; C3 C ; C3 O ; C3 C ; H31 C ; H31 C ; H31 O ; C5 O ; C5 C ; H51 H ; H51 C ; C6 H ; C6 O1 S13

14 ; H6 O ; H6 C ; C7 C ; O2 O ; H22 C2 [ angles ] ; ai aj ak fu c0, c1, ; C21 O4 C ; O4 C19 C ; O4 C19 C ; C20 C19 C ; C19 C20 H ; C19 C20 C ; H20 C20 C ; C19 C18 O ; C19 C18 C ; O5 C18 C ; C18 O5 H ; C18 C17 H ; C18 C17 C ; H17 C17 C ; C17 C16 H ; C17 C16 C ; H16 C16 C ; C20 C15 C ; C20 C15 C ; C16 C15 C ; C15 C14 C ; C14 C13 C ; C13 C12 O ; C13 C12 C ; O3 C12 C ; C12 O3 H ; C12 C11 C ; C11 C10 O ; C11 C10 C ; O6 C10 C ; C10 C9 C ; C9 C8 C ; C8 C4 C ; C8 C4 C ; C3 C4 C ; C4 C3 H ; C4 C3 C ; H31 C3 C ; C4 C5 H ; C4 C5 C ; H51 C5 C ; C5 C6 H ; C5 C6 C ; H6 C6 C ; C6 C7 O ; C6 C7 C ; O2 C7 C ; C7 O2 H ; C3 C2 C ; C3 C2 O ; C7 C2 O ; C2 O1 C1 [ dihedrals ] ; ai aj ak al fu c0, c1, m, ; imp C19 O4 C20 C ; imp C20 C19 C15 H ; imp C18 C17 O5 C ; imp C17 C18 C16 H ; imp C16 C17 C15 H ; imp C15 C14 C16 C ; imp C12 C11 O3 C ; imp C10 C9 O6 C ; imp C4 C8 C5 C ; imp C3 C4 C2 H ; imp C5 C4 C6 H51 S14

15 ; imp C6 C5 C7 H ; imp C7 C6 O2 C ; imp C2 C3 O1 C ; imp C19 C20 C15 C ; imp C20 C15 C16 C ; imp C15 C16 C17 C ; imp C16 C17 C18 C ; imp C17 C18 C19 C ; imp C18 C19 C20 C ; imp C4 C3 C2 C ; imp C3 C2 C7 C ; imp C2 C7 C6 C ; imp C7 C6 C5 C ; imp C6 C5 C4 C ; imp C5 C4 C3 C ; dih C18 C19 O4 C ; dih C19 C18 O5 H ; dih C13 C14 C15 C ; dih C12 C13 C14 C ; dih C11 C12 C13 C ; dih C13 C12 O3 H ; dih C10 C11 C12 C ; dih C9 C10 C11 C ; dih C8 C9 C10 C ; dih C4 C8 C9 C ; dih C5 C4 C8 C ; dih C6 C7 O2 H ; dih C3 C2 O1 C1 S15

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