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Asakura T, Williamson MP. A review on the structure of Bombyx mori silk fibroin fiber studied using solid-state NMR: An antipolar lamella with an 8-residue repeat. Int J Biol Macromol 2023:125537. [PMID: 37379946 DOI: 10.1016/j.ijbiomac.2023.125537] [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: 05/12/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
Silk fibroin (SF) fiber from the silkworm Bombyx mori in the Silk II form has been used as an excellent textile fiber for over 5000 years. Recently it has been developed for a range of biomedical applications. Further expansion of these uses builds on the excellent mechanical strength of SF fiber, which derives from its structure. This relationship between strength and SF structure has been studied for over 50 years, but it is still not well understood. In this review, we report the use of solid-state NMR to study stable-isotope labeled SF fiber and stable-isotope labeled peptides including (Ala-Gly)15 and (Ala-Gly-Ser-Gly-Ala-Gly)5 as models of the crystalline fraction. We show that the crystalline fraction is a lamellar structure with a repetitive folding using β-turns every eighth amino acid, and that the sidechains adopt an antipolar arrangement rather than the more well-known polar structure described by Marsh, Corey and Pauling (that is, the Ala methyls in each layer point in opposite directions in alternate strands). The amino acids Ser, Tyr and Val are the next most common in B. mori SF after Gly and Ala, and occur in the crystalline and semi-crystalline regions, probably defining the edges of the crystalline region. Thus, we now have an understanding of the main features of Silk II but there is still a long way to go.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan.
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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Gao Y, Guo C, Watzlawik JO, Randolph PS, Lee EJ, Huang D, Stagg SM, Zhou HX, Rosenberry TL, Paravastu AK. Out-of-Register Parallel β-Sheets and Antiparallel β-Sheets Coexist in 150-kDa Oligomers Formed by Amyloid-β(1-42). J Mol Biol 2020; 432:4388-4407. [PMID: 32470558 DOI: 10.1016/j.jmb.2020.05.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022]
Abstract
We present solid-state NMR measurements of β-strand secondary structure and inter-strand organization within a 150-kDa oligomeric aggregate of the 42-residue variant of the Alzheimer's amyloid-β peptide (Aβ(1-42)). We build upon our previous report of a β-strand spanned by residues 30-42, which arranges into an antiparallel β-sheet. New results presented here indicate that there is a second β-strand formed by residues 11-24. Contrary to expectations, NMR data indicate that this second β-strand is organized into a parallel β-sheet despite the co-existence of an antiparallel β-sheet in the same structure. In addition, the in-register parallel β-sheet commonly observed for amyloid fibril structure does not apply to residues 11-24 in the 150-kDa oligomer. Rather, we present evidence for an inter-strand registry shift of three residues that likely alternate in direction between adjacent molecules along the β-sheet. We corroborated this unexpected scheme for β-strand organization using multiple two-dimensional NMR and 13C-13C dipolar recoupling experiments. Our findings indicate a previously unknown assembly pathway and inspire a suggestion as to why this aggregate does not grow to larger sizes.
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Affiliation(s)
- Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Cong Guo
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai, China
| | - Jens O Watzlawik
- Departments of Neuroscience and Pharmacology, Mayo Clinic College of Medicine, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Peter S Randolph
- Institute of Molecular Biophysics, Florida State University, Tallahasse, FL 32306, USA
| | - Elizabeth J Lee
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Danting Huang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahasse, FL 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Chemistry and Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Terrone L Rosenberry
- Departments of Neuroscience and Pharmacology, Mayo Clinic College of Medicine, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332, USA.
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Abstract
This commentary summarizes the recent biophysical research conducted at the National Institute for Basic Biology, the National Institute for Physiological Sciences, and the Institute for Molecular Science in Okazaki, Japan.
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Asakura T, Nishimura A, Aoki A, Naito A. Packing Structure of Antiparallel β-Sheet Polyalanine Region in a Sequential Model Peptide of Nephila clavipes Dragline Silk Studied Using 13C Solid-State NMR and MD Simulation. Biomacromolecules 2019; 20:3884-3894. [PMID: 31449407 DOI: 10.1021/acs.biomac.9b00969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Packing structures of polyalanine regions, which are considered to be the reason for the extremely high strength of spider dragline silks, were studied using a series of sequential peptides: (Glu)4GlyGlyLeuGlyGlyGlnGlyAlaGly(Ala)nGlyGlyAlaGlyGlnGlyGlyTyrGlyGly(Glu)4 (n = 3-8) using 13C solid-state NMR spectroscopy. The conformations of (Ala)n in the freeze-dried peptides changed gradually with increasing n from random coils to α-helices with partial antiparallel β-sheet (AP-β) structures. Conversely, all the insolubilized peptides, n = 6-8 after low-pH treatment and n = 4-8 after formic acid/methanol treatment, formed AP-β structures with significant amounts of staggered packing arrangements. These results are different from previously obtained results for pure alanine oligopeptides, that is, AP-β (Ala)n formed rectangular packing for less than n = 6 but staggered packings for n ≥ 7. The 13C-labeled peptides were also used to confirm the staggered packing arrangements from NMR dynamics. Furthermore, a MD simulation supported the observed results.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei, Tokyo 184-8588 , Japan
| | - Akio Nishimura
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei, Tokyo 184-8588 , Japan
| | - Akihiro Aoki
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei, Tokyo 184-8588 , Japan
| | - Akira Naito
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei, Tokyo 184-8588 , Japan
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Naito A, Kametani S, Aoki A, Asakura T. Structural Analyses of Alanine Trimer and Tetramer Crystals with Antiparallel and Parallel β-Sheet Structures Using Solid-State 1H Spin-Diffusion 2D Correlation NMR Spectroscopy. J Phys Chem B 2018; 122:9373-9381. [PMID: 30234305 DOI: 10.1021/acs.jpcb.8b07859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Poly-l-alanine (PLA) sequences are key elements of the crystalline domains of spider dragline and wild silkworm silks. In the present work, 1H spin-diffusion two-dimensional (2D) correlation NMR spectra were observed for selectively deuterated (Ala)3 and (Ala)4 crystals to develop the analytical method for the structure of PLA sequences. The build-up curves of the cross peaks for three kinds of 1H pairs in selectively deuterated (Ala)3 and (Ala)4 crystals were observed to obtain spin-diffusion rate constant k j, k from relaxation master equations P i, j(τm). The k j, k values subsequently lead to effective interproton distance r j, keff (obs) values for individual proton-proton pairs, which include intra- and intermolecular contributions. The r j, keff (obs) values were compared to r j, keff (calc) values obtained from the experimentally determined atomic coordinates of antiparallel (AP) β-sheet (Ala)3 and (Ala)4 and parallel (P) β-sheet of (Ala)3 and (Ala)4 crystals. The agreement between the r j, keff (obs) and r j, keff (calc) values was good for AP β-sheet (Ala)3 and (Ala)4 crystals but poor for P β-sheet (Ala)3 and (Ala)4 crystals. These deviations were obtained from the interproton distances of the interchain contributions due to different packing arrangements. The packing arrangements of the PLA region are important when considering the relevant structure and the mechanical properties of silks.
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Affiliation(s)
- Akira Naito
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
| | - Shunsuke Kametani
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
| | - Akihiro Aoki
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
| | - Tetsuo Asakura
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
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