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1 Chrstopher Lockhart and Dmtr K. Klmov Molecular nteractons of Alzhemer's bomarker FDDNP wth A peptde Supportng Materals Parameterzaton of FDDNP molecule: CHARMM General Force Feld (CGenFF verson 2b6) was used to generate the parameters for FDDNP molecule [1]. CGenFF mplemented through the ParamChem web nterface produced FDDNP force feld parameters usng exstng parameterzatons of analogous chemcal structures. FDDNP atom charges were adjusted to keep the net charge of the compound as zero. The mass of alphatc monofluoro atom was manually changed to account for the mass of 18 F sotope. CHARMM MD program compled wth CGenFF was then used to dentfy the mssng parameters and energetcally mnmze the fnal molecular structure. Convergence of REMD smulatons: The convergence of REMD samplng was tested usng several methods descrbed n our prevous studes ([2] and ref. [40] n the man text). Below we evaluate REMD convergence for the system consstng of A monomer and 10 FDDNP lgands (system S1), although smlar results were obtaned for the system contanng three lgands (system S2). Frst, we have computed the number N s of unque states (E p,c) sampled at least once n the course of smulatons. Each state (E p,c) s determned by the potental energy E p and the number of ntrapeptde sde chan contacts, C. The energy nterval used to dscretze potental energes s 2 kcal/mol, whereas the full range of E p s approxmately 10,000 kcal/mol. The number N s as a functon of the cumulatve equlbrum smulaton tme sm s shown n Fg. S1. It s seen that N s starts to level off at sm >1.0 s ndcatng that REMD samplng gradually exhausts new states. To test the convergence of samplng of lgand bndng, we have consdered the states (E p,l), where L s the number of bound lgands. The number of unque states (E p,l) ndcate that REMD smulatons start to revst already sampled states at sm >0.6 s. Exhauston of the new states observed for two ndependent quanttes probng peptde conformatonal ensemble and lgand bndng suggests the convergence of REMD smulatons. To perform the second test of REMD convergence we computed the replca mxng parameter m(t) ntroduced by Han and Hansmann [3] m T 1, t t 2 where t s the total number of REMD steps spent by the replca at the REMD temperature T. If the total number of replcas s N=40 and all replcas are equally represented at the temperature T, m T 1 1/ N Then f constant m(t) 0.84 s observed for all REMD temperatures, t would ndcate effcent mxng of replcas over temperatures and no evdence of ther trappng at any temperature. Fg. S2 shows that m(t) s ndeed approxmately constant and equal to 0.8 for all REMD temperatures. S1

2 Fg. S1 The number N s of the unque states (E p,c) as a functon of the cumulatve equlbrum smulaton tme sm (contnuous lne). Dotted lne represents N s computed for the states (E p,l). Data are for the system S1. Mxng of replcas over temperatures s drectly vsualzed n Fg. S3. Ths fgure demonstrates random walk of replcas over temperatures as prescrbed by REMD. Fnally, we checked REMD convergence by dvdng the smulaton data nto two equal subsets and analyzng them separately. The thermodynamc quanttes probng A monomer structure from the two subsets dffered by no more than 4% at 330K. The errors n the quanttes descrbng lgand-peptde nteractons dd not exceed 16%. Correspondng errors for the system contanng three FDDNP lgands were wthn 10 and 17%. Fg. S2 Replca mxng parameter m(t) as a functon of REMD temperatures T. S2

3 Fg. S3 Random walk of replcas over temperatures n REMD trajectory for the system S1. Colors n the rght scale represent nstantaneous dstrbuton of replcas over temperatures at the begnnng of the REMD trajectory. Changes n polar accessble surface areas of amno acds and FDDNP bndng: We have computed changes n the relatve polar accessble surface areas (ASA) < pasa()> of amno acds caused by lgand bndng. Fg. S4 shows < pasa()> together wth the number of lgand-amno acd contacts <C l ()>. Lack of correlaton between < pasa()> and <C l ()> ndcates that the nteractons wth polar atoms do not play a sgnfcant role n FDDNP bndng. Fg. S4 The plot compares changes n the relatve polar ASA < pasa()> of amno acds (black crcles) wth the numbers of contacts formed by A sde chans wth FDDNP lgands, <C l ()> (shaded bars). The plot s computed at 330K for hgh lgand concentraton. S3

4 FDDNP molecules penetrate the core of A peptde: To explore the spatal dstrbuton of FDDNP lgands around A we computed the number denstes for varous atoms g(r) as a functon of the dstance to A center of mass r. Fg. S5 shows that the number densty of peptde atoms g p (r) rapdly decays reachng half of ts g p (0) value at r=r c (=10Å), whch we nterpret as the boundary of A core. Our computatons ndcate that about 59% of hydrophobc amno acds are confned to the core. The lgand number densty g l (r) also presented n Fg. S5 ndcates that some lgands penetrate A core. Indeed, t follows from Fg. S5 that 23% of lgand atoms are localzed n the core. Therefore, although most of FDDNP lgands concentrate around A core (the nset to Fg. S5), a notceable fracton resdes nsde ts core. Ths result can be expected, because A core contans large fracton of hydrophobc atoms and FDDNP bndng s manly governed by hydrophobc effect. Fg. S5 Number densty of A atoms g p (r) as a functon of the dstance to A center of mass r (thck black lne). Number densty of FDDNP atoms g l (r) s gven by thn lne. The nset presents the fracton of lgand atoms g l (r)/(g l (r)+g p (r)) vs r. Dashed vertcal lnes ndcate the boundary of A core. The fgure s obtaned for hgh lgand concentraton at 330K. Rgdty of A backbone s affected by R1-R2 ntrapeptde nteractons: Formaton of R1-R2 nteractons sgnfcantly enhances the rgdty of A backbone. As an llustraton consder Fg. S6, whch dsplays two dstrbutons of standard devatons of backbone dhedral angles, () and (), computed for the cases when R1-R2 nteractons are formed or broken. If R1-R2 nteractons are formed (.e., at least one contact n bold n Table 2 s establshed), the average of and n the sequence regon (15-24) s 36(±5). However, f R1-R2 nteractons are broken, ths average ncreases to 48(±1). The sequence regon wth the stff backbone (15-24) approxmately concdes wth the regon of elevated turn content n Fg. 4a. S4

5 R1-R2 off R1-R2 on Fg. S6 Dstrbutons of fluctuatons n A backbone measured by the standard devatons n backbone dhedral angles () (flled bars) and () (shaded bars) as a functon of sequence poston. The lower and upper panels are computed wth R1-R2 nteractons formed or dsrupted. The lst of R1-R2 nteractons s gven n bold n Table 2. The sequence regon wth stff backbone s boxed n the lower panel. The plots are obtaned for hgh lgand concentraton at 330K. Tertary structure of A monomer n lgand free water: To evaluate the changes n A tertary structure nduced by FDDNP we have computed the map of contacts <C(,j)> between A sde chans and j n lgand free water (Fg. S7). Ths fgure shows numerous local nteractons ( j- <5) and few long range contacts formed between the resdues near the central hydrophobc cluster (Phe19, Val24) and n the C-termnal (Gly29, Ileu31, Val34, Met35). The dstrbuton of long range (tertary) ntrapeptde nteractons n lgand free water s sharply dfferent from those observed at low or hgh FDDNP concentratons (Fgs. 4b and 5c). Fg. S7 Contact map <C(,j)> vsualzes the probabltes of formng sde chan contacts between resdues and j n lgand free water at 330K (<j). The map s computed usng REMD samplng of A monomer (ref. [40] n the man text). Local contacts ( j- <5) are shown above the man dagonal,.e., for those j<. S5

6 Testng the secondary structure dstrbuton n A peptde: Usng STRIDE program we have shown that FDDNP bndng does not change sgnfcantly the secondary structure of A peptde. To test ths concluson we have appled another commonly used program for secondary structure analyss, DSSP (ref. [48] n the man text). Fg. S8 compares the fractons of helx <h()>, turn <t()>, bend <s()>, and random col <rc()> formed by resdues at hgh FDDNP concentraton and n lgand free water. It s clear that apart from the sequence regon around Gln15 the dstrbutons are smlar. The average fractons of helx structure <h> n S1 and lgand free water are 0.11 and 0.13, respectvely. For turn <t>, random col <rc>, and bend <s> fractons the correspondng approxmate values are 0.25 and 0.23, 0.41 and 0.44, 0.21 and Hence, DSSP predcts mnor redstrbuton of secondary structure wth some ncrease n bend propensty near Gln15. Note that STRIDE, whch does not dstngush bend, predcts enhancement of turn structure n the same regon (Fg. 4a). Wth respect to lgand free water the RMSD values for the helx, turn, random col, and bend structures formed by ndvdual amno acds are 0.05, 0.07, 0.14, and 0.10, whch are smlar to those computed usng STRIDE. Therefore, DSSP and STRIDE suggest that FDDNP bndng causes mnor changes n A secondary structure. Fg. S8 Dstrbutons of A secondary structure computed usng DSSP at 330K: fractons of helx <h()>, turn <t()>, bend <s()>, and random col <rc()> structures formed by A resdues n hgh FDDNP concentraton soluton and n lgand free water are shown n black and grey, respectvely. Supportng references 1. Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shm, J., Daran, E., Guvench, O., Lopes, P., Vorobyov, I., and MacKerell, A. D., CHARMM general force feld: A force feld for drug-lke molecules compatble wth the CHARMM all-atom addtve bologcal force felds. J. Comp. Chem. 31: Km, S., Takeda, T., and Klmov, D.K., Globular state n the olgomers formed by Abeta peptdes J. Chem. Phys. 132: S6

7 3. Han, M., and Hansmann, U. H. E., Replca exchange molecular dynamcs of the thermodynamcs of fbrl growth of Alzhemer s A 42 peptde. J. Chem. Phys. 135: S7