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Robang A, Wong KM, Leisen J, Liu R, Radford WL, Rao Sudarshan T, Hudalla GA, Paravastu AK. Parallel β-Sheet Structure and Structural Heterogeneity Detected within Q11 Self-Assembling Peptide Nanofibers. J Phys Chem B 2024; 128:5387-5396. [PMID: 38787393 PMCID: PMC11163420 DOI: 10.1021/acs.jpcb.4c00825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Q11 peptide nanofibers are used as a biomaterial for applications such as antigen presentation and tissue engineering, yet detailed knowledge of molecular-level structure has not been reported. The Q11 peptide sequence was designed using heuristics-based patterning of hydrophobic and polar amino acids with oppositely charged amino acids placed at opposite ends of the sequence to promote antiparallel β-sheet formation. In this work, we employed solid-state nuclear magnetic resonance spectroscopy (NMR) to evaluate whether the molecular organization within Q11 self-assembled peptide nanofibers is consistent with the expectations of the peptide designers. We discovered that Q11 forms a distribution of molecular structures. NMR data from two-dimensional (2D) 13C-13C dipolar-assisted rotational resonance indicate that the K3 and E9 residues between Q11 β-strands are spatially proximate (within ∼0.6 nm). Frequency-selective rotational echo double resonance (fsREDOR) on K3 Nζ and E9 Cδ-labeled sites showed that approximately 9% of the sites are close enough for salt bridge formation to occur. Surprisingly, dipolar recoupling measurements revealed that Q11 peptides do not assemble into antiparallel β-sheets as expected, and structural analysis using Fourier-transform infrared spectroscopy and 2D NMR alone can be misleading. 13C PITHIRDS-CT dipolar recoupling measurements showed that the most abundant structure consists of parallel β-sheets, in contrast to the expected antiparallel β-sheet structure. Structural heterogeneity was detected from 15N{13C} REDOR measurements, with approximately 22% of β-strands having antiparallel nearest neighbors. We cannot propose a complete structural model of Q11 nanofibers because of the complexity involved when examining structurally heterogeneous samples using NMR. Altogether, our results show that while heuristics-based patterning is effective in promoting β-sheet formation, designing a peptide sequence to form a targeted β-strand arrangement remains challenging.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kong M. Wong
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Johannes Leisen
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Renjie Liu
- J. Crayton
Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Walker L. Radford
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Tarunya Rao Sudarshan
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gregory A. Hudalla
- J. Crayton
Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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2
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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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3
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Saklani R, Domb AJ. Peptide and Protein Stereocomplexes. ACS OMEGA 2024; 9:17726-17740. [PMID: 38680378 PMCID: PMC11044247 DOI: 10.1021/acsomega.4c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 05/01/2024]
Abstract
Stereocomplexation in peptides and proteins is a fascinating phenomenon arising from their inherent stereoisomerism. Peptides and proteins, with their three-dimensional helical structures, exhibit stereoselectivity and form intertwined complexes when complementary left- and right-handed structures are mixed together. Stereocomplexation provides an unprecedented opportunity to impart some valuable biological, chemical, and physical properties in peptide and protein polymeric platforms that can be employed in various applications such as catalysis and drug delivery and to improve the stability of these therapeutics. However, exploration of stereocomplexation in peptides and proteins remains limited. We report on a comprehensive understanding of stereocomplexation in peptides and proteins, compiling existing reports, discussing its implications, and highlighting its role in different applications, aiming to inspire further research and advancements in this direction.
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Affiliation(s)
- Ravi Saklani
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Abraham J. Domb
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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4
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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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5
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Koch KN, Teo AJ, Wheeler KA. Dual space divergence in small molecule quasiracemates: benzoyl leucine and phenylalanine assemblies. Chem Commun (Camb) 2024; 60:2800-2803. [PMID: 38362749 DOI: 10.1039/d3cc06212k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Quasiracemic materials constructed with two points of structural difference were used to understand the role molecular shape plays in molecular assembly. Hot stage, crystallographic and occupied cavity space assessments provide insight into how imposed CH3/Cl and H/CF3 structural variations placed on benzoyl leucine and phenylalanine scaffolds result in a remarkably high occurrence of cocrystal formation.
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Affiliation(s)
- Katelyn N Koch
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, Washington, 99251, USA.
| | - Aaron J Teo
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, Washington, 99251, USA.
| | - Kraig A Wheeler
- Department of Chemistry, Whitworth University, 300 West Hawthorne Road, Spokane, Washington, 99251, USA.
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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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