Amyloid fibril structure of peptides and proteins by magic angle spinning NMR spectroscopy and dynamic nuclear polarization

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2011.Vita. Cataloged from student-submitted PDF version of thesis.Includes bibliographical references.Amyloid fibrils are insoluble, non-crystalline protein filaments associated with a number of diseases such as Alzheimer's and Type Il diabetes. They can have a functional role in different organisms and many proteins and peptides have been found to form amyloid fibrils in vitro. We have used magic angle spinning (MAS) NMR spectroscopy to investigate the structure of two amyloid fibril systems - an 11- residue segment from the disease-related protein transthyretin (TTR); and P2- microglobulin (32m), a 99-residue protein associated with dialysis-related amyloidosis. The TTR(105-115) case exemplifies our efforts to characterize the hierarchy of structures present in the fibril form, including the organization of the Pstrands into P-sheets (tertiary structure), the P-sheet interface that defines each protofilament (quaternary structure), and the protofilament-to-protofilament contacts that lead to the formation of the complete fibril. Our efforts were guided by information obtained from other methods such as cryo-electron microscopy and atomic force microscopy, and resulted in the very first atomic resolution structure of a complete amyloid fibril. We have extended the methods used in the TTR(105-115) structure determination procedure to the fibrils formed by 2m, a process complicated not only by the much larger size of the protein involved but also by the high degree of dynamics exhibited in these fibrils. Nevertheless, we were able to characterize the secondary structure of the protein in the fibril form, and the tertiary and quaternary interactions within the fibrils. In addition, we have compared at the molecular level @2m fibrils formed under different conditions, in an effort to characterize the origins of fibril polymorphism for this protein sequence. Our work on amyloid fibrils has also benefited extensively from the development of dynamic nuclear polarization, a method used to enhance the sensitivity of MAS NMR experiments, leading to unprecedented gains in signal-to-noise ratios and acquisition times.by Galia Tzvetanova Debelouchina.Ph.D

Combining DNP NMR with segmental and specific labeling to study a yeast prion protein strain that is not parallel in-register

The yeast prion protein Sup35NM is a self-propagating amyloid. Despite intense study, there is no consensus on the organization of monomers within Sup35NM fibrils. Some studies point to a â-helical arrangement, whereas others suggest a parallel inregister organization. Intermolecular contacts are often determined by experiments that probe long-range heteronuclear contacts for fibrils templated from a 1:1 mixture of 13 C- and 15 N-labeled monomers. However, for Sup35NM, like many large proteins, chemical shift degeneracy limits the usefulness of this approach. Segmental and specific isotopic labeling reduce degeneracy, but experiments to measure long-range interactions are often too insensitive. To limit degeneracy and increase experimental sensitivity, we combined specific and segmental isotopic labeling schemes with dynamic nuclear polarization (DNP) NMR. Using this combination, we examined an amyloid form of Sup35NM that does not have a parallel in-register structure. The combination of a small number of specific labels with DNP NMR enables determination of architectural information about polymeric protein systems. Keyword: [PSI+] prion; solid-state NMR; amyloid; Sup35; dynamic nuclear polarizationNational Institutes of Health (U.S.) (Grants GM-025874)National Institutes of Health (U.S.) (Grants EB-003151)National Institutes of Health (U.S.) (Grants EB-002804)National Institutes of Health (U.S.) (Grants EB-002026

Dynamic Nuclear Polarization-Enhanced Solid-State NMR Spectroscopy of GNNQQNY Nanocrystals and Amyloid Fibrils

Dynamic nuclear polarization (DNP) utilizes the inherently larger polarization of electrons to enhance the sensitivity of conventional solid-state NMR experiments at low temperature. Recent advances in instrumentation development and sample preparation have transformed this field and have opened up new opportunities for its application to biological systems. Here, we present DNP-enhanced [superscript 13]C–[superscript 13]C and [superscript 15]N–[superscript 13]C correlation experiments on GNNQQNY nanocrystals and amyloid fibrils acquired at 9.4 T and 100 K and demonstrate that DNP can be used to obtain assignments and site-specific structural information very efficiently. We investigate the influence of temperature on the resolution, molecular conformation, structural integrity and dynamics in these two systems. In addition, we assess the low-temperature performance of two commonly used solid-state NMR experiments, proton-driven spin diffusion (PDSD) and transferred echo double resonance (TEDOR), and discuss their potential as tools for measurement of structurally relevant distances at low temperature in combination with DNP.National Institutes of Health (U.S.) (Grant EB002804)National Institutes of Health (U.S.) (Grant EB003151)National Institutes of Health (U.S.) (Grant EB002026

Intermolecular Structure Determination of Amyloid Fibrils with 2 Magic-Angle Spinning and Dynamic Nuclear Polarization NMR

We describe magic-angle spinning NMR experiments designed to elucidate the interstrand architecture of amyloid fibrils. Three methods are introduced for this purpose, two being based on the analysis of long-range [superscript 13]C–[superscript 13]C correlation spectra and the third based on the identification of intermolecular interactions in [superscript 13]C–[superscript 15]N spectra. We show, in studies of fibrils formed by the 86-residue SH3 domain of PI3 kinase (PI3-SH3 or PI3K-SH3), that efficient [superscript 13]C–[superscript 13]C correlation spectra display a resonance degeneracy that establishes a parallel, in-register alignment of the proteins in the amyloid fibrils. In addition, this degeneracy can be circumvented to yield direct intermolecular constraints. The [superscript 13]C–[superscript 13]C experiments are corroborated by [superscript 15]N–[superscript 13]C correlation spectra obtained from a mixed [[superscript 15]N,[superscript 12]C]/[[superscript 14]N,[superscript 13]C] sample which directly quantify interstrand distances. Furthermore, when the spectra are recorded with signal enhancement provided by dynamic nuclear polarization (DNP) at 100 K, we demonstrate a dramatic increase (from 23 to 52) in the number of intermolecular [superscript 15]N–[superscript 13]C constraints detectable in the spectra. The increase in the information content is due to the enhanced signal intensities and to the fact that dynamic processes, leading to spectral intensity losses, are quenched at low temperatures. Thus, acquisition of low temperature spectra addresses a problem that is frequently encountered in MAS spectra of proteins. In total, the experiments provide 111 intermolecular [superscript 13]C–[superscript 13]C and [superscript 15]N–[superscript 13]C constraints that establish that the PI3-SH3 protein strands are aligned in a parallel, in-register arrangement within the amyloid fibril.National Institutes of Health (U.S.) (Grant EB-003151)National Institutes of Health (U.S.) (Grant EB-002804)National Institutes of Health (U.S.) (Grant EB-002026

Z-Selective and Syndioselective Ring-Opening Metathesis Polymerization (ROMP) Initiated by MonoAryloxidePyrrolide (MAP) Catalysts

We report the Z-selective and syndioselective polymerization of 2,3-bis(trifluoromethyl)bicyclo[2.2.1]hepta-2,5-diene (NBDF6) and 3-methyl-3-phenylcyclopropene (MPCP) by monoaryloxide monopyrrolide imido alkylidene (MAP) catalysts of Mo. The mechanism of polymerization with syn-Mo(NAd)(CHCMe2Ph)(Pyr)(OHIPT) (1; Ad = 1-adamantyl, OHIPT = O-2,6-(2,4,6-i-Pr3C6H2)2C6H3) as the initiator is proposed to consist of addition of monomer to the syn initiator to yield a syn first insertion product and propagation via syn insertion products. In contrast, the mechanism of polymerization with syn-Mo(NAr)(CHCMe2Ph)(Pyr)(OTPP) (4; Ar = 2,6-i-Pr2C6H3, OTPP = 2,3,5,6-Ph4C6H) as the initiator at −78 °C consists of addition of monomer to the syn initiator to yield an anti first insertion product and propagation via anti insertion products. Polymerizations of NBDF6 and MPCP at room temperature initiated by 4 led to polymers without a regular structure. We propose that the syndiotacticity of cis polymers is the consequence of the required inversion at the metal center with each insertion of monomer, i.e., stereogenic metal control of the polymer structure. We also propose that the two mechanisms for forming cis,syndiotactic polymers arise as a consequence of the relative steric bulk of the imido and phenoxide ligands.United States. Army Research Office (Institute for Soldier Nanotechnologies, Contract No. DAAD-19-02-D-0002)United States. Dept. of Energy (DE-FG02-86ER13564)National Institutes of Health (U.S.) (GM066360)National Institutes of Health (U.S.) (EB002026

Magic Angle Spinning NMR Analysis of β[subscript 2]-Microglobulin Amyloid Fibrils in Two Distinct Morphologies

β[subscript 2]-Microglobulin (β[subscript 2]m) is the major structural component of amyloid fibrils deposited in a condition known as dialysis-related amyloidosis. Despite numerous studies that have elucidated important aspects of the fibril formation process in vitro, and a magic angle spinning (MAS) NMR study of the fibrils formed by a small peptide fragment, structural details of β[subscript 2]m fibrils formed by the full-length 99-residue protein are largely unknown. Here, we present a site-specific MAS NMR analysis of fibrils formed by the full-length β[subscript 2]m protein and compare spectra of fibrils prepared under two different conditions. Specifically, long straight (LS) fibrils are formed at pH 2.5, while a very different morphology denoted as worm-like (WL) fibrils is observed in preparations at pH 3.6. High-resolution MAS NMR spectra have allowed us to obtain [superscript 13]C and [superscript 15]N resonance assignments for 64 residues of β[subscript 2]m in LS fibrils, including part of the highly mobile N-terminus. Approximately 25 residues did not yield observable signals. Chemical shift analysis of the sequentially assigned residues indicates that these fibrils contain an extensive β-sheet core organized in a non-native manner, with a trans-P32 conformation. In contrast, WL fibrils exhibit more extensive dynamics and appear to have a smaller β-sheet core than LS fibrils, although both cores seem to share some common elements. Our results suggest that the distinct macroscopic morphological features observed for the two types of fibrils result from variations in structure and dynamics at the molecular level.National Institutes of Health (U.S.) (Grant Number EB003151)National Institutes of Health (U.S.) (Grant Number EB002026)Wellcome Trust (London, England) (Grant Number 075675)Wellcome Trust (London, England) (Grant Number 062164

Intermolecular Alignment in Beta 2-Microglobulin Amyloid Fibrils

The deposition of amyloid-like fibrils, composed primarily of the 99-residue protein β2-microglobulin (β2m), is one of the characteristic symptoms of dialysis-related amyloidosis. Fibrils formed in vitro at low pH and low salt concentration share many properties with the disease related fibrils and have been extensively studied by a number of biochemical and biophysical methods. These fibrils contain a significant β-sheet core and have a complex cryoEM electron density profile. Here, we investigate the intrasheet arrangement of the fibrils by means of [superscript 15]N−[superscript 13]C MAS NMR correlation spectroscopy. We utilize a fibril sample grown from a 50:50 mixture of [superscript 15]N,[superscript 12]C- and [superscript 14]N,[superscript 13]C-labeled β2m monomers, the latter prepared using 2-[superscript 13]C glycerol as the carbon source. Together with the use of ZF-TEDOR mixing, this sample allowed us to observe intermolecular [superscript 15]N−[superscript 13]C backbone-to-backbone contacts with excellent resolution and good sensitivity. The results are consistent with a parallel, in-register arrangement of the protein subunits in the fibrils and suggest that a significant structural reorganization occurs from the native to the fibril state.National Institutes of Health (U.S.) (grant no. EB003151)National Institutes of Health (U.S.) (grant no. EB002026)National Institutes of Health (U.S.) (grant no. P41 RR-01081)Wellcome Trust (London, England) (grant no. 075675)Wellcome Trust (London, England) (grant no. 062164

Distinct Prion Strains Are Defined by Amyloid Core Structure and Chaperone Binding Site Dynamics

Yeast prions are self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that produce distinct phenotypes. Using magic-angle spinning nuclear magnetic resonance spectroscopy, we provide a detailed look at the dynamic properties of these forms over a broad range of timescales. We establish that different prion strains have distinct amyloid structures, with many side chains in different chemical environments. Surprisingly, the prion strain with a larger fraction of rigid residues also has a larger fraction of highly mobile residues. Differences in mobility correlate with differences in interaction with the prion-partitioning factor Hsp104 in vivo, perhaps explaining strain-specific differences in inheritance.Howard Hughes Medical Institute (Investigator)Howard Hughes Medical Institute (HHMI fellow of the Life Science Research Foundation)National Institutes of Health (U.S.) (NIH grant GM025874)National Institutes of Health (U.S.) (NIH grant EB003151)National Institutes of Health (U.S.) (NIH grant EB002026

Higher Order Amyloid Fibril Structure by MAS NMR and DNP Spectroscopy

Protein magic angle spinning (MAS) NMR spectroscopy has generated structural models of several amyloid fibril systems, thus providing valuable information regarding the forces and interactions that confer the extraordinary stability of the amyloid architecture. Despite these advances, however, obtaining atomic resolution information describing the higher levels of structural organization within the fibrils remains a significant challenge. Here, we detail MAS NMR experiments and sample labeling schemes designed specifically to probe such higher order amyloid structure, and we have applied them to the fibrils formed by an eleven-residue segment of the amyloidogenic protein transthyretin (TTR(105–115)). These experiments have allowed us to define unambiguously not only the arrangement of the peptide β-strands into β-sheets but also the β-sheet interfaces within each protofilament, and in addition to identify the nature of the protofilament-to-protofilament contacts that lead to the formation of the complete fibril. Our efforts have resulted in 111 quantitative distance and torsion angle restraints (10 per residue) that describe the various levels of structure organization. The experiments benefited extensively from the use of dynamic nuclear polarization (DNP), which in some cases allowed us to shorten the data acquisition time from days to hours and to improve significantly the signal-to-noise ratios of the spectra. The β-sheet interface and protofilament interactions identified here revealed local variations in the structure that result in multiple peaks for the exposed N- and C-termini of the peptide and in inhomogeneous line-broadening for the residues buried within the interior of the fibrils.Biotechnology and Biological Sciences Research Council (Great Britain)Burroughs Wellcome FundLeverhulme TrustNational Institutes of Health (U.S.) (NIH grant EB-003151)National Institutes of Health (U.S.) (NIH grant EB-002026