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Transition of Metastable Cross-Α Crystals Into Cross-Β Fibrils by Β

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Transition of Metastable Cross-Α Crystals Into Cross-Β Fibrils by Β Article Cite This: J. Am. Chem. Soc. 2019, 141, 363−369 pubs.acs.org/JACS Transition of Metastable Cross‑α Crystals into Cross‑β Fibrils by β‑Turn Flipping Sudipta Mondal,† Guy Jacoby,‡ Michael R. Sawaya,§ Zohar A. Arnon,† Lihi Adler-Abramovich,∥ Pavel Rehak,⊥ Lela Vukovic,́# Linda J. W. Shimon,¶ Petr Kral,́⊥,□ Roy Beck,‡ and Ehud Gazit*,†,△ † Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel ‡ The Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel § Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, United States ∥ Department of Oral Biology, The Goldschleger School of Dental Medicine, Tel Aviv University, Tel Aviv 69978, Israel ⊥ Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States # Department of Chemistry, University of Texas at El Paso, El Paso, Texas 79968, United States ¶ Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel □ Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States △ Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel *S Supporting Information ABSTRACT: The ensemble of native, folded state was once considered to represent the global energy minimum of a given protein sequence. More recently, the discovery of the cross-β amyloid state revealed that deeper energy minima exist, often associated with pathogenic, fibrillar deposits, when the concentration of proteins reaches a critical value. Fortunately, a sizable energy barrier impedes the conversion from native to pathogenic states. However, little is known about the structure of the related transition state. In addition, there are indications of polymorphism in the amyloidogenic process. Here, we report the first evidence of the conversion of metastable cross- α-helical crystals to thermodynamically stable cross-β-sheet- like fibrils by a de novo designed heptapeptide. Furthermore, for the first time, we demonstrate at atomic resolution that the flip of a peptide plane from a type I to a type II′ turn facilitates transformation to cross-β structure and assembly of a dry steric zipper. This study establishes the potential of a peptide turn, a Downloaded via UNIV OF ILLINOIS CHICAGO on January 31, 2019 at 18:36:08 (UTC). common protein secondary structure, to serve as a principal gatekeeper between a native metastable folded state and the See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles. amyloid state. ■ INTRODUCTION aggregates with cross-β structure at high pH and elevated 9 The aggregation of many intrinsically disordered as well as temperature. Subsequently, it has been indicated that above a globular proteins into insoluble fibrillar deposits with cross-β critical concentration the natively folded soluble proteins may be metastable in nature and the corresponding Gibbs free architecture is the hallmark of various debilitating pathologies, fi including Alzheimer’s, Parkinson’s, and Huntington’s dis- energy may represent a local minimum in the energy pro le, 1−4 whereas amyloid fibrils are lower in energy (and thus more eases. Critical evidence suggests that several of the natively 10,11 unfolded sequences, en route to aggregation, populate an favorable) and may actually represent a global minimum. A intermediate oligomeric state rich in helix−helix associations, recent report further suggested that the amyloid state can populate different energy levels with novel structural features whereas the intermediate state of globular proteins proceeds 12 via assembly of partially unfolded native-like structures and and revealed the polymorphism within amyloid species. − many of them have helical conformation.5 8 In a pioneering Proteins can also assemble into crystal lattices composed of work, Dobson and co-workers demonstrated that myoglobin, a predominantly α-helical globular protein, not related to any Received: September 23, 2018 known disease conditions, converts to amyloid-like fibrillar Published: December 11, 2018 © 2018 American Chemical Society 363 DOI: 10.1021/jacs.8b10289 J. Am. Chem. Soc. 2019, 141, 363−369 Journal of the American Chemical Society Article native metastable conformations.13,14 Thus, an in situ characterization of the conformational conversion between the native crystalline and cross-β ensembles is expected to provide important atomic-level insights into the structural factors affecting the relative stability of the metastable and − amyloid states and the nature of the transition state.15 17 However, the inability of intrinsically disordered pathologically relevant sequences to form metastable crystalline assemblies has so far hindered such deliberation. Moreover, the different conditions required for in vitro fibril formation and crystallization of natively folded proteins,1,7,9 in contrast to the constant physiological conditions under which amyloido- genesis progresses in vivo,15,18 also comprise a major obstacle. Significant advancements toward understanding the struc- tural basis for amyloid formation came from the utilization of − minimal amyloidogenic fragments.19 21 Most notably, the first atomic resolution structure of amyloid cross-β spines was deciphered by microcrystal X-ray diffraction of the GNNQQNY heptapeptide, a truncated sequence of the prion-determining domain of the yeast protein Sup35.22 Recently, Mezzenga and co-workers studied several homolo- gous hexapeptides demonstrating that amyloid crystals, rather than amyloid fibrils, represent the true thermodynamic minima.23 Yet, a peptide aggregation system delineating the Figure 1. Supramolecular helical organization of SHR-FF. (a) atomic details of both the metastable state and amyloid fibers, Chemical structure of the SHR-FF heptapeptide. (b) Experimental fi formed under physiologically relevant conditions and separated WAXS (1) and PXRD (2) pro les of SHR-FF and a predicted PXRD pattern (3) generated from the crystal structure shown in (c). Major only by the time scale of aggregation, is still unavailable. Here, ff using a de novo designed heptapeptide sequence, we report the di erences in peaks are highlighted with shaded bars. (c) Single- crystal X-ray analysis of cross-α architecture of SHR-FF viewed first real-time observation and atomic resolution evidence of α parallel (top) and perpendicular (bottom, represented as solvent- the conversion of a metastable cross- -helical crystal into accessible surface) to the length of the crystal. Blue and red denote cross-β-like crystalline fibers. Furthermore, these experiments positively and negatively charged surfaces, respectively, and gray allowed us to examine the role of the peptide turn, a common denotes a hydrophobic surface. structural feature in a protein loop, in determining the transition of a native peptide into an amyloid structure. supported the helical conformation (Figure S1). Since a cross-α structure cannot account for the observed X-ray ■ RESULTS AND DISCUSSION scattering profile, it was concluded that SHR-FF could adopt Recently, we have demonstrated the ability of a short seven- two distinct higher order self-assembled states. Additional residue sequence, SHR-FF, to self-assemble into crystalline WAXS analysis established that the formation of a noncross-α supramolecular fibrillar structures (Figure 1a).24 To gain fibrillar state does not depend on the cosolvent or buffer further insight into the atomistic features of the SHR-FF compositions (Figure S2). fibrillar assembly, we performed X-ray powder diffraction To distinguish the boundaries between the two phases of (PXRD) analysis of the lyophilized fiber assemblies (Figure SHR-FF and ascertain their morphological differences, freshly 1b). Furthermore, to eliminate the possibility of structural prepared SHR-FF solutions (5 mg mL−1) were assembled at reorganization during drying, the wide-angle X-ray scattering different temperatures. Consistent with our diffraction studies, (WAXS) spectra of the self-assembled nanofibers were also two distinct types of self-assembled structures were evident by recorded in their original mother liquor without lyophilization. optical and transmission electron microscopy (Figures 2a,b The PXRD and WAXS analyses revealed the same diffraction and S3). At a low temperature (4 °C), SHR-FF assembly was profiles, both distinctly different from the predicted PXRD dominated by elongated flat tape-like microstructures, whereas pattern of the reported X-ray crystal structure (Figure 1b).24 at a relatively elevated temperature (30 °C), it formed The SHR-FF crystal was regrown under conditions native to nanofibers. We used microcrystal diffraction techniques to fibril assemblies as shown in Figure 1c. determine the atomic structure of the fibrillar assembly (Figure Single-crystal X-ray structural analysis revealed that the 2c). Unlike the cross-α structure, the dihedral angles of the peptide adopted an amphiphilic helical conformation, with peptide backbones, except for the α-aminoisobutyric acid adjacent helical molecules interacting through π-stacking and residues, reside in the allowed β-sheet region (Table S1). SHR- hydrophobic interactions, as reported earlier.24 These colum- FF adopted a looplike conformation
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