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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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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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3
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Kuhn AJ, Ehlke B, Johnstone TC, Oliver SRJ, Raskatov JA. A crystal-structural study of Pauling-Corey rippled sheets. Chem Sci 2022; 13:671-680. [PMID: 35173931 PMCID: PMC8768883 DOI: 10.1039/d1sc05731f] [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: 10/16/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Following the seminal theoretical work on the pleated β-sheet published by Pauling and Corey in 1951, the rippled β-sheet was hypothesized by the same authors in 1953. In the pleated β-sheet the interacting β-strands have the same chirality, whereas in the rippled β-sheet the interacting β-strands are mirror-images. Unlike with the pleated β-sheet that is now common textbook knowledge, the rippled β-sheet has been much slower to evolve. Much of the experimental work on rippled sheets came from groups that study aggregating racemic peptide systems over the course of the past decade. This includes MAX1/DMAX hydrogels (Schneider), L/D-KFE8 aggregating systems (Nilsson), and racemic Amyloid β mixtures (Raskatov). Whether a racemic peptide mixture is “ripple-genic” (i.e., whether it forms a rippled sheet) or “pleat-genic” (i.e., whether it forms a pleated sheet) is likely governed by a complex interplay of thermodynamic and kinetic effects. Structural insights into rippled sheets remain limited to only a very few studies that combined sparse experimental structural constraints with molecular modeling. Crystal structures of rippled sheets are needed so we can rationally design rippled sheet architectures. Here we report a high-resolution crystal structure, in which (l,l,l)-triphenylalanine and (d,d,d)-triphenylalanine form dimeric antiparallel rippled sheets, which pack into herringbone layer structures. The arrangements of the tripeptides and their mirror-images in the individual dimers were in excellent agreement with the theoretical predictions by Pauling and Corey. A subsequent mining of the PDB identified three orphaned rippled sheets among racemic protein crystal structures. Following the seminal theoretical work on the pleated β-sheet published by Pauling and Corey in 1951, the rippled β-sheet was hypothesized by the same authors in 1953.![]()
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Affiliation(s)
- Ariel J Kuhn
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
| | - Beatriz Ehlke
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
| | - Timothy C Johnstone
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
| | - Scott R J Oliver
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California USA
| | - Jevgenij A Raskatov
- Dept. of Chemistry and Biochemistry, UCSC 1156 High Street Santa Cruz California 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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Foley AR, Raskatov JA. Understanding and controlling amyloid aggregation with chirality. Curr Opin Chem Biol 2021; 64:1-9. [PMID: 33610939 PMCID: PMC8368077 DOI: 10.1016/j.cbpa.2021.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 12/22/2022]
Abstract
Amyloid aggregation and human disease are inextricably linked. Examples include Alzheimer disease, Parkinson disease, and type II diabetes. While seminal advances on the mechanistic understanding of these diseases have been made over the last decades, controlling amyloid fibril formation still represents a challenge, and it is a subject of active research. In this regard, chiral modifications have increasingly been proved to offer a particularly well-suited approach toward accessing to previously unknown aggregation pathways and to provide with novel insights on the biological mechanisms of action of amyloidogenic peptides and proteins. Here, we summarize recent advances on how the use of mirror-image peptides/proteins and d-amino acid incorporations have helped modulate amyloid aggregation, offered new mechanistic tools to study cellular interactions, and allowed us to identify key positions within the peptide/protein sequence that influence amyloid fibril growth and toxicity.
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Affiliation(s)
- Alejandro R Foley
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
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Raskatov JA, Foley A, Louis JM, Yau WM, Tycko R. Constraints on the Structure of Fibrils Formed by a Racemic Mixture of Amyloid-β Peptides from Solid-State NMR, Electron Microscopy, and Theory. J Am Chem Soc 2021; 143:13299-13313. [PMID: 34375097 PMCID: PMC8456612 DOI: 10.1021/jacs.1c06339] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Previous studies have shown that racemic mixtures of 40- and 42-residue amyloid-β peptides (d,l-Aβ40 and d,l-Aβ42) form amyloid fibrils with accelerated kinetics and enhanced stability relative to their homochiral counterparts (l-Aβ40 and l-Aβ42), suggesting a "chiral inactivation" approach to abrogating the neurotoxicity of Aβ oligomers (Aβ-CI). Here we report a structural study of d,l-Aβ40 fibrils, using electron microscopy, solid-state nuclear magnetic resonance (NMR), and density functional theory (DFT) calculations. Two- and three-dimensional solid-state NMR spectra indicate molecular conformations in d,l-Aβ40 fibrils that resemble those in known l-Aβ40 fibril structures. However, quantitative measurements of 13C-13C and 15N-13C distances in selectively labeled d,l-Aβ40 fibril samples indicate a qualitatively different supramolecular structure. While cross-β structures in mature l-Aβ40 fibrils are comprised of in-register, parallel β-sheets, our data indicate antiparallel β-sheets in d,l-Aβ40 fibrils, with alternation of d and l molecules along the fibril growth direction, i.e., antiparallel "rippled sheet" structures. The solid-state NMR data suggest the coexistence of d,l-Aβ40 fibril polymorphs with three different registries of intermolecular hydrogen bonds within the antiparallel rippled sheets. DFT calculations support an energetic preference for antiparallel alignments of the β-strand segments identified by solid-state NMR. These results provide insight into the structural basis for Aβ-CI and establish the importance of rippled sheets in self-assembly of full-length, naturally occurring amyloidogenic peptides.
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Affiliation(s)
- Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Alejandro Foley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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Grelich-Mucha M, Garcia AM, Torbeev V, Ożga K, Berlicki Ł, Olesiak-Bańska J. Autofluorescence of Amyloids Determined by Enantiomeric Composition of Peptides. J Phys Chem B 2021; 125:5502-5510. [PMID: 34008978 PMCID: PMC8182742 DOI: 10.1021/acs.jpcb.1c00808] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Amyloid fibrils are
peptide or protein aggregates possessing a
cross-β-sheet structure. They possess intrinsic fluorescence
property, which is still not fully understood. Herein, we compare
structural and optical properties of fibrils formed from L- and D-enantiomers
of the (105–115) fragment of transthyretin (TTR) and from their
racemic mixture. Our results show that autofluorescence of fibrils
obtained from enantiomers differs from that of fibrils from the racemic
mixture. In order to elucidate the origin of observed differences,
we analyzed the structure and morphology of fibrils and showed how
variations in β-sheet organization influence optical properties
of fibrils. We clarified the contribution of aromatic rings and the
amyloid backbone to the final blue-green emission of fibrils. This
work demonstrates how enantiomeric composition of amino acids allows
us to modulate the self-assembly and final morphology of well-defined
fibrillar bionanostructures with optical properties controlled by
supramolecular organization.
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Affiliation(s)
- Manuela Grelich-Mucha
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ana M Garcia
- Institute de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006) Strasbourg 67000, France
| | - Vladimir Torbeev
- Institute de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006) Strasbourg 67000, 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
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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Raskatov JA, Schneider JP, Nilsson BL. Defining the Landscape of the Pauling-Corey Rippled Sheet: An Orphaned Motif Finding New Homes. Acc Chem Res 2021; 54:2488-2501. [PMID: 33901396 PMCID: PMC8154201 DOI: 10.1021/acs.accounts.1c00084] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
When peptides are mixed with their mirror images in an equimolar
ratio, two-dimensional periodic structural folds can form, in which
extended peptide strands are arrayed with alternating chirality. The
resultant topography class, termed the rippled β-sheet, was
introduced as a theoretical concept by Pauling and Corey in 1953.
Unlike other fundamental protein structural motifs identified around
that time, including the α-helix and the pleated β-sheet,
it took several decades before conclusive experimental data supporting
the proposed rippled β-sheet motif were gained. Much of the
key experimental evidence was provided over the course of the past
decade through the concurrent efforts of our three laboratories. Studies
that focused on developing new self-assembling hydrogel materials
have shown that certain amphiphilic peptides form fibrils and hydrogel
networks that are more rigid and have a higher thermodynamic stability
when made from racemic peptide mixtures as opposed to pure enantiomers.
Related interrogation of assemblies composed of mixtures of l- and d-amphiphilic peptides confirmed that the resulting
fibrils were composed of alternating l/d peptides
consistent with rippled β-sheets. It was also demonstrated that
mirror-image amyloid beta (Aβ) could act as a molecular chaperone
to promote oligomer-to-fibril conversion of the natural Aβ enantiomer,
which was found to reduce Aβ neurotoxicity against different
neuronal cell models. With a cross-disciplinary approach that combines
experiment and theory, our three laboratories have demonstrated the
unique biophysical, biochemical, and biological properties that arise
upon mixing of peptide enantiomers, in consequence of rippled β-sheet
formation. In this Account, we give an overview of the early history
of the rippled β-sheet and provide a detailed structural description/definition
of this motif relative to the pleated β-sheet. We then summarize
the key findings, obtained on three unique sets of aggregating mirror-image
peptide pairs through independent efforts of our three laboratories,
and use these results to delineate the landscape of the rippled β-sheet
structural motif to inspire future studies. Peptide sequence parameters
that favor rippled β-sheet assembly are described, along with
the accompanying kinetic and thermodynamic properties, as well as
the resulting emergent physical properties of the assemblies. The
Account then concludes with a brief overview of some key unresolved
challenges in this nascent field. There is much potential for future
applications of this unique supramolecular motif in the realm of materials
design and biomedical research. We hope this Account will stimulate
much-needed discussion of this fascinating structural class to eventually
produce a fully quantitative, rational framework for the molecular
engineering of rippled β-sheets in the future.
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Affiliation(s)
- Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joel P. Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Bradley L. Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
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