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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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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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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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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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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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