Amyloid Toxicity of Misfolded Amyloidogenic Peptides

Misfolding vs. Amyloid Diseases

The aggregation of proteins is normally tightly controlled,and misfolded proteins are generally removed by the proteosome before aggregation of the misfolded protein can occur. For reasons not clearly understood, in some individuals this degradation process breaks down and misfolded proteins accumulate in insoluble protein aggregates as time progresses. Out of the many proteins within the human genome, a small but growing number have been found to form the long, highly ordered β-sheet protein fibers that comprise amyloid deposits. A high percentage of these proteins have been linked to common and incurable disorders including Alzheimer’s, type II diabetes and Parkinson’s.

This link has led to an explosion of interest in amyloidogenic proteins. However, despite their prevalence in diseased tissue, most amyloid fibers are surprisingly inert. Instead of

mature fibers, small oligomers of amyloid proteins disrupt the cellular membranes and cause cell death. We are currently using a variety of biophysical techniques, including solution and solid-state NMR spectroscopy, to understand the folding/misfolding pathways of amyloid proteins and investigate compounds able to suppress the amyloid fibril formation and toxicity.

Interaction with membranes. To perform this task, we need to understand exactly how amyloid forming proteins kill cells. The toxicity of amyloid-forming proteins has been hypothesized to reside in the ability of protein oligomers to interact with and disrupt the cell membrane. Much of the evidence for this hypothesis comes from in vitro experiments using model membranes. Our goal is to shed light on the membrane

disruption process, studying the interaction of amyloidogenic protein with model membranes that more closely resemble the properties of biologic membranes. One idea is to vary the membrane lipid composition to understand how different kinds of membranes, e.g. plasma membrane, intracellular organelles' membrane, raft domain, etc. interact with and are affected by amyloidogenic proteins.

High resolution structure of protein monomers and aggregates. To date the structure of amyloidogenic proteins, especially small oligomers, which are believed to be the most toxic species, are largely unknown. This lack of information presents a problem in designing compounds designed to block amyloid-induced toxicity. Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful techniques to study the structure of proteins and aggregates. Our interest is to develop and apply NMR spectroscopy to solve the structure of amyloidogenic proteins in different environments.

Role of metal ions in the fiber formation process. Homeostasis of metal ions is essential for the proper functioning of the cell. Since it is known that many metal ions can interact with amyloidogenic proteins, the dysregulation of metal ions could be one of the key points underlying the etiology of protein conformational diseases. Some metal ions inhibit the fiber formation process, but others seem to enhance the toxicity of amyloid. Our studies are focused on the nature of the interaction between metal ions and amyloid proteins, the structure of the protein-metal complex, as well as the role that several metals play in the fiber formation and/or membrane disruption process.

Inhibitors. There is a growing interest in studying natural compounds that inhibit the formation of fibrils and oligomers. The goal is to develop new drugs useful for preventing protein conformational diseases. Although several studies have shown the ability of some natural compounds to interfere with the formation of fibrils, to date the mechanisms underlying this behavior are not fully known. Our goal is to study and shed light on the mechanisms of interaction of various natural inhibitors, such as EGCG, resveratrol, curcumin, with amyloidogenic proteins.

Our publications on amyloid proteins

Kotler SA, Walsh P, Breander JR, Ramamoorthy A. Differences between amyloid-beta aggregation in solution and on the membrane: Insights in to elucidation of the mechanistic details of Alzheimer's disease. Chem. Soc. Rev. (In press).
- Zhao J, Hu R, Sciacca MF, Brender JR, Chen H, Ramamoorthy A, Zheng J. Non-selective ion channel activity of polymorphic human islet amyloid polypeptide (amylin) double channels. Phys. Chem. Chem. Phys. (In press)
Lee S, Zheng X, Krishnamoorthy J, Savelieff M, Park M, Brender J, Kim H, Derrick S, Kochi A, Lee J, Kim C, Ramamoorthy A, Bowers T, Lim MH. Rational design of a structural framework with potential use to develop chemical reagents that target and modulate multiple facets of Alzheimer's disease. J. Am. Chem. Soc. 136(2014) 299-310.
Ramamoorthy A and Lim MH. Structural characterization and inhibition of toxic amyloid-beta oligomeric intermediates. Biophys J. 105(2013) 287-288.
Ramamoorthy A. Insights in to protein misfolding and amyloidogenesis. Phys. Chem. Chem. Phys. 15(2013) 8867-8867.
- Hyung SJ, DeToma AS, Brender JR, Lee S, Vivekanandan S, Kochi A, Choi J, Ramamoorthy A, Ruotolo BT, Lim MH. Insights into antiamyloidogenic properties of the green tea extract(-)-epigallocatechin-3-gallate toward metal-associated amyloid-beta species. Proc. Natl. Acad. Sci. U S A. (In press).
Hartman K, Brender JR, Monde K, Ono A, Evans ML, Popovych N, Chapman MR, Ramamoorthy A. Bacterial curli protein promotes the conversion of PAP(248-286) into the amyloid SEVI: cross-seeding of dissimiliar amyloid sequences. Peer J. (2013) DOI:10.7717/peerj.5
J. R. Brender, D. L. Heyl, S. Samisetti, S. A. Kotler, J. M. Osborne, R. R. Pesaru, A. Ramamoorthy, Membrane disordering is not sufficient for membrane permeabilization by islet amyloidogenic polypeptide: studies of IAPP(20–29) fragments, Phys. Chem. Chem. Phys. (in press).
- Sciacca MF, Milardi D, Messina GM, Marletta G, Brender JR, Ramamoorthy A, La Rosa C. Cations as switches of amyloid-mediated membrane disruption mechanisms: Calcium and IAPP. Biophys. J., 104, 173-184 (2013).
- J. R. Brender, J. Krishnamoorthy, G. M. L. Messina, A. Deb, S. Vivekanandan, C. La Rosa, J. E. Penner-Hahn, A. Ramamoorthy, Zinc stabilization of prefibrillar oligomers of human islet amyloid polypeptide, Chem. Commun., 49, 3339-3341 (2013).
Suzuki Y, Brender JR, Soper MT, Krishnamoorthy J, Zhou Y, Ruotolo BT, Kotov NA, Ramamoorthy A*, Marsh EN*, Resolution of Oligomeric Species during the Aggregation of Aβ1-40 Using 19F NMR, Biochemistry (in press). (* Corresponding Authors).
- Popovych N, Brender JR, Soong R, Vivekanandan S, Hartman K, Basrur V, MacDonald PM, Ramamoorthy A. Site specific interaction of the polyphenol EGCG with the SEVI amyloid peptide PAP(248-286), J. Phys. Chem. B., 116, 3650-3658 (2012).
- Krishnamoorthy J, Brender JR, Vivekanandan S, Jahr N, Ramamoorthy A. Side chain dynamics reveals transient association of Ab(1-40) monomers with amyloid fibers, J. Phys. Chem., B.116, 13618-13623 (2012).
- Sciacca MFM, Kotler SA, Brender JR, Chen J, Lee DK, Ramamoorthy A. Two step mechanism of membrane disruption by Aβ through membrane fragmentation and pore formation, Biophys. J., 103, 702-710 (2012).
- Suzuki Y, Brender JR, Hartman K, Ramamoorthy A, Marsh EN. Alternative pathways of human islet amyloid polypeptide aggregation distinguished by 19F NMR-detected kinetics of monomer consumption, Biochemistry., 51, 8154-8162 (2012).
- Jones MR, Service EL, Thompson JR, Wang MCP, Kimsey IJ, DeToma AS, Ramamoorthy A, Lim MH, Storr T. Dual-function triazole-pyridine derivatives as inhibitors of metal-induced amyloid-beta aggregation, Metallomics., 4, 910-920 (2012).
- Sciacca MF, Brender JR, Lee DK, Ramamoorthy A. Phosphatidylethanolamine enhances amyloid fiber-dependent membrane fragmentation, Biochemistry., 51, 7676-7684 (2012).
Brender J, Salamekh S, Ramamoorthy A. Membrane-disruption and early events in the aggregation of the diabetes related peptide IAPP from a molecular perspective, Acc. Chem. Res., 45, 454-463 (2012).
Detoma AS, Salamekh S, Ramamoorthy A, Lim MH. Misfolded proteins in Alzheimer's disease and type II diabetes. Chem. Soc. Rev., 41, 608-621 (2012).
Huang R, Vivekanandan S, Brender JR, Abe Y, Naito A, Ramamoorthy A. NMR Characterization of monomeric and oligomeric conformations of human calcitonin and its interaction with EGCG, J. Mol. Biol., 416, 108-120 (2012).
Braymer J, Choi J-S, DeToma A, Wang C, Nam K, Kampf J, Ramamoorthy A, Lim MH. Development of Bifunctional Stillbene Derivatives for Targeting and Modulating Metal-Amyloid-beta species, Inorg. Chem., 50, 10724-10734 (2011).
Nanga RPR, Brender JR, Vivekanandan S, Ramamoorthy A. Structure and Membrane Orientation of IAPP in its Natively Amidated Form at Physiological pH in a Membrane Environment, Biochim. Biophys. Acta., 10, 2337-2342 (2011).
Vivekanandan S, Brender JR, Lee SY, Ramamoorthy A. A Partially Folded Structure of Amyloid-Beta(1-40) in an Aqueous Environment, Biochem. Biophys. Res. Commun., 411, 312-316 (2011).
Salamekh S, Brender JR, Hyung S-J, Nanga RP, Vivekanandan S, Ruotolo BT, Ramamoorthy A. A Two Site Mechanism for the Inhibition of IAPP Amyloidogenesis by Zinc, J. Mol. Biol., 410, 294-306 (2011).
Yoo S II, Yang M, Brender JR, Vivekanandan S, Sun K, Joo NE, Jeong S-H, Ramamoorthy A, and Kotov NA. Inhibition of Amyloid Peptide Fibrillation by Inorganic Nanoparticles: Functional Similarities with Proteins, Angew. Chem. Int. Ed., 50, 1-7 (2011).
Brender JR, Lee EL, Hartman K, Wong PT, Ramamoorthy A, Steel DG, Gafni A. Biphasic effects of insulin on islet amyloid polypeptide membrane disruption, Biophys. J., 100, 685-692 (2011).
Brender JR, Nanga RP, Popovych N, Soong R, Macdonald PM, Ramamoorthy A. The amyloidogenic SEVI precursor, PAP248-286, is highly unfolded in solution despite an underlying helical tendency, Biochim. Biophys. Acta., 1808, 1161-1169 (2011).
Choi J-S, Braymer JJ, Nanga RPR, Ramamoorthy A, Lim MH. Design of small molecules that target metal-Abeta species and regulate metal-induced Abeta aggregation and neurotoxicity, Proc. Natl. Acad. Sci. U S A., 107, 21990-21995 (2010).
J. R. Brender, K. Hartman, R. P. R. Nanga, N. Popovych, R. de la Salud Bea, Vivekanandan S, E. N. G. Marsh, A. Ramamoorthy, Role of Zinc in Human Amyloid Polypeptide Aggregation, J. Am. Chem. Soc., 132, 8973-8983 (2010).
R. P. R. Nanga, J. R. Brender, Vivekanandan S, N. Popovych, and A. Ramamoorthy, NMR Structure in a Membrane Environment Reveals Putative Amyloidogenic Regions of the SEVI Precursor Peptide PAP248-286, J. Am. Chem. Soc., 131, 17972-17979 (2009).
S. S. Hindo, A. M. Mancino, J. J. Braymer, Y. H. Liu, Vivekanandan S, A. Ramamoorthy, and M. H. Lim, Small Molecule Modulators of Copper-Induced Abeta Aggregation, J. Am. Chem. Soc., 131, 16663-16665 (2009).
J. R. Brender, K. Hartman, L. M. Gottler, M. E. Cavitt, D. W. Youngstrom, and A. Ramamoorthy, Helical Conformation of the SEVI Precursor Peptide PAP(248-286), a Dramatic Enhancer of HIV Infectivity, Promotes Lipid Aggregation and Fusion, Biophys. J., 97, 2474-2483 (2009).
R. P. R. Nanga, J. R. Brender, J. D. Xu, K. Hartman, Vivekanandan S, and A. Ramamoorthy, Three-Dimensional Structure and Orientation of Rat Islet Amyloid Polypeptide Protein in a Membrane Environment by Solution NMR Spectroscopy, J. Am. Chem. Soc., 131, 8252-8261 (2009).
R. Soong, J. R. Brender, P. M. Macdonald, and A. Ramamoorthy, Association of Highly Compact Type II Diabetes Related Islet Amyloid Polypeptide Intermediate Species at Physiological Temperature Revealed by Diffusion NMR Spectroscopy, J. Am. Chem. Soc., 131, 7079-7085 (2009).
P. E. S. Smith, J. R. Brender, and A. Ramamoorthy, Induction of Negative Curvature as a Mechanism of Cell Toxicity by Amyloidogenic Peptides: The Case of Islet Amyloid Polypeptide, J. Am. Chem. Soc., 131, 4470-4478 (2009).
R. P. R. Nanga, J. R. Brender, J. Xu, G. Veglia, and A. Ramamoorthy, Structures of Rat and Human Islet Amyloid Polypeptide (IAPP)1-19 in Micelles by NMR Spectroscopy, Biochemistry 47, 12689-12697 (2008).
J. R. Brender, K. Hartman, K. R. Reid, R. T. Kennedy, and A. Ramamoorthy, A Single Mutation in the Non-Amyloidogenic Region of IAPP (Amylin) Greatly Reduces Toxicity, Biochemistry 47, 12680-12688 (2008).
J. R. Brender, E. L. Lee, M. A. Cavitt, A. Gafni, D. G. Steel, and A. Ramamoorthy, Amyloid Fiber Formation and Membrane Disruption are Separate Processes Localized in Two Distinct Regions of the Amylin Peptide. J. Am. Chem. Soc., 130, 6424-6429 (2008).
J. R. Brender, U. H. N. Dürr, D. Heyl, M. B. Budarapu, A. Ramamoorthy, Membrane fragmentation by human islet amyloid polypeptide detected by solid-state NMR spectroscopy of membrane nanotubes. BBA Biomembranes, 1768, 2026-2029 (2007).
A. Mascioni, F. Porcelli, U. Ilangovan, A. Ramamoorthy, and G. Veglia, Conformational Preferences of the Amylin Nucleation Site in SDS Micelles: an NMR study. Biopolymers 69, 29 (2003).
U. Ilangovan, A. Ramamoorthy, Conformational studies of human islet amyloid peptide using molecular dynamics and simulated annealing methods. Biopolymers, 45, 9-20 (1998).

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