Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Impacts of D-aspartate on the Aggregation Kinetics and Structural Polymorphism of Amyloid β Peptide 1-42.
Journal, issue, pages	J Mol Biol, Vol. 437, Issue 12, Page 169092, Year 2025
Publish date	Mar 14, 2025
Authors	Li-Ching Hsiao / Chih-Hsuan Lee / Karine Mazmanian / Masaya Yoshida / Genta Ito / Takuya Murata / Naoko Utsunomiya-Tate / Takeharu Haino / Shih-Ichi Tate / Shang-Te Danny Hsu /
PubMed Abstract	Isomerization of L-Aspartate (L-Asp) into D-aspartate (D-Asp) occurs naturally in proteins at a rate that is much faster than that of other amino acid types. Accumulation of D-Asp is age-dependent, ...Isomerization of L-Aspartate (L-Asp) into D-aspartate (D-Asp) occurs naturally in proteins at a rate that is much faster than that of other amino acid types. Accumulation of D-Asp is age-dependent, which could alter protein structures and, therefore, functions. Site-specific introduction of D-Asp can accelerate aggregation kinetics of a variety of proteins associated with misfolding diseases. Here, we showed by thioflavin T fluorescence that the isomerization of L-Asp at different positions of amyloid β peptide 1-42 (Aβ42) generates opposing effects on its aggregation kinetics. We further determined the atomic structures of Aβ42 amyloid fibrils harboring a single D-Asp at position 23 and two D-Asp at positions 7 and 23 by cryo-electron microscopy helical reconstruction - cross-validated by cryo-electron tomography and atomic force microscopy - to reveal how D-Asp contributes to the formation of a unique triple stranded amyloid fibril structure stabilized by two threads of well-ordered water molecules. These findings provide crucial insights into how the conversion from L- to D-Asp influences the aggregation propensity and amyloid polymorphism of Aβ42.
External links	J Mol Biol / PubMed:40090459
Methods	EM (helical sym.)
Resolution	2.5 - 3.0 Å
Structure data	61302 9jaz EMDB-61302, PDB-9jaz: Cryo-EM structure of the class I amyloid-beta 42 fibril containing a D-Asp at position 23 Method: EM (helical sym.) / Resolution: 3.0 Å 61303 9jb0 EMDB-61303, PDB-9jb0: Cryo-EM structure of the class II amyloid-beta 42 fibril containing a D-Asp at position 23 Method: EM (helical sym.) / Resolution: 2.9 Å 61304 9jb1 EMDB-61304, PDB-9jb1: Cryo-EM structure of the type I amyloid-beta 42 fibril containing a D-Asp at positions 7 and 23 Method: EM (helical sym.) / Resolution: 2.5 Å 61305 9jb2 EMDB-61305, PDB-9jb2: Cryo-EM structure of the type II amyloid-beta 42 fibril containing a D-Asp at positions 7 and 23 Method: EM (helical sym.) / Resolution: 2.9 Å
Source	homo sapiens (human)
Keywords	PROTEIN FIBRIL / aggregation