The aim of my laboratory is to create a better understanding of the pathological and functional aspects of protein disorder and aggregation. In particular, we are interested in the differences between functional and pathological amyloid fibrils and the importance of intrinsically disordered protein domains (i.e. domains that lack stable tertiary or secondary structure) for the formation of amyloid.
Amyloid formation is important for many neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's disease. The aggregation of monomeric proteins into a variety of oligomeric and fibrillar (amyloid) states can lead to cell death and, therefore, disease. However, amyloid fibrils can also have non-pathological, positive functions such as cell signaling or scaffolding functions. One of the most important goals of the lab is to understand what distinguishes functional and pathological amyloid fibrils. Understanding the difference between these types of amyloid could lead to the development of new therapeutics and will deepen our understanding of the role of amyloid in biology.
A second area of research in my laboratory is protein disorder as prerequisite for amyloid formation. Intrinsic disorder or partial unfolding is necessary for a protein to aggregate from its soluble state into an amyloid fibril. Furthermore, many proteins can be forced to fold into an amyloid by partial denaturation in vitro. The structural aspects of the unfolded state is, therefore, important for the understanding of amyloid formation and may lead to new strategies to prevent the formation of amyloid in neurodegenerative diseases. However, partially unfolded, intrinsically disordered proteins also carry important functional aspects, especially in eukaryotic organisms, where up to 40% of all proteins contain disordered regions. Our second goal is to understand how aggregation is prevented in most disordered proteins and why it occurs in some disease-related cases.
To address these questions, my lab will use primarily solid-state nuclear magnetic resonance (NMR) in conjunction with other biochemical methods. Solid-state NMR is an emerging technique that enables us to investigate protein structures that are otherwise inaccessible to atomic-resolution structural methods such as X-ray crystallography and liquid-state NMR, thereby permitting us to investigate systems such as protein fibrils with atomic resolution.
Falk AS, Siemer AB. Dynamic domains of amyloid fibrils can be site-specifically assigned with proton detected 3D NMR spectroscopy. J Biomol NMR. 2016 Oct 20. View in: PubMed
Isas JM, Langen R, Siemer AB. Solid-State Nuclear Magnetic Resonance on the Static and Dynamic Domains of Huntingtin Exon-1 Fibrils. Biochemistry. 2015 Jun 30; 54(25):3942-9. View in: PubMed
Raveendra BL, Siemer AB, Puthanveettil SV, Hendrickson WA, Kandel ER, McDermott AE. Characterization of prion-like conformational changes of the neuronal isoform of Aplysia CPEB. Nat Struct Mol Biol. 2013 Apr; 20(4):495-501. View in: PubMed
Li J, McQuade T, Siemer AB, Napetschnig J, Moriwaki K, Hsiao YS, Damko E, Moquin D, Walz T, McDermott A, Chan FK, Wu H. The RIP1/RIP3 necrosome forms a functional amyloid signaling complex required for programmed necrosis. Cell. 2012 Jul 20; 150(2):339-50. View in: PubMed
Siemer AB, Huang KY, McDermott AE. Protein linewidth and solvent dynamics in frozen solution NMR. PLoS One. 2012; 7(10):e47242. View in: PubMed
Huang KY, Siemer AB, McDermott AE. Homonuclear mixing sequences for perdeuterated proteins. J Magn Reson. 2011 Jan; 208(1):122-7. View in: PubMed
Siemer AB, Huang KY, McDermott AE. Protein-ice interaction of an antifreeze protein observed with solid-state NMR. Proc Natl Acad Sci U S A. 2010 Oct 12; 107(41):17580-5. View in: PubMed
Siemer AB, McDermott AE. Solid-state NMR on a type III antifreeze protein in the presence of ice. J Am Chem Soc. 2008 Dec 24; 130(51):17394-9. View in: PubMed
Wasmer C, Lange A, Van Melckebeke H, Siemer AB, Riek R, Meier BH. Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core. Science. 2008 Mar 14; 319(5869):1523-6. View in: PubMed
Verel R, Manolikas T, Siemer AB, Meier BH. Improved resolution in (13)C solid-state spectra through spin-state-selection. J Magn Reson. 2007 Feb; 184(2):322-9. View in: PubMed
Siemer AB, Arnold AA, Ritter C, Westfeld T, Ernst M, Riek R, Meier BH. Observation of highly flexible residues in amyloid fibrils of the HET-s prion. J Am Chem Soc. 2006 Oct 11; 128(40):13224-8. View in: PubMed
Siemer AB, Ritter C, Steinmetz MO, Ernst M, Riek R, Meier BH. 13C, 15N resonance assignment of parts of the HET-s prion protein in its amyloid form. J Biomol NMR. 2006 Feb; 34(2):75-87. View in: PubMed
Ritter C, Maddelein ML, Siemer AB, Lührs T, Ernst M, Meier BH, Saupe SJ, Riek R. Correlation of structural elements and infectivity of the HET-s prion. Nature. 2005 Jun 9; 435(7043):844-8. View in: PubMed
Siemer AB, Ritter C, Ernst M, Riek R, Meier BH. High-resolution solid-state NMR spectroscopy of the prion protein HET-s in its amyloid conformation. Angew Chem Int Ed Engl. 2005 Apr 15; 44(16):2441-4. View in: PubMed
Siemer A, Masip M, Carreras N, García-Ortega L, Oñaderra M, Bruix M, Del Pozo AM, Gavilanes JG. Conserved asparagine residue 54 of alpha-sarcin plays a role in protein stability and enzyme activity. Biol Chem. 2004 Dec; 385(12):1165-70. View in: PubMed