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Lee H, Yang MY, Raskatov JA, Kim H, Goddard WA. Molecular Dynamics Studies of Atomistically Determined Fibrillar Assemblies: Comparison of the Rippled β-Sheet, Pleated β-Sheet, and Herringbone Structures. J Phys Chem Lett 2024; 15:4568-4574. [PMID: 38639377 DOI: 10.1021/acs.jpclett.4c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Pauling and Corey expected that a racemic mixture would result in a rippled β-sheet, however, it has been known from experiments that the racemic mixtures of triphenylalanine lead to a herringbone structure. Because of the theoretical limitations concerning crystal structures such as rippled β-sheet, it is inevitable to understand how the interplay of the amino acids prefers a specific structural motif. In this paper we use molecular dynamics to understand the sequence- and enantiomer-dependent structures by comparisons between rippled β-sheet and pleated β-sheet, solvated and anhydrous rippled β-sheet, and rippled β-sheet and the herringbone structure, based on thermodynamics and structures at the atomic level. The tripeptides select the favored structure that can be stabilized through aromatic or hydrogen bonding interactions between tripeptides. Furthermore, the solubility is determined by the environment of space that is created around the side chains. Our findings provide comprehensive insight into the crystallized fibril motif of the polypeptide.
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Affiliation(s)
- Hyeonju Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, Republic of Korea
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Moon Young Yang
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Jevgenij A Raskatov
- UC Santa Cruz Department of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-Ro, Yuseong-Gu, Daejeon 34141, Republic of Korea
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - William A Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
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Grelich-Mucha M, Bachelart T, Torbeev V, Ożga K, Berlicki Ł, Olesiak-Bańska J. Amyloid engineering - how terminal capping modifies morphology and secondary structure of supramolecular peptide aggregates. Biomater Sci 2024; 12:1590-1602. [PMID: 38323504 DOI: 10.1039/d3bm01641b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The effects of peptide N- and C-termini on aggregation behavior have been scarcely studied. Herein, we examine (105-115) peptide fragments of transthyretin (TTR) containing various functional groups at both termini and study their impact on the morphology and the secondary structure. We synthesized TTR(105-115) peptides functionalized with α-amino (H-), N-acetyl-α-amino (Ac-) or N,N-dimethyl-α-amino (DiMe-) groups at the N-terminus, and with amide (-NH2) or carboxyl (-OH) functions at the C-terminus. We also investigated quasi-racemic mixtures by mixing the L-enantiomers with the D-enantiomer capped by H- and -NH2 groups. We observed that fibril formation is promoted by the sufficient number of hydrogen bonds at peptides' termini. Moreover, the final morphology of the aggregates can be controlled by the functional groups at the N-terminus. Remarkably, all quasi-racemic mixtures resulted in the robust formation of fibrils. Overall, this work illustrates how modifications of peptide termini may help to engineer supramolecular aggregates with a predicted morphology.
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Affiliation(s)
- Manuela Grelich-Mucha
- Institute of Advanced Materials, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Thomas Bachelart
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400 Illkirch, France
| | - Vladimir Torbeev
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg, 67400 Illkirch, France
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Bańska
- Institute of Advanced Materials, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
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Hazari A, Sawaya MR, Sajimon M, Vlahakis N, Rodriguez J, Eisenberg D, Raskatov JA. Racemic Peptides from Amyloid β and Amylin Form Rippled β-Sheets Rather Than Pleated β-Sheets. J Am Chem Soc 2023; 145:25917-25926. [PMID: 37972334 DOI: 10.1021/jacs.3c11712] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The rippled β-sheet was theorized by Pauling and Corey in 1953 as a structural motif in which mirror image peptide strands assemble into hydrogen-bonded periodic arrays with strictly alternating chirality. Structural characterization of the rippled β-sheet was limited to biophysical methods until 2022 when atomic resolution structures of the motif were first obtained. The crystal structural foundation is restricted to four model tripeptides composed exclusively of aromatic residues. Here, we report five new rippled sheet crystal structures derived from amyloid β and amylin, the aggregating toxic peptides of Alzheimer's disease and type II diabetes, respectively. Despite the variation in peptide sequence composition, all five structures form antiparallel rippled β-sheets that extend, like a fibril, along the entire length of the crystalline needle. The long-range packing of the crystals, however, varies. In three of the crystals, the sheets pack face-to-face and exclude water, giving rise to cross-β architectures grossly resembling the steric zipper motif of amyloid fibrils but differing in fundamental details. In the other two crystals, the solvent is encapsulated between the sheets, yielding fibril architectures capable of host-guest chemistry. Our study demonstrates that the formation of rippled β-sheets from aggregating racemic peptide mixtures in three-dimensional (3D) assemblies is a general phenomenon and provides a structural basis for targeting intrinsically disordered proteins.
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Affiliation(s)
- Amaruka Hazari
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
| | - Michael R Sawaya
- Dept. of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - Maria Sajimon
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
| | - Niko Vlahakis
- Dept. of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - Jose Rodriguez
- Dept. of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - David Eisenberg
- Dept. of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Box 951569, Los Angeles, California 90095-1569, United States
| | - Jevgenij A Raskatov
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
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Identification of heterochirality-mediated stereochemical interactions in peptide architectures. Colloids Surf B Biointerfaces 2023; 224:113200. [PMID: 36774824 DOI: 10.1016/j.colsurfb.2023.113200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/26/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
In this work, we illustrate a strategy for constructing heterochiral peptide architectures with distinct structural, mechanical and thermal characteristics. A series of nanotube structures based on diphenylalanine (FF) and its chiral derivatives were examined. Pronounced effects relating to heterochirality on mechanostability and thermal stability can be identified. The homochiral peptide FF and its enantiomer ff formed nanotubes with high thermal and mechanical stabilities (Young's modulus: 20.3 ± 5.9 GPa for FF and 21.2 ± 4.7 GPa for ff). In contrast, heterochiral nanotubes formed by Ff and fF manifest superstructures along the axial direction with differed thermal and mechanical strength (Young's modulus: 7.3 ± 2.4 GPa for Ff and 8.3 ± 2.1 GPa for fF). Combining their single-crystal XRD structure and in silico results, it was demonstrated that the spatial orientations of aromatic moieties were subtly changed by heterochirality of peptide building blocks, which led to intramolecular face-to-face interactions. As the result, both intermolecular axial and interchannel interactions in heterochiral nanotubes were weakened as reflected in the strikingly deteriorated mechanical and thermal stabilities. Conversely, two aromatic side chains of the homochiral peptides were staggered and formed interdigitated steric zippers, which served as strong glues that secured the robustness of nanotubes in both axial and radial orientation. Furthermore, the generality of the heterochiral-mediated stereochemical effects was demonstrated in other "FF class" dipeptides, including fluorinated Ff, FW and FL. Our results unequivocally revealed the relationship between amino acid chirality, peptide molecule packing, and physical stabilities of "FF class" dipeptide self-assembled materials and provide valuable molecular insights into chirality-mediated stereochemical interactions in determining the properties of peptide architectures.
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Hazari A, Sawaya MR, Vlahakis N, Johnstone TC, Boyer D, Rodriguez J, Eisenberg D, Raskatov JA. The rippled β-sheet layer configuration-a novel supramolecular architecture based on predictions by Pauling and Corey. Chem Sci 2022; 13:8947-8952. [PMID: 36091211 PMCID: PMC9365095 DOI: 10.1039/d2sc02531k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
The rippled β-sheet is a peptidic structural motif related to but distinct from the pleated β-sheet. Both motifs were predicted in the 1950s by Pauling and Corey. The pleated β-sheet was since observed in countless proteins and peptides and is considered common textbook knowledge. Conversely, the rippled β-sheet only gained a meaningful experimental foundation in the past decade, and the first crystal structural study of rippled β-sheets was published as recently as this year. Noteworthy, the crystallized assembly stopped at the rippled β-dimer stage. It did not form the extended, periodic rippled β-sheet layer topography hypothesized by Pauling and Corey, thus calling the validity of their prediction into question. NMR work conducted since moreover shows that certain model peptides rather form pleated and not rippled β-sheets in solution. To determine whether the periodic rippled β-sheet layer configuration is viable, the field urgently needs crystal structures. Here we report on crystal structures of two racemic and one quasi-racemic aggregating peptide systems, all of which yield periodic rippled antiparallel β-sheet layers that are in excellent agreement with the predictions by Pauling and Corey. Our study establishes the rippled β-sheet layer configuration as a motif with general features and opens the road to structure-based design of unique supramolecular architectures.
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Affiliation(s)
- Amaruka Hazari
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz CA 95064 USA
| | - Michael R Sawaya
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - Niko Vlahakis
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - Timothy C Johnstone
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz CA 95064 USA
| | - David Boyer
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - Jose Rodriguez
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - David Eisenberg
- Dept. of Chemistry and Biochemistry, UCLA 607 Charles E. Young Drive East Box 951569 Los Angeles CA 90095-1569 USA
| | - Jevgenij A Raskatov
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz CA 95064 USA
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Li X, Rios SE, Nowick JS. Enantiomeric β-sheet peptides from Aβ form homochiral pleated β-sheets rather than heterochiral rippled β-sheets. Chem Sci 2022; 13:7739-7746. [PMID: 35865901 PMCID: PMC9258340 DOI: 10.1039/d2sc02080g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/11/2022] [Indexed: 12/18/2022] Open
Abstract
In 1953, Pauling and Corey postulated “rippled” β-sheets, composed of a mixture of d- and l-peptide strands, as a hypothetical alternative to the now well-established structures of “pleated” β-sheets, which they proposed as a component of all-l-proteins. Growing interest in rippled β-sheets over the past decade has led to the development of mixtures of d- and l-peptides for biomedical applications, and a theory has emerged that mixtures of enantiomeric β-sheet peptides prefer to co-assemble in a heterochiral fashion to form rippled β-sheets. Intrigued by conflicting reports that enantiomeric β-sheet peptides prefer to self-assemble in a homochiral fashion to form pleated β-sheets, we set out address this controversy using two β-sheet peptides derived from Aβ17–23 and Aβ30–36, peptides 1a and 1b. Each of these peptides self-assembles to form tetramers comprising sandwiches of β-sheet dimers in aqueous solution. Through solution-phase NMR spectroscopy, we characterize the different species formed when peptides 1a and 1b are mixed with their respective d-enantiomers, peptides ent-1a and ent-1b. 1H NMR, DOSY, and 1H,15N-HSQC experiments reveal that mixing peptides 1a and ent-1a results in the predominant formation of homochiral tetramers, with a smaller fraction of a new heterochiral tetramer, and mixing peptides 1b and ent-1b does not result in any detectable heterochiral assembly. 15N-edited NOESY reveals that the heterochiral tetramer formed by peptides 1a and ent-1a is composed of two homochiral dimers. Collectively, these NMR studies of Aβ-derived peptides provide compelling evidence that enantiomeric β-sheet peptides prefer to self-assemble in a homochiral fashion in aqueous solution. In aqueous solution, mixtures of l- and d- macrocyclic β-sheet peptides derived from Aβ self-assemble to form homochiral pleated β-sheets but do not co-assemble to form heterochiral rippled β-sheets.![]()
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Affiliation(s)
- Xingyue Li
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA 92697-2025, USA
| | - Stephanie E. Rios
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA 92697-2025, USA
| | - James S. Nowick
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA 92697-2025, USA
- Department of Pharmaceutical Sciences, University of California Irvine, 4126 Natural Sciences I, Irvine, CA 92697-2025, USA
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