Prediction of the Absolute Aggregation Rates of Amyloidogenic Polypeptide Chains Kateri F. DuBay 1 , Amol P. Pawar 1 , Fabrizio Chiti 2 , Jesu ´ s Zurdo 1 Christopher M. Dobson 1 * and Michele Vendruscolo 1 * 1 Department of Chemistry University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK 2 Dipartimento di Scienze Biochimiche, Viale Morgagni 50, Universita ´ degli Studi di Firenze, 50134 Firenze, Italy Protein aggregation is associated with a variety of pathological conditions, including Alzheimer’s and Creutzfeldt-Jakob diseases and type II dia- betes. Such degenerative disorders result from the conversion of the nor- mal soluble state of specific proteins into aggregated states that can ultimately form the characteristic amyloid fibrils found in diseased tissue. Under appropriate conditions it appears that many, perhaps all, proteins can be converted in vitro into amyloid fibrils. The aggregation propensities of different polypeptide chains have, however, been observed to vary sub- stantially. Here, we describe an approach that uses the knowledge of the amino acid sequence and of the experimental conditions to reproduce, with a correlation coefficient of 0.92 and over five orders of magnitude, the in vitro aggregation rates of a wide range of unstructured peptides and proteins. These results indicate that the formation of protein aggre- gates can be rationalised to a considerable extent in terms of simple physico-chemical parameters that describe the properties of polypeptide chains and their environment. q 2004 Elsevier Ltd. All rights reserved. Keywords: amyloid fibrils; aggregation rates; sequence analysis; hydrophobic patterns; misfolding diseases *Corresponding authors Introduction Pathological conditions such as type II diabetes and neurodegenerative disorders such as Alzheimer’s and Creutzfeldt-Jakob diseases have been linked with the deposition in tissue of insoluble protein aggregates. 1–5 These deposits, often in the form of amyloid plaques, are largely composed of misfolded proteins that assemble to form extended fibrillar structures. 6 Despite the lack of detectable similarities among the amino acid sequences or the native structures of amyl- oidogenic proteins, amyloid fibrils from different sources share common morphological and struc- tural features. 7 Electron and atomic force microscopy have shown that amyloid fibrils are formed from protofilaments that associate laterally or twist together to form fibrils of larger diameter. 6,8 – 10 Moreover, amyloid fibrils show a common cross-b pattern in which the polypeptide chains form b-strands oriented perpendicularly to the long axis of the fibril, resulting in b-sheets pro- pagating in the direction of the fibril. 7 Although amyloid deposits were initially discovered in association with several human disorders, it has recently become apparent that a wide range of other proteins, unrelated to any known disease, can form amyloid structures in vitro when incubated under appropriate conditions. 4,11 – 13 As a consequence it has been suggested that the ability to form amyloid fibrils is a common charac- teristic of polypeptide chains, although the ease with which they form varies greatly with the sequence. 11,14,15 Given the increasing number of diseases that are recognised to be related to amyloid formation, and the apparent generic ability of natural and syn- thetic polypeptide chains to form amyloid fibrils, it is important to understand the determinants of this process. Diverse factors, both intrinsic and extrinsic to the proteins, have been reported to influence the rate of aggregation of amyloidogenic peptides and proteins. Extrinsic factors that affect the formation of protein aggregates include the interaction with cellular components such as 0022-2836/$ - see front matter q 2004 Elsevier Ltd. All rights reserved. Present address: Kateri F. DuBay, Department of Chemistry, UC Berkeley, 419 Latimer Hall, Berkeley, CA 94720-1460, USA. E-mail addresses of the corresponding authors: mv245@cam.ac.uk; cmd44@cam.ac.uk Abbreviations used: AcP, acylphosphatase. doi:10.1016/j.jmb.2004.06.043 J. Mol. Biol. (2004) 341, 1317–1326