Journal of Peptide Science J. Pept. Sci. 2006; 12: 780–789 Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/psc.813 Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides INTA LIEPINA, a * SALVADOR VENTURA, b CEZARY CZAPLEWSKI c and ADAM LIWO c a Latvian Institute of Organic Synthesis, Riga, LV1006, Latvia b Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, E-08193 Bellaterra, Spain c Faculty of Chemistry, University of Gdansk, 80-952 Gdansk, Poland Received 31 July 2006; Revised 27 September 2006; Accepted 28 September 2006 Abstract: Molecular dynamics (MD) simulations were carried out for two-strand and ten-strand β-sheets constructed from two peptides corresponding to the diverging turn of two homologous Abl-SH3 domains, DLSFMKGE (MK; from Drosophila) and DLSFKKGE (KK; from man), in explicit water at the temperatures of 30, 170/190 and 300 K. It was found that the 2 × MK β-sheet is more stable than the 2 × KK β-sheet, and that the 10 × MK β-sheet is more stable than the 10 × KK β-sheet; this suggests that the MK systems are fibril-creating and the KK systems are not. These results might explain why most SH3 domains possess two conserved basic residues at the diverging turn, which may act as gatekeepers in order to avoid aggregation. Copyright  2006 European Peptide Society and John Wiley & Sons, Ltd. Keywords: amyloid; amyloid peptides; amyloid formation; molecular dynamics; β-sheet INTRODUCTION Amyloidosis is deposition of soluble proteins as insoluble fibrils or other supramolecular structures in living organisms. The mechanism of amyloid formation is still unclear and it has become one of the leading subjects of biomolecular research. Amyloid formation and deposition is connected with conformation-related diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Finnish familial amyloidosis, type II diabetes, and the prion-related diseases. No sequence or structural similarities are apparent among any of the proteins that display the ability to form amyloids. In spite of this diversity, all amyloid fibrils display similar features regardless of their source: (i) they are long, straight and unbranched fibrils; (ii) they bind to dyes, such as Congo Red and Thioflavin-T (Th-T), and (iii) X-ray fibril diffraction studies have indicated that they all exhibit a cross-β -structure. In the last few years, globular proteins unrelated to any known human disease have been found to be converted into amyloid fibrils in vitro. These nonpathogenic proteins have become paradigmatic models to study protein aggregation. One of the most extensively studied amyloidogenic proteins not related to any classical amyloid disease is the SH3 domain from PI3 kinase [1,2]. In globular proteins, amyloidogenesis starts neces- sarily with a total or partial unfolding [3–6]. After protein misfolding, short-peptide sequences may act * Correspondence to: I. Liepina, Latvian Institute of Organic Synthesis, Riga, LV1006, Latvia; e-mail: inta@osi.lv as the ‘hot spots’ that provide the driving force for pro- tein aggregation in amyloid fibrils [7–11]. These regions are usually in the inner hydrophobic core in native pro- teins, but in unfolded proteins they become exposed to solvent and ready to establish intermolecular contacts [7–11]. Previously, we identified and characterized in detail one of these ‘hot spots’ in the diverging turn of the PI3-SH3 domain. The diverging turn is a member of a particular subset of type IIβ turns and forms part of the folding nucleus of SH3 domains. The diverging turn of PI3-SH3 shows a number of unusual features compared to the rest of the proteins in the family. First, while most SH3 proteins have two consecutive basic residues at the diverging turn (usually two Lys), in PI3-SH3 one of these positions is occupied by Leu, which appears exposed to solvent in the native struc- ture of the domain. This finding is extremely unusual, given that only 10% of the SH3 sequences shows a hydrophobic residue at this position. The presence of this unusual residue converts this sequence into an aggregation of ‘hot spot’. In contrast, Spectrin SH3, a protein domain with a canonical diverging turn, does not form amyloid fibrils under any of the conditions we have so far explored. We have shown that these sequential differences account, at least partially, for the different amyloidogenicity of these two domains. On the basis of a homology search, we have identified an aggregation-prone region in the same structural element of the related Abl-SH3 domain of Drosophila, with the sequence DLSFMKGE (hereafter referred to as [MK]), whereas the human homologous region with the canonical sequence DLSFKKGE (hereafter referred to as [KK]) is predicted to be less amyloidogenic, as is the case with the Spectrin SH3 domain. Preliminary Copyright  2006 European Peptide Society and John Wiley & Sons, Ltd.