X-ray Crystallographic Structures of Trimers and Higher-Order Oligomeric Assemblies of a Peptide Derived from Aβ<sub>17–36</sub>

Spencer, Ryan K.; Li, Hao; Nowick, James S.

doi:10.1021/ja5017409

Cited by 86 publications

(124 citation statements)

References 38 publications

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“…have reported a X-ray crystal structure for a cyclic peptidomimetic analog of Aβ(17–36), in which twisted β-hairpins are arranged into 3-fold symmetric antiparallel β-strand subunits. 41 …”

Section: Discussionmentioning

confidence: 99%

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Antiparallel β-Sheet Structure within the C-Terminal Region of 42-Residue Alzheimer's Amyloid-β Peptides When They Form 150-kDa Oligomers

Huang

Zimmerman

Martin

et al. 2015

Journal of Molecular Biology

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Understanding the molecular structures of amyloid-β (Aβ) oligomers and underlying assembly pathways will advance our understanding of Alzheimer’s disease (AD) at the molecular level. This understanding could contribute to disease prevention, diagnosis, and treatment strategies, as oligomers play a central role in AD pathology. We have recently presented a procedure for production of 150 kDa oligomeric samples of Aβ(1–42) (the 42-residue variant of the Aβ peptide) that are compatible with solid state NMR analysis, and we have shown that these oligomers and amyloid fibrils differ in intermolecular arrangement of β-strands. Here we report new solid state NMR constraints that indicate antiparallel intermolecular alignment of β-strands within the oligomers. Specifically, 150 kDa Aβ(1–42) oligomers with uniform 13C and 15N isotopic labels at I32, M35, G37 and V40 exhibit β-strand secondary chemical shifts in 2D fpRFDR NMR spectra, spatial proximities between I32 and V40 as well as between M35 and G37 in 2D DARR spectra, and close proximity between M35 Hα and G37 Hα in 2D CHHC spectra. Furthermore, 2D DARR analysis of an oligomer sample prepared with 30% labeled peptide indicates that the I32-V40 and M35-G37 contacts are between residues on different molecules. We employ molecular modeling to compare the newly derived experimental constraints with previously proposed geometries for arrangement of Aβ molecules into oligomers.

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Section: Discussionmentioning

confidence: 99%

“…suggest that oligomers could have similar structure, others including our own group have proposed incompatible oligomer structural models. 22–24, 40, 41 More structural knowledge is needed to explain how oligomers differ structurally from protofibrils and fibrils.…”

Section: Introductionmentioning

confidence: 99%

Antiparallel β-Sheet Structure within the C-Terminal Region of 42-Residue Alzheimer's Amyloid-β Peptides When They Form 150-kDa Oligomers

Huang

Zimmerman

Martin

et al. 2015

Journal of Molecular Biology

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“…The central part of this hairpin structure consists of a hydrophilic region flanked by hydrophobic ␤-sheet-forming segments at both ends (5)(6)(7)(8)(9)(10). This particular shape is believed to be dictated by the specific pattern of hydrophobic and charged residues in the A␤ sequence and has been identified even in soluble A␤ aggregates (7,(11)(12)(13)(14)(15)(16)(17), including the very early stage oligomers of A␤ (18). Chemically constraining the side chains of Asp 23 and Lys 28 accelerates the kinetics of A␤ aggregation by stabilizing the hairpin structure (5).…”

mentioning

confidence: 99%

Steric Crowding of the Turn Region Alters the Tertiary Fold of Amyloid-β18–35 and Makes It Soluble

Chandrakesan

Bhowmik

Sarkar

et al. 2015

Journal of Biological Chemistry

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A␤ self-assembles into parallel cross-␤ fibrillar aggregates, which is associated with Alzheimer's disease pathology. A central hairpin turn around residues 23-29 is a defining characteristic of A␤ in its aggregated state. Major biophysical properties of A␤, including this turn, remain unaltered in the central fragment A␤ 18 -35 . Here, we synthesize a single deletion mutant, ⌬G25, with the aim of sterically hindering the hairpin turn in A␤ 18 -35 . We find that the solubility of the peptide goes up by more than 20-fold. Although some oligomeric structures do form, solution state NMR spectroscopy shows that they have mostly random coil conformations. Fibrils ultimately form at a much higher concentration but have widths approximately twice that of A␤ 18 -35 , suggesting an opening of the hairpin bend. Surprisingly, two-dimensional solid state NMR shows that the contact between Phe 19 and Leu 34 residues, observed in full-length A␤ and A␤ 18 -35 , is still intact in these fibrils. This is possible if the monomers in the fibril are arranged in an antiparallel ␤-sheet conformation. Indeed, IR measurements, supported by tyrosine cross-linking experiments, provide a characteristic signature of the antiparallel ␤-sheet. We conclude that the self-assembly of A␤ is critically dependent on the hairpin turn and on the contact between the Phe 19 and Leu 34 regions, making them potentially sensitive targets for Alzheimer's therapeutics. Our results show the importance of specific conformations in an aggregation process thought to be primarily driven by nonspecific hydrophobic interactions.Alzheimer's disease pathology has been associated with the aggregation of amyloid ␤ (A␤), 6 a 39 -43-amino acid-long peptide (1, 2). In this process, the unstructured monomers of A␤ get converted into amyloid fibrils composed of hairpin-shaped monomeric units assembled in a parallel ␤ sheet arrangement (3, 4). The central part of this hairpin structure consists of a hydrophilic region flanked by hydrophobic ␤-sheet-forming segments at both ends (5-10). This particular shape is believed to be dictated by the specific pattern of hydrophobic and charged residues in the A␤ sequence and has been identified even in soluble A␤ aggregates (7,(11)(12)(13)(14)(15)(16)(17), including the very early stage oligomers of A␤ (18 , and stabilizes the soluble monomeric and oligomeric assemblies of A␤ (19). This hairpin turn thus seems to be a critical factor dictating the self-assembly of A␤ under physiological conditions. Studying the influence of the turn region on the properties of A␤, separately from that of the distal terminal regions and without changing the electrostatics, can yield valuable information on the logic of A␤ assembly.A␤ aggregation appears to be primarily hydrophobic in nature. In fact a contact between hydrophobic regions containing Phe 19 and Leu 34 is one of the earliest contacts formed during the aggregation of amyloid ␤ (18). In a generic hydrophobic aggregate, the burial of the hydrophobic surface can in principle proceed in an ...

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“…We initially used p -bromophenylalanine to incorporate a Br atom within our macrocylic β-sheet peptides; [4] recently we have switched to p -iodophenylalanine to quickly solve our peptide structures using Cu radiation on an in-house X-ray diffractometer. [5] Although both bromine and iodine are suitable for anomalous diffraction data collection on a synchrotron, only the iodine permits the collection of anomalous diffraction data on an X-ray diffractometer with a Cu anode. [6] The choice of an appropriate heavy atom will become more apparent during the discussion of the generation of an electron density map (Section 2.6).…”

Section: Peptide Crystallographymentioning

confidence: 99%

“…[5] We designed macrocyclic peptides 1 and 2 to fold into a β-sheet that incorporates two heptapeptide sequences from Aβ – the central region Aβ 17–23 (LVFFAED) and the C-terminal region Aβ 30–36 (AIIGLMV). The heptapeptides are connected together with two δ-linked ornithine residues to form a macrocycle.…”

Section: Case Studymentioning

confidence: 99%

A Newcomer′s Guide to Peptide Crystallography

Spencer

Nowick

2015

Israel Journal of Chemistry

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Here we provide a guide for adapting the tools developed for protein X-ray crystallography to study the structures and supramolecular assembly of peptides. Peptide crystallography involves selecting a suitable peptide, crystallizing the peptide, collecting X-ray diffraction data, processing the diffraction data, determining the crystallographic phases and generating an electron density map, building and refining models, and depositing the crystallographic structure in the Protein Data Bank (PDB). Advances in technology make this process easy for a newcomer to adopt. This paper describes techniques for determining the X-ray crystallographic structures of peptides: incorporation of amino acids containing heavy atoms for crystallographic phase determination, commercially available kits to crystallize peptides, modern techniques for X-ray crystallographic data collection, and free user-friendly software for data processing and producing a crystallographic structure.

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X-ray Crystallographic Structures of Trimers and Higher-Order Oligomeric Assemblies of a Peptide Derived from Aβ_17–36

Cited by 86 publications

References 38 publications

Antiparallel β-Sheet Structure within the C-Terminal Region of 42-Residue Alzheimer's Amyloid-β Peptides When They Form 150-kDa Oligomers

Antiparallel β-Sheet Structure within the C-Terminal Region of 42-Residue Alzheimer's Amyloid-β Peptides When They Form 150-kDa Oligomers

Steric Crowding of the Turn Region Alters the Tertiary Fold of Amyloid-β18–35 and Makes It Soluble

A Newcomer′s Guide to Peptide Crystallography

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X-ray Crystallographic Structures of Trimers and Higher-Order Oligomeric Assemblies of a Peptide Derived from Aβ17–36

Cited by 86 publications

References 38 publications

Antiparallel β-Sheet Structure within the C-Terminal Region of 42-Residue Alzheimer's Amyloid-β Peptides When They Form 150-kDa Oligomers

Antiparallel β-Sheet Structure within the C-Terminal Region of 42-Residue Alzheimer's Amyloid-β Peptides When They Form 150-kDa Oligomers

Steric Crowding of the Turn Region Alters the Tertiary Fold of Amyloid-β18–35 and Makes It Soluble

A Newcomer′s Guide to Peptide Crystallography

Contact Info

Product

Resources

About

X-ray Crystallographic Structures of Trimers and Higher-Order Oligomeric Assemblies of a Peptide Derived from Aβ_17–36