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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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Structure of Silk I ( Bombyx mori Silk Fibroin before Spinning) -Type II β-Turn, Not α-Helix. Molecules 2021; 26:molecules26123706. [PMID: 34204550 PMCID: PMC8234240 DOI: 10.3390/molecules26123706] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/04/2022] Open
Abstract
Recently, considerable attention has been paid to Bombyx mori silk fibroin by a range of scientists from polymer chemists to biomaterial researchers because it has excellent physical properties, such as strength, toughness, and biocompatibility. These appealing physical properties originate from the silk fibroin structure, and therefore, structural determinations of silk fibroin before (silk I) and after (silk II) spinning are a key to make wider applications of silk. There are discrepancies about the silk I structural model, i.e., one is type II β-turn structure determined using many solid-state and solution NMR spectroscopies together with selectively stable isotope-labeled model peptides, but another is α-helix or partially α-helix structure speculated using IR and Raman methods. In this review, firstly, the process that led to type II β-turn structure by the authors was introduced in detail. Then the problems in speculating silk I structure by IR and Raman methods were pointed out together with the problem in the assignment of the amide I band in the spectra. It has been emphasized that the conformational analyses of proteins and peptides from IR and Raman studies are not straightforward and should be very careful when the proteins contain β-turn structure using many experimental data by Vass et al. In conclusion, the author emphasized here that silk I structure should be type II β-turn, not α-helix.
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The Silk I and Lamella Structures of (Ala-Gly)15 as the Model of Bombyx mori Silk Fibroin Studied with Solid State NMR. BIOTECHNOLOGY OF SILK 2014. [DOI: 10.1007/978-94-007-7119-2_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Asakura T, Suzuki Y, Nakazawa Y, Yazawa K, Holland GP, Yarger JL. Silk structure studied with nuclear magnetic resonance. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 69:23-68. [PMID: 23465642 DOI: 10.1016/j.pnmrs.2012.08.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
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Yazawa K, Yamaguchi E, Aoki A, Nakazawa Y, Suzuki Y, Asakura T. A two-dimensional spin-diffusion NMR study on the local structure of a water-soluble model peptide for Nephila clavipes dragline silk (MaSp1) before and after spinning. Polym J 2012. [DOI: 10.1038/pj.2012.98] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wen X, Peng X, Fu H, Dong Y, Han K, Su J, Wang Z, Wang R, Pan X, Huang L, Wu C. Preparation and in vitro evaluation of silk fibroin microspheres produced by a novel ultra-fine particle processing system. Int J Pharm 2011; 416:195-201. [DOI: 10.1016/j.ijpharm.2011.06.041] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/29/2011] [Accepted: 06/23/2011] [Indexed: 11/25/2022]
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Spiess K, Ene R, Keenan CD, Senker J, Kremer F, Scheibel T. Impact of initial solvent on thermal stability and mechanical properties of recombinant spider silk films. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm11700a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Li XG, Wu LY, Huang MR, Shao HL, Hu XC. Conformational transition and liquid crystalline state of regenerated silk fibroin in water. Biopolymers 2008; 89:497-505. [DOI: 10.1002/bip.20905] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hu BW, Zhou P, Noda I, Ruan QX. Generalized Two-Dimensional Correlation Analysis of NMR and Raman Spectra for Structural Evolution Characterizations of Silk Fibroin. J Phys Chem B 2006; 110:18046-51. [PMID: 16956296 DOI: 10.1021/jp062461y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Generalized two-dimensional (2D) correlation spectroscopy was used to characterize the structural evolution of silk fibroin as the pH changed from 6.8 to 4.8, demonstrating that the conformational transitions of silk fibroin are induced step by step as the pH decreases. 2D homo- and hetero-spectral correlation spectroscopy was used to establish the relationship between information extracted from NMR and Raman spectroscopy. This novel method reveals the structural evolution using two probes with different frequency scales (10(5-9) Hz for nuclear spin motion and 10(12-14) Hz for molecular vibration motion), reflecting the different spatial scale sensitivity to the molecular conformational change. The transition order is identified as silk I state (helix dominant) --> silk I intermediate state --> silk II intermediate state --> silk II state (beta-sheet dominant), as the pH decreases. The results may rationalize the silkworm spinning process, which undergoes the conformational transition steadily from the soluble helix state to the insoluble beta-sheet state as the pH decreases from the posterior to anterior glands.
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Affiliation(s)
- Bing-Wen Hu
- The Key Laboratory of Molecular Engineering of Polymers, Ministry of Education, Department of Macromolecular Science, Fudan University, Shanghai 200433, P. R. China
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Borsacchi S, Cappellozza S, Catalano D, Geppi M, Ierardi V. Solid State NMR Investigation of the Molecular Dynamics of Cocoon Silks Produced by Different Bombyx mori (Lepidoptera) Strains. Biomacromolecules 2006; 7:1266-73. [PMID: 16602748 DOI: 10.1021/bm0510092] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cocoons produced by different strains of Bombyx mori larvae were investigated by a combination of several high- and low-resolution 1H and 13C solid-state NMR techniques in order to characterize and compare their dynamic behavior at a molecular level. A detailed interpretation in terms of molecular motions in these very complex systems was possible thanks to the integrated analysis of different relaxation measurements and high-resolution selective experiments. Untreated cocoons of all strains were found to be mainly constituted by two different types of rigid domains and by a third one, more mobile, due to physisorbed water molecules. Dynamic processes in the MHz and kHz ranges were characterized by means of different 1H and 13C relaxation times. Cocoons arising from different strains exhibit a different content of physisorbed water and also slightly different dynamic behavior, especially in the MHz regime.
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Affiliation(s)
- Silvia Borsacchi
- Dipartimento di Chimica e Chimica Industriale, Università degli Studi di Pisa, v. Risorgimento 35, 56126 Pisa, Italy
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Witter R, Sternberg U, Ulrich AS. NMR Chemical Shift Powder Pattern Recoupling at High Spinning Speed and Theoretical Tensor Evaluation Applied to Silk Fibroin. J Am Chem Soc 2006; 128:2236-43. [PMID: 16478177 DOI: 10.1021/ja051730f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The NMR pulse sequence RAI (recoupling of anisotropy information) has been improved to obtain powder patterns at high MAS spinning speeds. The 2D iso-aniso experiment displays the static chemical shift spectra on the indirect dimension and the MAS spectra on the direct dimension; hence overlapping chemical shift tensor patterns can be well resolved. This efficient technique is applicable to compounds containing (13)C sp(3) (C(alpha), C(beta)) and sp(2) (C=O) sites with higher chemical shift (CS) anisotropy (CSA), and the reliability of the method was tested here on the (13)C chemical shift tensors of polycrystalline glycine, alanine, and serine. Subsequently, the same experiment was applied to the native silk protein fibroin from Bombyx mori, which consists mainly of these three amino acids. Molecular dynamics (MD) simulations of the silk II crystal structure of Takahashi et al. (Takahashi et al. Int. J. Biol. Macromol. 1999, 24, 127-138) were carried out to study the influence of motions on the chemical shift tensors. The (13)C chemical shift tensors were calculated using the bond polarization theory BPT on 200 structures created by an MD simulation. Very good agreement of the theoretical chemical shift anisotropy values with the experimental NMR results was obtained. The tensor orientations in the protein structure could thus be reliably derived.
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Affiliation(s)
- Raiker Witter
- Forschungszentrum Karlsruhe, IBG, POB 3640, 76021 Karlsruhe, Germany.
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Ohgo K, Ashida J, Kumashiro KK, Asakura T. Structural Determination of an Elastin-Mimetic Model Peptide, (Val-Pro-Gly-Val-Gly)6, Studied by 13C CP/MAS NMR Chemical Shifts, Two-Dimensional off Magic Angle Spinning Spin-Diffusion NMR, Rotational Echo Double Resonance, and Statistical Distribution of Torsion Angles from Protein Data Bank. Macromolecules 2005. [DOI: 10.1021/ma050052e] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kosuke Ohgo
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan, Varian Technologies Japan Ltd., Minato, Tokyo 108-0023, Japan, and Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822
| | - Jun Ashida
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan, Varian Technologies Japan Ltd., Minato, Tokyo 108-0023, Japan, and Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822
| | - Kristin K. Kumashiro
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan, Varian Technologies Japan Ltd., Minato, Tokyo 108-0023, Japan, and Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan, Varian Technologies Japan Ltd., Minato, Tokyo 108-0023, Japan, and Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822
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Ohgo K, Kurano TL, Kumashiro KK, Asakura T. Structure of the model peptides of Bombyx mori silk-elastin like protein studied with solid state NMR. Biomacromolecules 2005; 5:744-50. [PMID: 15132656 DOI: 10.1021/bm034355x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The peptides (AG)(6)(VPGVG)(AG)(7) and (AG)(5)(VPGVG)(2)(AG)(5) are models for a new type of protein with both composition and properties such as Bombyx mori silk and elastin. In this paper, we report the solid-state NMR results for these samples and related peptides; the structures after dialysis of the 9 M LiBr aqueous solution and after treatment with formic acid were determined and compared. The detailed structural analyses were performed using deconvolution subroutines assuming Gaussian line shapes for the Ala Cbeta peaks of the (AG)(n) sequences in these peptides. The peptide (AG)(6)(VPGVG)(AG)(7) took the silk II structure after the dialysis, which is in contrast to the silk I form of (AG)(15) after the same treatment. However, a drastic structural change of the (AG)(n) sequences was observed for (AG)(5)(VPGVG)(2)(AG)(5); the fraction of distorted beta-turn was 81% after the dialysis, but the distorted beta-sheet became dominant (84%) after treatment with formic acid. The local structures of the Gly residue of the VG units in the elastin-like subunits, (VPGVG) and (VPGVG)(2), were the distorted structures with a distribution of the torsion angles, which was derived from the 2D spin diffusion NMR spectral pattern of (AG)(5)VPG[1-(13)C]V[1-(13)C]GVPGVG(AG)(5). Observation of this distribution of the Gly residue was independent of the treatment, dialysis or formic acid.
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Affiliation(s)
- Kosuke Ohgo
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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Sine-modulated two-dimensional pure exchange solid-state NMR as a tool for characterizing dynamics in solids. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)01186-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Nakazawa Y, Asakura T. Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods. J Am Chem Soc 2003; 125:7230-7. [PMID: 12797796 DOI: 10.1021/ja0300721] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.
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Affiliation(s)
- Yasumoto Nakazawa
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588 Japan
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Asakura T, Nitta K, Yang M, Yao J, Nakazawa Y, Kaplan DL. Synthesis and characterization of chimeric silkworm silk. Biomacromolecules 2003; 4:815-20. [PMID: 12741803 DOI: 10.1021/bm034020f] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A synthetic gene encoding a chimeric silklike protein was constructed that combined a polyalanine encoding region (Ala)(18), a sequence slightly longer than the (Ala)(12-13) found in the silk fibroin from the wild silkworm Samia cynthia ricini, and a sequence encoding GVGAGYGAGAGYGVGAGYGAGVGYGAGAGY, found in the silk fibroin from the silkworm Bombyx mori. A tetramer of the chimeric repeat sequence encoding a approximately 29 kDa protein was expressed as a fusion protein in Escherichia coli. In comparison to S. c. ricini silk, the chimeric protein demonstrated improved solubility because it could be dissolved in 8 M urea. The purified protein assumed an alpha-helical structure based on solid-state (13)C CP/MAS NMR and was less prone to conformational transition to a beta-sheet, unlike native silk proteins from S. c. ricini. Model peptides representing the crystalline region of S. c. ricini silk fibroin, (Ala)(12) and (Ala)(18), formed beta-sheet structures. Therefore, the solubility and structural transitions of the chimeric protein were significantly altered through the formation of this chimeric silk. This experimental strategy to the study of silk structure and function can be used to develop an improved understanding of the contributions of protein domains in repetitive silkworm and spider silk sequences to structure development and structural transitions.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
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