Probing the Initial Stage of Aggregation of the Ab 10-35 -protein: Assessing the Propensity for Peptide Dimerization Bogdan Tarus 1 , John E. Straub 1 * and D. Thirumalai 2,3 * 1 Department of Chemistry Boston University, Boston MA 02215, USA 2 Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA 3 Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA Characterization of the early stages of peptide aggregation is of fundamental importance in elucidating the mechanism of the formation of deposits associated with amyloid disease. The initial step in the pathway of aggregation of the Ab-protein, whose monomeric NMR structure is known, was studied through the simulation of the structure and stability of the peptide dimer in aqueous solution. A protocol based on shape complementarity was used to generate an assortment of possible dimer structures. The structures generated based on shape complementarity were evaluated using rapidly computed estimates of the desolvation and electrostatic interaction energies to identify a putative stable dimer structure. The potential of mean force associated with the dimerization of the peptides in aqueous solution was computed for both the hydrophobic and the electrostatic driven forces using umbrella sampling and classical molecular dynamics simulation at constant temperature and pressure with explicit solvent and periodic boundary conditions. The comparison of the two free energy profiles suggests that the structure of the peptide dimer is determined by the favorable desolvation of the hydrophobic residues at the interface. Molecular dynamics trajectories originating from two putative dimer structures indicate that the peptide dimer is stabilized primarily through hydrophobic interactions, while the conformations of the peptide monomers undergo substantial structural reorganization in the dimeriza- tion process. The finding that the 4-dimer may constitute the ensemble of stable Ab 10-35 dimer has important implications for fibril formation. In particular, the expulsion of water molecules at the interface might be a key event, just as in the oligomerization of Ab 16-22 fragments. We conjecture that events prior to the nucleation process themselves might involve crossing free energy barriers which depend on the peptide–peptide and peptide–water interactions. Consistent with existing experimental studies, the peptides within the ensemble of aggregated states show no signs of formation of secondary structure. q 2004 Elsevier Ltd. All rights reserved. Keywords: Alzheimer’s disease; amyloid b-protein; dimer; molecular dynamics simulation; potential of mean force *Corresponding authors Introduction Amyloid b-protein (Ab) is involved in the pathogenesis of Alzheimer’s disease (AD). 1,2 Early studies illustrated the presence of amyloid plaques in the human brain of AD victims, and these conglomerates have been related to the evolution of AD. 3 It is still not established whether amyloid protein aggregates, fibrils or plaques are causative agents of the pathological manifestations or whether they are only collateral products of this disease. 3 However, the toxic influence of the amyloid plaques on the proximate neurons has been demonstrated. 4–6 Recent studies have found that the neurotoxicity may be provoked even by 0022-2836/$ - see front matter q 2004 Elsevier Ltd. All rights reserved. Abbreviations used: Ab, amyloid b-protein; AD, Alzheimer’s disease; LMW, low molecular weight; PMF, potential of mean force; RMSD, root-mean-square displacement; CD, circular dichroism; ACE, atomic contact energy; DCOM, distance between centers-of- mass. E-mail addresses of the corresponding authors: straub@bu.edu; thirum@glue.umd.edu doi:10.1016/j.jmb.2004.11.022 J. Mol. Biol. (2005) 345, 1141–1156