proteins STRUCTURE O FUNCTION O BIOINFORMATICS Comparing the folding free-energy landscapes of Ab42 variants with different aggregation properties Simon Mitternacht, 1,2 Iskra Staneva, 1 Torleif Ha ¨rd, 3 and Anders Irba ¨ck 1 * 1 Computational Biology and Biological Physics, Lund University, So ¨lvegatan 14A, SE-223 62 Lund, Sweden 2 Department of Informatics, University of Bergen, PB 7803, N-5020 Bergen, Norway 3 Department of Molecular Biology, Swedish University of Agricultural Sciences (SLU), Box 590, SE-751 24 Uppsala, Sweden INTRODUCTION The amyloid-b peptide is the dominant component of amyloid plaques in the brains of patients with Alzheimer’s disease (AD). Understanding the formation and character of different Ab aggregates, from oligomers to amy- loid fibrils, and their roles in AD is currently the focus of intense research efforts. Ab is present in two major forms, Ab40 and Ab42, with 40 and 42 resi- dues, respectively. Of these, Ab42 is most strongly linked to AD. Ab42 is also more neurotoxic 1–3 and aggregates more rapidly into oligomers, pro- tofibrils, and fibrils. 4–7 Some familial early-onset forms of AD are associated with single amino acid mutations of Ab. It is well known from in vitro studies that such mutations can significantly alter the propensity of Ab to aggregate. It is not obvious, however, how much one can learn from in vitro aggregation studies about the behavior of Ab under complex in vivo conditions. This issue was recently addressed by studies of Drosophila flies expressing different Ab42 variants. 8,9 A clear correlation was found between a variant’s in vitro aggregation rate and its influence on fly lon- gevity and locomotion. A first step toward a molecular understanding of Ab aggregation is to characterize the Ab monomer. The solution behavior of Ab has been studied by both NMR 10–12 and atomic-level computer simulations. 13–17 The NMR results suggest that Ab40 and Ab42 both are largely unstructured in aqueous solution. 10–12 The main difference seems to be that Ab42 is more rigid than Ab40 at the C-terminus. 12 This conclusion is supported by explicit water molecular dynamics simulations at the microsecond time scale. 16 Another region of Ab that might be crucial for its aggregation properties is the segment 21–30, which has been identified as a protease-resistant part of the molecule. 18 NMR 18 and computational 19–21 studies found the excised Ab(21–30) fragment to adopt a bend structure in solution. It was further found that several familial AD mutations reduce the stability of this bend. 22,23 Simon Mitternacht’s current address is Department of Informatics, University of Bergen, PB 7803, N-5020 Bergen, Norway *Correspondence to: A. Irba ¨ck, Computational Biology and Biological Physics, Lund University, So ¨lvegatan 14A, SE-223 62 Lund, Sweden Received 13 April 2010; Revised 12 May 2010; Accepted 14 May 2010 Published online 24 May 2010 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/prot.22775 ABSTRACT The properties of the amyloid-b peptide that lead to aggregation associated with Alzheimer’s disease are not fully under- stood. This study aims at identifying conformational differences among four variants of full-length Ab42 that are known to display very different aggrega- tion properties. By extensive all-atom Monte Carlo simulations, we find that a variety of b-sheet structures with dis- tinct turns are readily accessible for full-length Ab42. In the simulations, wild type (WT) Ab42 preferentially pop- ulates two major classes of conforma- tions, either extended with high b-sheet content or more compact with lower b- sheet content. The three mutations stud- ied alter the balance between these classes. Strong mutational effects are observed in a region centered at resi- dues 23–26, where WT Ab42 tends to form a turn. The aggregation-accelerat- ing E22G mutation associated with early onset of Alzheimer’s disease makes this turn region conformationally more diverse, whereas the aggregation-deceler- ating F20E mutation has the reverse effect, and the E22G/I31E mutation reduces the turn population. Comparing results for the four Ab42 variants, we identify specific conformational proper- ties of residues 23–26 that might play a key role in aggregation. Proteins 2010; 78:2600–2608. V V C 2010 Wiley-Liss, Inc. Key words: amyloid-b; mutations; all atom; implicit solvent; Monte Carlo; J- coupling constants; chemical shifts. 2600 PROTEINS V V C 2010 WILEY-LISS, INC.