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Núñez-Villanueva D, Plata-Ruiz A, Romero-Muñiz I, Martín-Pérez I, Infantes L, González-Muñiz R, Martín-Martínez M. β-Turn Induction by a Diastereopure Azepane-Derived Quaternary Amino Acid. J Org Chem 2023; 88:14688-14696. [PMID: 37774108 PMCID: PMC10594656 DOI: 10.1021/acs.joc.3c01689] [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] [Received: 07/28/2023] [Indexed: 10/01/2023]
Abstract
β-Turns are one of the most common secondary structures found in proteins. In the interest of developing novel β-turn inducers, a diastereopure azepane-derived quaternary amino acid has been incorporated into a library of simplified tetrapeptide models in order to assess the effect of the azepane position and peptide sequence on the stabilization of β-turns. The conformational analysis of these peptides by molecular modeling, NMR spectroscopy, and X-ray crystallography showed that this azepane amino acid is an effective β-turn inducer when incorporated at the i + 1 position. Moreover, the analysis of the supramolecular self-assembly of one of the β-turn-containing peptide models in the solid state reveals that it forms a supramolecular helical arrangement while maintaining the β-turn structure. The results here presented provide the basis for the use of this azepane quaternary amino acid as a strong β-turn inducer in the search for novel peptide-based bioactive molecules, catalysts, and biomaterials.
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Affiliation(s)
| | - Adrián Plata-Ruiz
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Ignacio Romero-Muñiz
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
- Universidad
Autónoma de Madrid, Química Orgánica, Francisco Tomás y Valiente,
7, 28049 Madrid, Spain
| | - Ignacio Martín-Pérez
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Lourdes Infantes
- Instituto
de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
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2
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Recombinant Spider Silk Fiber with High Dimensional Stability in Water and Its NMR Characterization. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238479. [PMID: 36500566 PMCID: PMC9739919 DOI: 10.3390/molecules27238479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Spider dragline silk has unique characteristics of strength and extensibility, including supercontraction. When we use it as a biomaterial or material for textiles, it is important to suppress the effect of water on the fiber by as much as possible in order to maintain dimensional stability. In order to produce spider silk with a highly hydrophobic character, based on the sequence of ADF-3 silk, we produced recombinant silk (RSSP(VLI)) where all QQ sequences were replaced by VL, while single Q was replaced by I. The artificial RSSP(VLI) fiber was prepared using formic acid as the spinning solvent and methanol as the coagulant solvent. The dimensional stability and water absorption experiments of the fiber were performed for eight kinds of silk fiber. RSSP(VLI) fiber showed high dimensional stability, which is suitable for textiles. A remarkable decrease in the motion of the fiber in water was made evident by 13C solid-state NMR. This study using 13C solid-state NMR is the first trial to put spider silk to practical use and provide information regarding the molecular design of new recombinant spider silk materials with high dimensional stability in water, allowing recombinant spider silk proteins to be used in next-generation biomaterials and materials for textiles.
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3
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Asakura T, Matsuda H, Aoki A, Naito A. Acetylation and hydration treatment of recombinant spider silk fiber, and their characterization using 13C NMR spectroscopy. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Wu A, Ramakrishna I, Hattori T, Yamamoto H. Silicon-based hydrophobic tags applied in liquid-phase peptide synthesis: protected DRGN-1 and poly alanine chain synthesis. Org Biomol Chem 2022; 20:8685-8692. [DOI: 10.1039/d2ob01795d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Two types of silicon-based hydrophobic tags, including a siloxy group containing tag and an arylsilyl group containing tag, were developed for applying them in tag-assisted liquid-phase peptide synthesis (Tag LPPS) to synthesize long peptides.
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Affiliation(s)
- An Wu
- Peptide Research Centre, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Isai Ramakrishna
- Peptide Research Centre, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Tomohiro Hattori
- Peptide Research Centre, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hisashi Yamamoto
- Peptide Research Centre, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
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5
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Rani A, De Leon-Rodriguez LM, Kavianinia I, McGillivray DJ, Williams DE, Brimble MA. Synthesis and characterization of mono S-lipidated peptide hydrogels: a platform for the preparation of reactive oxygen species responsive materials. Org Biomol Chem 2021; 19:3665-3677. [PMID: 33908574 DOI: 10.1039/d1ob00355k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we report the synthesis of mono lipidated peptides containing a 3-mercaptopropionate linker in the N-terminus by means of a photoinitiated thiol-ene reaction (S-lipidation). We evaluate the self-assembling and hydrogelation properties of a library of mono S-lipidated peptides containing lipid chains of various lengths and demonstrate that hydrogelation was driven by a balance between the lipid chain's hydrophobicity and the peptide's facial hydrophobicity. We further postulate that a simple calculation using estimated values of log D could be used as a predictor of hydrogelation when designing similar systems. A mono S-lipidated peptide containing a short lipid chain that formed hydrogels was fully characterized and a mechanism for the peptide hydrogelation developed. Finally, we demonstrate that the presence of the thioether group in the mono S-lipidated peptide hydrogels, which is a feature lacking in conventional N-acyl lipidated systems, enables the controlled disassembly of the gel via oxidation to the sulfoxide by reactive oxygen species in accordance with a hydrophobicity-modulated strategy. Thus, we conclude that mono S-lipidated peptide hydrogels constitute a novel and simple tool for the development of tissue engineering and targeted drug delivery applications of diseases with overexpression of reactive oxygen species (e.g. degenerative and metabolic diseases, and cancers).
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Affiliation(s)
- Aakanksha Rani
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - Luis M De Leon-Rodriguez
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand.
| | - Iman Kavianinia
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - David E Williams
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand. and School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand and MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
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6
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Rani A, Kavianinia I, De Leon-Rodriguez LM, McGillivray DJ, Williams DE, Brimble MA. Nanoribbon self-assembly and hydrogel formation from an NOctanoyl octapeptide derived from the antiparallel β-Interface of a protein homotetramer. Acta Biomater 2020; 114:233-243. [PMID: 32682054 DOI: 10.1016/j.actbio.2020.07.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/09/2020] [Accepted: 07/09/2020] [Indexed: 12/26/2022]
Abstract
The effect of installing different lipid chains (C6, C8, C10, and C16) on the N-terminus of an octapeptide derived from the antiparallel β-interface of the diaminopimelate decarboxylase protein homotetramer has been investigated. Notably, the C8 peptide conjugate assembled into wide twisted nanoribbons and formed hydrogels, which to the best of our knowledge constitutes the first example of a peptide containing an eight carbon alkyl chain that demonstrates these properties, a space typically occupied by peptide amphiphiles with long lipid chains. Furthermore, this self-assembling lipopeptide exhibited pH and temperature stability with shear thinning properties suitable for biomedical applications. Importantly, in this work the application of the polystyrene-based sorbent Diaion™ HP20SS for the simple large-scale purification of self-assembling peptides is presented as an alternative to the use of time-consuming and labor-intensive reverse-phase high-performance liquid chromatography. STATEMENT OF SIGNIFICANCE: Peptides that can self-assemble into defined nanostructures are highly attractive for many biomedical applications given their unique physical and chemical properties. It is recognized that self-assembling peptides derived from naturally occurring proteins offer an unlimited source of functionalities and structures, which are hard to uncover with designed sequences. In this study, we have investigated the effect of installing different lipids chains on the N-terminus of an octapeptide derived from the antiparallel β-interface of the diaminopimelate decarboxylase protein homo tetramer. We also reported the use of polymeric DiaionⓇ HP20SS beads as an alternative solid support to purify self-assembling peptides.
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Affiliation(s)
- Aakanksha Rani
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand; School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - Iman Kavianinia
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand; School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand
| | - Luis M De Leon-Rodriguez
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand; School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - David E Williams
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand; School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1010, New Zealand; School of Biological Sciences, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3A Symonds St., Auckland 1010, New Zealand.
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7
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Del Giudice A, Rüter A, Pavel NV, Galantini L, Olsson U. Self-Assembly of Model Amphiphilic Peptides in Nonaqueous Solvents: Changing the Driving Force for Aggregation Does Not Change the Fibril Structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:8451-8460. [PMID: 32597180 PMCID: PMC8009514 DOI: 10.1021/acs.langmuir.0c00876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Within the homologous series of amphiphilic peptides AnK, both A8K and A10K self-assemble in water to form twisted ribbon fibrils with lengths around 100 nm. The structure of the fibrils can be described in terms of twisted β-sheets extending in the direction of the fibrils, laminated to give a constant cross section of 4 nm by 8 nm. The finite width of the twisted ribbons can be reasonably explained within a simple thermodynamic model, considering a free energy penalty for the stretching of hydrogen bonds along the twisted β-sheets and an interfacial free energy gain for the lamination of the hydrophobic β-sheets. In this study, we characterize the self-assembly behavior of these peptides in nonaqueous solutions as a route to probe the role of hydrophobic interaction in fibril stabilization. Both peptides, in methanol and N,N-dimethylformamide, were found to form fibrillar aggregates with the same β-sheet structure as in water but with slightly smaller cross-sectional sizes. However, the gel-like texture, the slow relaxation in dynamic light scattering experiments, and a correlation peak in the small-angle X-ray scattering pattern highlighted enhanced interfibril interactions in the nonaqueous solvents in the same concentration range. This could be ascribed to a higher effective volume of the aggregates because of enhanced fibril growth and length, as suggested by light scattering and cryogenic transmission electron microscopy analyses. These effects can be discussed considering how the solvent properties affect the different energetic contributions (hydrophobic, electrostatic, and hydrogen bonding) to fibril formation. In the analyzed case, the decreased hydrogen bonding propensity of the nonaqueous solvents makes the hydrogen bond formation along the fibril a key driving force for peptide assembly, whereas it represents a nonrelevant contribution in water.
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Affiliation(s)
- Alessandra Del Giudice
- Department
of Chemistry, Sapienza University of Rome, P. le A. Moro 5, Rome 00185, Italy
| | - Axel Rüter
- Division
of Physical Chemistry, Lund University, Lund SE-22100, Sweden
| | - Nicolae Viorel Pavel
- Department
of Chemistry, Sapienza University of Rome, P. le A. Moro 5, Rome 00185, Italy
| | - Luciano Galantini
- Department
of Chemistry, Sapienza University of Rome, P. le A. Moro 5, Rome 00185, Italy
| | - Ulf Olsson
- Division
of Physical Chemistry, Lund University, Lund SE-22100, Sweden
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8
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Asakura T. Structure and Dynamics of Spider Silk Studied with Solid-State Nuclear Magnetic Resonance and Molecular Dynamics Simulation. Molecules 2020; 25:E2634. [PMID: 32517041 PMCID: PMC7321385 DOI: 10.3390/molecules25112634] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 01/01/2023] Open
Abstract
This review will introduce very recent studies using solid-state nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulation on the structure and dynamics of spider dragline silks conducted by the author's research group. Spider dragline silks possess extraordinary mechanical properties by combining high tensile strength with outstanding elongation before breaking, and therefore continue to attract attention of researchers in biology, biochemistry, biophysics, analytical chemistry, polymer technology, textile technology, and tissue engineering. However, the inherently non-crystalline structure means that X-ray diffraction and electron diffraction methods provide only limited information because it is difficult to study the molecular structure of the amorphous region. The most detailed picture of the structure and dynamics of the silks in the solid state experimentally have come from solid-state NMR measurements coupled with stable isotope labeling of the silks and the related silk peptides. In addition, combination of solid-state NMR and MD simulation was very powerful analytical tools to understand the local conformation and dynamics of the spider dragline silk in atomic resolution. In this review, the author will emphasize how solid-state NMR and MD simulation have contributed to a better understanding of the structure and dynamics in the spider dragline silks.
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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
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
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9
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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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10
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Asakura T, Okonogi M, Naito A. Toward Understanding the Silk Fiber Structure: 13C Solid-State NMR Studies of the Packing Structures of Alanine Oligomers before and after Trifluoroacetic Acid Treatment. J Phys Chem B 2019; 123:6716-6727. [PMID: 31304756 DOI: 10.1021/acs.jpcb.9b04565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyalanine (poly-A) sequences with tightly packed antiparallel β sheet (AP-β) structures are frequently observed in silk fibers and serve as a key contributor to the exceptionally high-fiber tensile strength. In general, the poly-A sequence embedded in the amorphous glycine-rich regions has different lengths depending on the fiber type from spiders or wild silkworms. In this paper, the packing structures of AP-β alanine oligomers with different lengths were studied using 13C solid-state NMR as a model of the poly-A sequences. These included alanine oligomers with and without the protection groups (i.e., 9-fluorenylmethoxycarbonyl and polyethylene glycol groups at the N- and C-terminals, respectively). The fractions of the packing structures as well as the conformations were determined by deconvolution analyses of the methyl NMR peaks. Trifluoroacetic acid was used to promote the staggered packing structures, and the line shapes changed significantly for oligomers without the protected groups but only slightly for oligomers with the protected groups. Through NMR analysis of the 3-13C singly labeled alanine heptamer and refined crystal structure of the staggered packing units, a possible mechanism of the staggered packing formation is proposed for the AP-β alanine heptamer.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
| | - Michi Okonogi
- 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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11
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Asakura T, Matsuda H, Aoki A, Kataoka N, Imai A. Conformational change of 13C-labeled 47-mer model peptides of Nephila clavipes dragline silk in poly(vinyl alcohol) film by stretching studied by 13C solid-state NMR and molecular dynamics simulation. Int J Biol Macromol 2019; 131:654-665. [PMID: 30902719 DOI: 10.1016/j.ijbiomac.2019.03.112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 12/23/2022]
Abstract
For determination of the conformation of irregular sequences in glycine-rich region of the Nephila clavipes spider dragline silk, the combination of 13C selectively labeled model peptides for the typical primary structure and their 13C solid-state NMR observations is very useful (T. Asakura et al. Macromolecules. 51 (2018) 3608-3619). However, spiders produce the fiber through the stretching process in nature and therefore, it is difficult to study conformational change by stretching as mimic using the model peptides because these are generally in the powder form. In this paper, 13C selectively labeled three model peptides, (Glu)4(Ala)6GlyGly12Ala13Gly14GlnGlyGlyTyrGlyGlyLeuGlySerGlnGly25Ala26Gly27ArgGly-GlyLeuGlyGlyGlnGly35Ala36Gly37(Ala)6(Glu)4 with three underlined 13C labeled blocks and their poly(vinyl alcohol) blend films were prepared and the conformational changes of these peptides were monitored by stretching of the films using 13C solid-state NMR. In addition, the molecular dynamics simulation was done to evaluate change in the conformation of the sequence by stretching theoretically. The fractions of β-sheet of Ala36 and Gly37 residues in glycine-rich region adjacent to the C-terminal (Ala)6 sequence increased significantly by stretching compared with those of other 13C labeled Ala and Gly residues.
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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.
| | - Hironori Matsuda
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Akihiro Aoki
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Naomi Kataoka
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Akiko Imai
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
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12
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Holland C, Numata K, Rnjak‐Kovacina J, Seib FP. The Biomedical Use of Silk: Past, Present, Future. Adv Healthc Mater 2019; 8:e1800465. [PMID: 30238637 DOI: 10.1002/adhm.201800465] [Citation(s) in RCA: 387] [Impact Index Per Article: 77.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/04/2018] [Indexed: 11/07/2022]
Abstract
Humans have long appreciated silk for its lustrous appeal and remarkable physical properties, yet as the mysteries of silk are unraveled, it becomes clear that this outstanding biopolymer is more than a high-tech fiber. This progress report provides a critical but detailed insight into the biomedical use of silk. This journey begins with a historical perspective of silk and its uses, including the long-standing desire to reverse engineer silk. Selected silk structure-function relationships are then examined to appreciate past and current silk challenges. From this, biocompatibility and biodegradation are reviewed with a specific focus of silk performance in humans. The current clinical uses of silk (e.g., sutures, surgical meshes, and fabrics) are discussed, as well as clinical trials (e.g., wound healing, tissue engineering) and emerging biomedical applications of silk across selected formats, such as silk solution, films, scaffolds, electrospun materials, hydrogels, and particles. The journey finishes with a look at the roadmap of next-generation recombinant silks, especially the development pipeline of this new industry for clinical use.
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Affiliation(s)
- Chris Holland
- Department of Materials Science and Engineering The University of Sheffield Sir Robert Hadfield Building, Mappin Street Sheffield South Yorkshire S1 3JD UK
| | - Keiji Numata
- Biomacromolecules Research Team RIKEN Center for Sustainable Resource Science 2‐1 Hirosawa Wako Saitama 351‐0198 Japan
| | - Jelena Rnjak‐Kovacina
- Graduate School of Biomedical Engineering The University of New South Wales Sydney NSW 2052 Australia
| | - F. Philipp Seib
- Leibniz Institute of Polymer Research Dresden Max Bergmann Center of Biomaterials Dresden Dresden 01069 Germany
- Strathclyde Institute of Pharmacy and Biomedical Sciences University of Strathclyde Glasgow G4 0RE UK
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13
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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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14
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Asakura T, Matsuda H, Kataoka N, Imai A. Changes in the Local Structure of Nephila clavipes Dragline Silk Model Peptides upon Trifluoroacetic Acid, Low pH, Freeze-Drying, and Hydration Treatments Studied by 13C Solid-State NMR. Biomacromolecules 2018; 19:4396-4410. [DOI: 10.1021/acs.biomac.8b01267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Hironori Matsuda
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Naomi Kataoka
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Akiko Imai
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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15
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Asakura T, Tasei Y, Matsuda H, Naito A. Dynamics of Alanine Methyl Groups in Alanine Oligopeptides and Spider Dragline Silks with Different Packing Structures As Studied by 13C Solid-State NMR Relaxation. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Yugo Tasei
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Hironori Matsuda
- 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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16
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Naito A, Tasei Y, Nishimura A, Asakura T. Unusual Dynamics of Alanine Residues in Polyalanine Regions with Staggered Packing Structure of Samia cynthia ricini Silk Fiber in Dry and Hydrated States Studied by 13C Solid-State NMR and Molecular Dynamics Simulation. J Phys Chem B 2018; 122:6511-6520. [DOI: 10.1021/acs.jpcb.8b03509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Akira Naito
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Yugo Tasei
- 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
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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17
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Hong YL, Asakura T, Nishiyama Y. 3D 14 N/ 1 H Double Quantum/ 1 H Single Quantum Correlation Solid-State NMR for Probing the Parallel and Anti-Parallel Beta-Sheet Arrangement of Oligo-Peptides at Natural Abundance. Chemphyschem 2018; 19:1841-1845. [PMID: 29737041 DOI: 10.1002/cphc.201800392] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Indexed: 02/28/2024]
Abstract
The beta (β)-sheet structures of oligopeptides and polypeptides can be formed in anti-parallel (AP) and parallel (P) forms, which is an important feature to understand such structures. In principle, P- and AP-β-sheet structures can be identified by the presence (AP) or absence (P) of inter-strand 1 HNH /1 HNH correlations on a diagonal in the corresponding 2D 1 H double quantum (DQ)/1 H single quantum (SQ) spectrum due to the different inter-strand 1 HNH /1 HNH distances between the two arrangements. However, the 1 HNH /1 HNH peaks overlap with the 1 HNH3+ /1 HNH3+ peaks, which always give cross-peaks regardless of the β-sheet arrangement. The 1 HNH3+ /1 HNH3+ peaks disturb the observation of the presence/absence of 1 HNH /1 HNH correlations and the assignment of 1 HNH and 1 HNH3+ is not always available. Here, 3D 14 N/1 H DQ/1 H SQ correlation solid-state NMR experiments at fast magic angle spinning (70 kHz) are introduced to distinguish AP- and P-β-sheet structures. The 14 N dimension allows the distinction of 1 HNH /1 HNH peaks from 1 HNH3+ /1 HNH3+ peaks with clear assignments of 1 HNH and 1 HNH3+ . In addition, the high natural abundance of 1 H and 14 N enables 3D 14 N/1 H DQ/1 H SQ experiments of oligo-alanines (Ala3-6 ) in four hours without isotope labelling.
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Affiliation(s)
- You-Lee Hong
- RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184-8588, Japan
| | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa, 230-0045, Japan
- JEOL RESONANCE Inc., 3-1-2 Musaino, Akishima, Tokyo, 196-8558, Japan
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18
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Asakura T, Nishimura A, Tasei Y. Determination of Local Structure of 13C Selectively Labeled 47-mer Peptides as a Model for Gly-Rich Region of Nephila clavipes Dragline Silk Using a Combination of 13C Solid-State NMR and MD Simulation. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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
| | - Yugo Tasei
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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19
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Naito A, Okushita K, Nishimura K, Boutis GS, Aoki A, Asakura T. Quantitative Analysis of Solid-State Homonuclear Correlation Spectra of Antiparallel β-Sheet Alanine Tetramers. J Phys Chem B 2018; 122:2715-2724. [PMID: 29420030 DOI: 10.1021/acs.jpcb.7b11126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Poly-l-alanine (PLA) sequences are a key element in the structure of the crystalline domains of spider dragline silks, wild silkworm silks, antifreeze proteins, and amyloids. To date, no atomic-level structures of antiparallel (AP)-PLA longer than Ala4 have been reported using the single-crystal X-ray diffraction analysis. In this work, dipolar-assisted rotational resonance solid-state NMR spectra were observed to determine the effective internuclear distances of 13C uniformly labeled alanine tetramer with antiparallel (AP) β-sheet structure whose atomic coordinates are determined from the X-ray crystallographic analysis. Initial build-up rates, R j, k, were obtained from the build-up curves of the cross peaks by considering the internuclear distances arising in the master equation. Subsequently, experimentally obtained effective internuclear distances, reffj, k(obs), were compared with the calculated reffj, k(calc) values obtained from the X-ray crystallographic data. Fairly good correlation between reffj, k(obs) and reffj, k(calc) was obtained in the range of 1.0-6.0 Å, with the standard deviation of 0.244 Å, without considering the zero-quantum line-shape functions. It was further noted that the internuclear distances of intermolecular contributions provide details relating to the molecular packing in solid-state samples. Thus, the present data agree well with AP-β-sheet packing but do not agree with P-β-sheet packing.
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Affiliation(s)
- Akira Naito
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
| | - Keiko Okushita
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan.,Institute for Molecular Science , 38 Nishigo-Naka , Myodaiji, Okazaki 444-8585 , Japan
| | - Katsuyuki Nishimura
- Institute for Molecular Science , 38 Nishigo-Naka , Myodaiji, Okazaki 444-8585 , Japan
| | - Gregory S Boutis
- Department of Physics , Brooklyn College of The City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Department of Physics , The Graduate Center of The City University of New York , 365 5th Avenue , New York , New York 10016 , United States
| | - 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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20
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Asakura T, Tasei Y, Aoki A, Nishimura A. Mixture of Rectangular and Staggered Packing Arrangements of Polyalanine Region in Spider Dragline Silk in Dry and Hydrated States As Revealed by 13C NMR and X-ray Diffraction. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02627] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Yugo Tasei
- 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
| | - Akio Nishimura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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21
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Tasei Y, Nishimura A, Suzuki Y, Sato TK, Sugahara J, Asakura T. NMR Investigation about Heterogeneous Structure and Dynamics of Recombinant Spider Silk in the Dry and Hydrated States. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01862] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yugo Tasei
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Akio Nishimura
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Yu Suzuki
- Tenure-Track
Program for Innovative Research, University of Fukui, 3-9-1 Bunkyo, Fukui-shi, Fukui 910-8507, Japan
| | - Takehiro K. Sato
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Junichi Sugahara
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tetsuo Asakura
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16, Nakacho, Koganei, Tokyo 184-8588, Japan
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22
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Naito A, Tasei Y, Nishimura A, Asakura T. Packing Arrangements and Intersheet Interaction of Alanine Oligopeptides As Revealed by Relaxation Parameters Obtained from High-Resolution 13C Solid-State NMR. J Phys Chem B 2017; 121:8946-8955. [DOI: 10.1021/acs.jpcb.7b07068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akira Naito
- Department of Biotechnology, Tokyo University of Agriculture and Technology Koganei, Tokyo 184-8588 Japan
| | - Yugo Tasei
- 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
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology Koganei, Tokyo 184-8588 Japan
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23
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Asakura T, Nishimura A, Kametani S, Kawanishi S, Aoki A, Suzuki F, Kaji H, Naito A. Refined Crystal Structure of Samia cynthia ricini Silk Fibroin Revealed by Solid-State NMR Investigations. Biomacromolecules 2017; 18:1965-1974. [DOI: 10.1021/acs.biomac.7b00441] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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
| | - Shunsuke Kametani
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Shuto Kawanishi
- 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
| | - Furitsu Suzuki
- Institute
for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hironori Kaji
- Institute
for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akira Naito
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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24
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Asakura T, Nishimura A, Sato Y. Quantitative Correlation between Primary Sequences and Conformations in 13C-Labeled Samia cynthia ricini Silk Fibroin during Strain-Induced Conformational Transition by 13C Solid State NMR. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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
| | - Yuya Sato
- Department of Biotechnology, Tokyo University of Agriculture and Technology Koganei, Tokyo 184-8588, Japan
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25
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Kametani S, Tasei Y, Nishimura A, Asakura T. Distinct solvent- and temperature-dependent packing arrangements of anti-parallel β-sheet polyalanines studied with solid-state 13C NMR and MD simulation. Phys Chem Chem Phys 2017; 19:20829-20838. [DOI: 10.1039/c7cp03693k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Change from rectangular arrangement to staggered arrangement of (Ala)6 by heat treatment.
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Affiliation(s)
- Shunsuke Kametani
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
- Mitsui Chemical Analysis & Consulting Service, Inc
| | - Yugo Tasei
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Akio Nishimura
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
| | - Tetsuo Asakura
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Koganei
- Japan
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26
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Asakura T, Miyazawa K, Tasei Y, Kametani S, Nakazawa Y, Aoki A, Naito A. Packing arrangement of 13C selectively labeled sequence model peptides of Samia cynthia ricini silk fibroin fibers studied by solid-state NMR. Phys Chem Chem Phys 2017; 19:13379-13386. [DOI: 10.1039/c7cp01199g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Samia cynthia ricini silk fibroin fiber was proposed to take anti-parallel β-sheet structure with staggered arrangement.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Kenta Miyazawa
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Yugo Tasei
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Shunsuke Kametani
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
- Mitsui Chemical Analysis & Consulting Service
| | - Yasumoto Nakazawa
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
| | - Akihiro Aoki
- Department of Biotechnology
- Tokyo University of Agriculture and Technology
- Tokyo 184-8588
- Japan
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27
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Riekel C, Burghammer M, Dane TG, Ferrero C, Rosenthal M. Nanoscale Structural Features in Major Ampullate Spider Silk. Biomacromolecules 2016; 18:231-241. [PMID: 28001374 DOI: 10.1021/acs.biomac.6b01537] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spider major ampullate silk is often schematically represented as a two-phase material composed of crystalline nanodomains in an amorphous matrix. Here we are interested in revealing its more complex nanoscale organization by probing Argiope bruennichi dragline-type fibers using scanning X-ray nanodiffraction. This allows resolving transversal structural features such as an about 1 μm skin layer composed of around 100 nm diameter nanofibrils serving presumably as an elastic sheath. The core consists of a composite of several nm size crystalline nanodomains with poly(l-alanine) microstructure, embedded in a polypeptide network with short-range order. Stacks of nanodomains separated by less ordered nanosegments form nanofibrils with a periodic axial density modulation which is particularly sensitive to radiation damage. The precipitation of larger β-type nanocrystallites in the outer core-shell is attributed to MaSp1 protein molecules.
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Affiliation(s)
- Christian Riekel
- The European Synchrotron (ESRF) , CS40220, F-38043 Grenoble Cedex 9, France
| | - Manfred Burghammer
- The European Synchrotron (ESRF) , CS40220, F-38043 Grenoble Cedex 9, France.,Department of Analytical Chemistry, Ghent University , Krijgslaan 281, S12B-9000 Ghent, Belgium
| | - Thomas G Dane
- The European Synchrotron (ESRF) , CS40220, F-38043 Grenoble Cedex 9, France
| | - Claudio Ferrero
- The European Synchrotron (ESRF) , CS40220, F-38043 Grenoble Cedex 9, France
| | - Martin Rosenthal
- The European Synchrotron (ESRF) , CS40220, F-38043 Grenoble Cedex 9, France
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28
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Asakura T, Horiguchi K, Aoki A, Tasei Y, Naito A. Parallel β-Sheet Structure of Alanine Tetrapeptide in the Solid State As Studied by Solid-State NMR Spectroscopy. J Phys Chem B 2016; 120:8932-41. [PMID: 27482868 DOI: 10.1021/acs.jpcb.6b06292] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural analysis of alanine oligopeptides is important for understanding the crystalline region in silks from spiders and wild silkworms and also the mechanism of cellular toxicity of human diseases arising from expansion in polyalanine sequences. The atomic-level structures of alanine tripeptide and tetrapeptide with antiparallel β-sheet structures (AP-Ala3 and AP-Ala4, respectively) together with alanine tripeptide with parallel β-sheet structures (P-Ala3) have been determined, but alanine tetrapeptide with a parallel β-sheet structure (P-Ala4) has not been reported yet. In this article, first, we established the preparation protocol of P-Ala4 from more stable AP-Ala4. Second, complete assignments of the (13)C, (15)N, and (1)H solid-state NMR spectra were performed with (13)C- and (15)N-labeled Ala4 samples using several solid-state NMR techniques. Then, the structural constraints were obtained, for example, the amide proton peaks of P-Ala4 in the (1)H double-quantum magic-angle spinning NMR spectrum were heavily overlapped and observed at about 7.4 ppm, which was a much higher field than that of 8.7-9.1 ppm observed for AP-Ala4, indicating that the intermolecular hydrogen-bond lengths across strands (N-H···O═C) were considerably longer for P-Ala4, that is, 2.21-2.34 Å, than those reported for AP-Ala4, that is, 1.8-1.9 Å. The structural model was proposed for P-Ala4 by NMR results and MD calculations.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology , 2-24-16 Koganei, Tokyo 184-8588, Japan
| | - Kumiko Horiguchi
- Department of Biotechnology, Tokyo University of Agriculture and Technology , 2-24-16 Koganei, Tokyo 184-8588, Japan
| | - Akihiro Aoki
- Department of Biotechnology, Tokyo University of Agriculture and Technology , 2-24-16 Koganei, Tokyo 184-8588, Japan
| | - Yugo Tasei
- Department of Biotechnology, Tokyo University of Agriculture and Technology , 2-24-16 Koganei, Tokyo 184-8588, Japan
| | - Akira Naito
- Department of Biotechnology, Tokyo University of Agriculture and Technology , 2-24-16 Koganei, Tokyo 184-8588, Japan
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29
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Greenwald J, Friedmann MP, Riek R. Amyloid Aggregates Arise from Amino Acid Condensations under Prebiotic Conditions. Angew Chem Int Ed Engl 2016; 55:11609-13. [DOI: 10.1002/anie.201605321] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/14/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Jason Greenwald
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Michael P. Friedmann
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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30
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Greenwald J, Friedmann MP, Riek R. Amyloid Aggregates Arise from Amino Acid Condensations under Prebiotic Conditions. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jason Greenwald
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Michael P. Friedmann
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, D-CHAB; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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31
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Asakura T, Yazawa K, Horiguchi K, Suzuki F, Nishiyama Y, Nishimura K, Kaji H. Difference in the structures of alanine tri- and tetra-peptides with antiparallel β-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW. Biopolymers 2016; 101:13-20. [PMID: 23526402 DOI: 10.1002/bip.22241] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/23/2013] [Accepted: 03/07/2013] [Indexed: 11/09/2022]
Abstract
Alanine oligomers provide a key structure for silk fibers from spider and wild silkworms.We report on structural analysis of L-alanyl-L-alanyl-L-alanyl-L-alanine (Ala)4 with anti-parallel (AP) β-structures using X-ray and solid-state NMR. All of the Ala residues in the (Ala)4 are in equivalent positions, whereas for alanine trimer (Ala)3 there are two alternative locations in a unit cell as reported previously (Fawcett and Camerman, Acta Cryst., 1975, 31, 658-665). (Ala)4 with AP β-structure is more stable than AP-(Ala)3 due to formation of the stronger hydrogen bonds. The intermolecular structure of (Ala)4 is also different from polyalanine fiber structure, indicating that the interchain arrangement of AP β-structure changes with increasing alanine sequencelength. Furthermore the precise (1)H positions, which are usually inaccesible by X-ray diffraction method, are determined by high resolution (1)H solid state NMR combined with the chemical shift calculations by the gauge-including projector augmented wave method.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Koganei, Tokyo, Japan; Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
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32
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Numata K, Sato R, Yazawa K, Hikima T, Masunaga H. Crystal structure and physical properties of Antheraea yamamai silk fibers: Long poly(alanine) sequences are partially in the crystalline region. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.09.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Asakura T, Okushita K, Williamson MP. Analysis of the Structure of Bombyx mori Silk Fibroin by NMR. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00160] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Tetsuo Asakura
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Institute for
Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Keiko Okushita
- Department
of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Mike P. Williamson
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Firth Court,
Western Bank, Sheffield S10 2TN, U.K
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Peng Y, Li G, Hua J, Shi Z, Feng S. Syntheses, topological structures and properties of six metal–organic frameworks constructed from a flexible tetracarboxylate ligand. CrystEngComm 2015. [DOI: 10.1039/c5ce00078e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Six new metal–organic frameworks (MOFs), Co2O(odip)(py)2(DMSO)2·3H2O (1), Co2(odip)(H2O)(DMA)2·2DMA (2), Co4(odip)2(H2O)4(DMSO)2·5DMSO (3), [Zn2(odip)(DMF)2(H2O)]·2DMF·2H2O (4), Zn2(odip)(H2O) (5) and In(odip)·3ACN (6), have been synthesized from the 5,5′-oxydiisophthalic acid (H4odip) ligand under solvothermal conditions.
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Affiliation(s)
- Yu Peng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun, PR China
| | - Guanghua Li
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun, PR China
| | - Jia Hua
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun, PR China
| | - Zhan Shi
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun, PR China
| | - Shouhua Feng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry
- College of Chemistry
- Jilin University
- Changchun, PR China
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35
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Çenker CÇ, Bucak S, Olsson U. Aqueous self-assembly within the homologous peptide series AnK. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:10072-9. [PMID: 25072740 DOI: 10.1021/la5016324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We compare the aqueous self-assembly behavior within the homologous peptide series AnK, where A is alanine, K is lysine, and n = 4, 6, 8, and 10. The aqueous peptide solubility, ϕ(s) (volume fraction), depends strongly on the number of hydrophobic alanine residues and decreases approximately as ϕ(s) ≈ 10(-n). Also the self-assembly structure depends on n. A4K is highly water-soluble and shows no relevant self-assembly. A6K, which has been extensively studied previously, forms hollow nanotubes in water. A8K and A10K self-assembly is characterized here using a combination of small- and wide-angle X-ray scattering, static and dynamic light scattering, cryo transmission electron microscopy, and circular dichroism spectroscopy. They both form similar thin rodlike aggregates with lengths on the order of 100 nm and a biaxial cross-section with dimensions of 4 nm × 8 nm. We show that different sample preparation protocols result in different lengths of the A10K rodlike aggregates. On the basis of these findings, the question of thermodynamic equilibrium of peptide self-assembly is discussed.
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Affiliation(s)
- Celen Çağrı Çenker
- Division of Physical Chemistry, Chemistry Department, Lund University , Box 124, SE-22100 Lund, Sweden
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36
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Smith AJ, Ali FI, Soldatov DV. Glycine homopeptides: the effect of the chain length on the crystal structure and solid state reactivity. CrystEngComm 2014. [DOI: 10.1039/c4ce00630e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of linear oligoglycines has been studied to reveal the trends in their crystal structure, molecular conformation and thermally induced reactions.
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Affiliation(s)
- Aaron J. Smith
- Department of Chemistry
- University of Guelph
- Guelph, Canada
| | - Farukh I. Ali
- Department of Chemistry
- University of Guelph
- Guelph, Canada
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37
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Ling S, Qi Z, Knight DP, Huang Y, Huang L, Zhou H, Shao Z, Chen X. Insight into the structure of single Antheraea pernyi silkworm fibers using synchrotron FTIR microspectroscopy. Biomacromolecules 2013; 14:1885-92. [PMID: 23607809 DOI: 10.1021/bm400267m] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synchrotron FTIR (S-FTIR) microspectroscopy was used to monitor both protein secondary structures (conformations) and their orientations in single cocoon silk fibers of the Chinese Tussah silk moth ( Antheraea pernyi ). In addition, to understand further the relationship between structure and properties of single silk fibers, we studied the changes of orientation and content of different secondary structures in single A. pernyi silk fibers when subjected to different strains. The results showed that the content and orientation of β-sheet was almost unchanged for strains from 0 to 0.3. However, the orientation of α-helix and random coil improved progressively with increasing strain, with a parallel decrease in α-helix content and an increase in random coil. This clearly indicates that most of the deformation upon stretching of the single fiber is due to the change of orientation in the amorphous regions coupled with a conversion of some of the α-helix to random coil. These observations provide an explanation for the supercontraction behavior of certain animal silks and are likely to facilitate understanding and optimization of postdrawing used in the conjunction with the wet-spinning of silk fibers from regenerated silk solutions. Thus, our work demonstrates the power of S-FTIR microspectroscopy for studying biopolymers.
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Affiliation(s)
- Shengjie Ling
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University , Shanghai, 200433, People's Republic of China
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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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