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Asakura T, Nishimura A, Naito A. Stretching-Induced Conformational Transition of [3- 13C]Ser- and [3- 13C]Tyr- Antheraea yamamai Silk Fibroin before Spinning Investigated with 13C Solid-State NMR Spectroscopy. Biomacromolecules 2022; 23:5095-5105. [PMID: 36449573 DOI: 10.1021/acs.biomac.2c00937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The conformational transition of [3-13C]Ser- and [3-13C]Tyr-Antheraea yamamai silk fibroin before spinning induced by stretching was investigated with 13C CP/MAS NMR spectroscopy. The α-helix content of the silk fibroin before stretching was found to be 31.6% based on the Ala and Ser peaks. With increasing stretching ratio, the α-helix and the random coil Ala Cβ peaks decreased gradually, while the β-sheet peak was observed at a stretching ratio of ×5 and increased rapidly upon further stretching. For Ser residue, the α-helix peak decreased monotonically with increasing stretching ratio, but the random coil peak increased slightly till the stretching ratio of ×5 and then decreased. A small β-sheet peak was observed before stretching and then increased rapidly starting from the stretching ratio of ×7. In contrast, a gradual decrease of random coil peak and an increase of β-sheet peak were observed for the Tyr residue. The results of this investigation may be helpful for further studies of fiber formation mechanism in A. yamamai and in the future design of artificial silk materials.
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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
| | - Akio Nishimura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Akira Naito
- Department of Biotechnology, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
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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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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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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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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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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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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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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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Guo C, Zhang J, Jordan JS, Wang X, Henning RW, Yarger JL. Structural Comparison of Various Silkworm Silks: An Insight into the Structure-Property Relationship. Biomacromolecules 2018; 19:906-917. [PMID: 29425447 DOI: 10.1021/acs.biomac.7b01687] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Silkworm silk has attracted considerable attention in recent years due to its excellent mechanical properties, biocompatibility, and promising applications in biomedical sector. However, a clear understanding of the molecular structure and the relationship between the excellent mechanical properties and the silk protein sequences are still lacking. This study carries out a thorough comparative structural analysis of silk fibers of four silkworm species ( Bombyx mori, Antheraea pernyi, Samia cynthia ricini, and Antheraea assamensis). A combination of characterization techniques including scanning electron microscopy, mechanical test, synchrotron X-ray diffraction, Fourier transform infrared spectroscopy (FTIR), and NMR spectroscopy was applied to investigate the morphologies, mechanical properties, amino acid compositions, nanoscale organizations, and molecular structures of various silkworm silks. Furthermore, the structure-property relationship is discussed by correlating the molecular structural features of silks with their mechanical properties. The results show that a high content of β-sheet structures and a high crystallinity would result in a high Young's modulus for silkworm silk fibers. Additionally, a low content of β-sheet structures would result in a high extensibility.
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Affiliation(s)
- Chengchen Guo
- School of Molecular Sciences, Magnetic Resonance Research Center , Arizona State University , Tempe , Arizona 85287-1604 , United States
| | - Jin Zhang
- Australian Future Fibers Research and Innovation Centre, Institute for Frontier Materials , Deakin University , Burwood VIC 3216 , Australia
| | - Jacob S Jordan
- School of Molecular Sciences, Magnetic Resonance Research Center , Arizona State University , Tempe , Arizona 85287-1604 , United States
| | - Xungai Wang
- Australian Future Fibers Research and Innovation Centre, Institute for Frontier Materials , Deakin University , Burwood VIC 3216 , Australia
| | - Robert W Henning
- Center for Advanced Radiation Sources , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Jeffery L Yarger
- School of Molecular Sciences, Magnetic Resonance Research Center , Arizona State University , Tempe , Arizona 85287-1604 , United States
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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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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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12
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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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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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