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Article ; Online: Unusual p

Oktaviani, Nur Alia / Malay, Ali D / Matsugami, Akimasa / Hayashi, Fumiaki / Numata, Keiji

Biomacromolecules

2023 Volume 24, Issue 4, Page(s) 1604–1616

Abstract: Spider dragline silk is a remarkably tough biomaterial and composed primarily of spidroins MaSp1 and MaSp2. During fiber self-assembly, the spidroin N-terminal domains (NTDs) undergo rapid dimerization in response to a pH gradient. However, obtaining a ... ...

Abstract	Spider dragline silk is a remarkably tough biomaterial and composed primarily of spidroins MaSp1 and MaSp2. During fiber self-assembly, the spidroin N-terminal domains (NTDs) undergo rapid dimerization in response to a pH gradient. However, obtaining a detailed understanding of this mechanism has been hampered by a lack of direct evidence regarding the protonation states of key ionic residues. Here, we elucidated the solution structures of MaSp1 and MaSp2 NTDs from
MeSH term(s)	Animals ; Fibroins/chemistry ; Silk/chemistry ; Dimerization ; Magnetic Resonance Spectroscopy ; Spiders/metabolism
Chemical Substances	Fibroins (9007-76-5) ; Silk
Language	English
Publishing date	2023-03-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1526-4602
ISSN (online)	1526-4602
DOI	10.1021/acs.biomac.2c01344
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Article ; Online: The Residual Structure of Unfolded Proteins was Elucidated from the Standard Deviation of NMR Intensity Differences.

Mizuno, Fuko / Aoki, Saeko / Matsugami, Akimasa / Hayashi, Fumiaki / Nishimura, Chiaki

Protein and peptide letters

2022 Volume 30, Issue 2, Page(s) 103–107

Abstract: Introduction: Sensitive methods are necessary to identify the residual structure in an unfolded protein, which may be similar to the functionally native structure. Signal intensity in NMR experiments is useful for analyzing the line width for a dynamic ... ...

Abstract	Introduction: Sensitive methods are necessary to identify the residual structure in an unfolded protein, which may be similar to the functionally native structure. Signal intensity in NMR experiments is useful for analyzing the line width for a dynamic structure; however, another contribution is contained. Methods: Here, the signal-intensity difference along the sequence was used for probability to calculate the standard deviation. Results: The relative values of the standard deviations were 0.57, 0.57, and 0.66 for alpha-synuclein wild-type, A53T, and A30P, respectively. This revealed that the flexible region was mainly in the Cterminal region of alpha-synuclein at higher temperatures as observed by the amide-proton exchange studies. Conclusion: In particular, the flexible structure was induced by the A30P mutation.
MeSH term(s)	alpha-Synuclein/chemistry ; Magnetic Resonance Spectroscopy ; Mutation
Chemical Substances	alpha-Synuclein
Language	English
Publishing date	2022-12-07
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1280776-x
ISSN	1875-5305 ; 0929-8665
ISSN (online)	1875-5305
ISSN	0929-8665
DOI	10.2174/0929866530666230104140830
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Zs.A 4452: Show issues

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Article ; Online: Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability.

Sato, Yusuke / Matsugami, Akimasa / Watanabe, Satoru / Hayashi, Fumiaki / Arai, Munehito / Kigawa, Takanori / Nishimura, Chiaki

Protein science : a publication of the Protein Society

2021 Volume 30, Issue 11, Page(s) 2233–2245

Abstract: HIV-1 capsid is comprised of over a hundred p24 protein molecules, arranged as either pentamers or hexamers. Three p24 mutants with amino acid substitutions in capsid N-terminal domain protein were examined: G60W (α3-4 loop), M68T (helix 4), and P90T (α4- ...

Abstract	HIV-1 capsid is comprised of over a hundred p24 protein molecules, arranged as either pentamers or hexamers. Three p24 mutants with amino acid substitutions in capsid N-terminal domain protein were examined: G60W (α3-4 loop), M68T (helix 4), and P90T (α4-5 loop), which exhibited no viability for biological activity. One common structural feature of the three p24 N-domain mutants, examined by NMR, was the long-range effect of more β-structures at the β2-strand in the N-terminal region compared with the wild-type. In addition, the presence of fewer helical structures was observed in M68T and P90T, beyond the broad area from helix 1 to the C-terminal part of helix 4. This suggests that both N-terminal beta structures and helices play important roles in the formation of p24 hexamers and pentamers. Next, compared with P90T, we examined cis-conformation or trans-conformation of wild-type adopted by isomerization at G89-P90. Since P90T mutant adopts only a trans-conformation, comparison of chemical shifts and signal intensities between each spectra revealed that the major peaks (about 85%) in the spectrum of wild-type correspond to trans-conformation. Furthermore, it was indicated that the region in cis-conformation (minor; 15%) was more stabilized than that observed in trans-conformation, based on the analyses of heteronuclear Overhauser effect as well as the order-parameter. Therefore, it was concluded that the cis-conformation is more favorable than the trans-conformation for the interaction between the p24 N-terminal domain and cyclophilin-A. This is because HIV-1 with a P90T protein, which adopts only a trans-conformation, is associated with non-viability of biological activity.
MeSH term(s)	Amino Acid Substitution ; HIV Core Protein p24/chemistry ; HIV Core Protein p24/genetics ; HIV Core Protein p24/metabolism ; HIV-1/chemistry ; HIV-1/genetics ; HIV-1/metabolism ; Models, Molecular ; Mutation, Missense ; Protein Conformation, alpha-Helical ; Protein Domains
Chemical Substances	HIV Core Protein p24
Language	English
Publishing date	2021-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4184
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Distinct residual and disordered structures of alpha-synuclein analyzed by amide-proton exchange and NMR signal intensity

Okuwaki, Rina / Shinmura, Iori / Morita, Shiki / Matsugami, Akimasa / Hayashi, Fumiaki / Goto, Yuji / Nishimura, Chiaki

Biochimica et biophysica acta. 2020 Sept., v. 1868, no. 9

2020

Abstract: The residual solution structures of two alpha-synuclein mutants, A30P and A53T, observed in family members of patients with Parkinson's disease were compared with that of wild-type by NMR. The A53T substitution had been shown to accelerate fibril ... ...

Abstract	The residual solution structures of two alpha-synuclein mutants, A30P and A53T, observed in family members of patients with Parkinson's disease were compared with that of wild-type by NMR. The A53T substitution had been shown to accelerate fibril formation of alpha-synuclein, whereas the A30P mutation has the negative and positive effects on the formation of the fibril and spherical oligomer, respectively. The remaining structure was analyzed via amide-proton exchange and signal intensity measurements using NMR. Amide-proton exchange was used for both the calculation of kₑₓ values and ratio of kₑₓ at different temperatures. Effects of the A30P (N-terminal region) mutation were observed at the C-terminal region as a more flexible structure, suggesting that long-range interactions exist between the N- and C-terminal regions in alpha-synuclein. In addition, the N-terminal region adopted a more rigid structure in the A53T and A30P mutants than in the wild-type. It was concluded that the structural change caused by the mutations is related to the formation of a beta-hairpin at the initiation site of the N-terminal core structure. Furthermore, the signal intensity was used to estimate the rigidity of the structure. Higher signal intensities were observed for A30P at the 112, 113, and 116 C-terminal residues, suggesting that this region adopts more flexible structure. The ratio of the intensities at different temperatures indicated more flexible or rigid structures in the N-terminal region of A30P than in that of wild-type. Thus, using different approaches and temperatures is a good method to analyze residual structure in intrinsically disordered proteins.
Keywords	Parkinson disease ; measurement ; mutants ; mutation ; patients ; proteins ; solutions ; temperature
Language	English
Dates of publication	2020-09
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2020.140464
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Article ; Online: Ion effects on the conformation and dynamics of repetitive domains of a spider silk protein: implications for solubility and β-sheet formation.

Oktaviani, Nur Alia / Matsugami, Akimasa / Hayashi, Fumiaki / Numata, Keiji

Chemical communications (Cambridge, England)

2019 Volume 55, Issue 66, Page(s) 9761–9764

Abstract: The effect of ions on the structure and dynamics of a spider silk protein is elucidated. Chaotropic ions prevent intra- and inter-molecular interactions on the repetitive domain, which are required to maintain the solubility, while kosmotropic ions ... ...

Abstract	The effect of ions on the structure and dynamics of a spider silk protein is elucidated. Chaotropic ions prevent intra- and inter-molecular interactions on the repetitive domain, which are required to maintain the solubility, while kosmotropic ions promote hydrogen bond interactions in the glycine-rich region, which are a prerequisite for β-sheet formation.
MeSH term(s)	Animals ; Chlorides/chemistry ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Nuclear Magnetic Resonance, Biomolecular/methods ; Protein Conformation, beta-Strand ; Recombinant Proteins/chemistry ; Silk/chemistry ; Sodium/chemistry ; Solubility ; Spiders
Chemical Substances	Chlorides ; Recombinant Proteins ; Silk ; Sodium (9NEZ333N27)
Language	English
Publishing date	2019-07-09
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/c9cc03538a
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Article ; Online: The origins of binding specificity of a lanthanide ion binding peptide.

Hatanaka, Takaaki / Kikkawa, Nobuaki / Matsugami, Akimasa / Hosokawa, Yoichi / Hayashi, Fumiaki / Ishida, Nobuhiro

Scientific reports

2020 Volume 10, Issue 1, Page(s) 19468

Abstract: Lanthanide ions ( ... ...

Abstract	Lanthanide ions (Ln
MeSH term(s)	Binding Sites ; Calorimetry/methods ; Cations/chemistry ; Cations/metabolism ; Crystallography, X-Ray ; Lanthanoid Series Elements/chemistry ; Lanthanoid Series Elements/metabolism ; Magnetic Resonance Spectroscopy/methods ; Molecular Dynamics Simulation ; Molecular Structure ; Peptides/chemistry ; Peptides/metabolism ; Thermodynamics ; Water/chemistry
Chemical Substances	Cations ; Lanthanoid Series Elements ; Peptides ; Water (059QF0KO0R)
Language	English
Publishing date	2020-11-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-76527-y
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Article ; Online: Nearly complete

Oktaviani, Nur Alia / Malay, Ali D / Matsugami, Akimasa / Hayashi, Fumiaki / Numata, Keiji

Biomolecular NMR assignments

2020 Volume 14, Issue 2, Page(s) 335–338

Abstract: Spider dragline silk is well recognized due to its excellent mechanical properties. Dragline silk protein mainly consists of two proteins, namely, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2). The MaSp N-terminal domain (NTD) ...

Abstract	Spider dragline silk is well recognized due to its excellent mechanical properties. Dragline silk protein mainly consists of two proteins, namely, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2). The MaSp N-terminal domain (NTD) conformation displays a strong dependence on ion and pH gradients, which is crucial for the self-assembly behavior of spider silk. In the spider major ampullate gland, where the pH is neutral and concentration of NaCl is high, the NTD forms a monomer. In contrast, within the spinning duct, where pH becomes more acidic (to pH ~ 5) and the concentration of salt is low, NTD forms a dimer in antiparallel orientation. In this study, we report near-complete backbone and side chain chemical shift assignment of the monomeric form of NTD of MaSp2 from Nephila clavipes at pH 7 in the presence of 300 mM NaCl. Our NMR data demonstrate that secondary structure of monomeric form of NTD MaSp2 consists of five helix regions.
MeSH term(s)	Amino Acid Sequence ; Animal Structures ; Animals ; Carbon-13 Magnetic Resonance Spectroscopy ; Fibroins/chemistry ; Hydrogen-Ion Concentration ; Nitrogen Isotopes ; Protein Domains ; Protein Structure, Secondary ; Proton Magnetic Resonance Spectroscopy ; Spiders/metabolism
Chemical Substances	Nitrogen Isotopes ; Nitrogen-15 ; spidroin 2 (147883-43-0) ; Fibroins (9007-76-5)
Language	English
Publishing date	2020-08-06
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2388861-1
ISSN	1874-270X ; 1874-2718
ISSN (online)	1874-270X
ISSN	1874-2718
DOI	10.1007/s12104-020-09972-5
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Article ; Online: Distinct residual and disordered structures of alpha-synuclein analyzed by amide-proton exchange and NMR signal intensity.

Okuwaki, Rina / Shinmura, Iori / Morita, Shiki / Matsugami, Akimasa / Hayashi, Fumiaki / Goto, Yuji / Nishimura, Chiaki

Biochimica et biophysica acta. Proteins and proteomics

2020 Volume 1868, Issue 9, Page(s) 140464

Abstract	The residual solution structures of two alpha-synuclein mutants, A30P and A53T, observed in family members of patients with Parkinson's disease were compared with that of wild-type by NMR. The A53T substitution had been shown to accelerate fibril formation of alpha-synuclein, whereas the A30P mutation has the negative and positive effects on the formation of the fibril and spherical oligomer, respectively. The remaining structure was analyzed via amide-proton exchange and signal intensity measurements using NMR. Amide-proton exchange was used for both the calculation of k
MeSH term(s)	Amides/chemistry ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/genetics ; Magnetic Resonance Imaging ; Magnetic Resonance Spectroscopy ; Mutant Proteins/chemistry ; Mutation ; Parkinson Disease/genetics ; Protein Structure, Secondary ; Protons ; Temperature ; alpha-Synuclein/chemistry ; alpha-Synuclein/genetics
Chemical Substances	Amides ; Intrinsically Disordered Proteins ; Mutant Proteins ; Protons ; alpha-Synuclein
Language	English
Publishing date	2020-06-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2020.140464
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Article: Ion effects on the conformation and dynamics of repetitive domains of a spider silk protein: implications for solubility and β-sheet formation

Oktaviani, Nur Alia / Matsugami, Akimasa / Hayashi, Fumiaki / Numata, Keiji

Chemical communications. 2019 Aug. 13, v. 55, no. 66

2019

Abstract	The effect of ions on the structure and dynamics of a spider silk protein is elucidated. Chaotropic ions prevent intra- and inter-molecular interactions on the repetitive domain, which are required to maintain the solubility, while kosmotropic ions promote hydrogen bond interactions in the glycine-rich region, which are a prerequisite for β-sheet formation.
Keywords	chemical compounds ; chemical reactions ; glycine (amino acid) ; hydrogen bonding ; ions ; solubility ; spidroins
Language	English
Dates of publication	2019-0813
Size	p. 9761-9764.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/c9cc03538a
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Article ; Online: Conformation and dynamics of soluble repetitive domain elucidates the initial β-sheet formation of spider silk.

Oktaviani, Nur Alia / Matsugami, Akimasa / Malay, Ali D / Hayashi, Fumiaki / Kaplan, David L / Numata, Keiji

Nature communications

2018 Volume 9, Issue 1, Page(s) 2121

Abstract: The β-sheet is the key structure underlying the excellent mechanical properties of spider silk. However, the comprehensive mechanism underlying β-sheet formation from soluble silk proteins during the transition into insoluble stable fibers has not been ... ...

Abstract	The β-sheet is the key structure underlying the excellent mechanical properties of spider silk. However, the comprehensive mechanism underlying β-sheet formation from soluble silk proteins during the transition into insoluble stable fibers has not been elucidated. Notably, the assembly of repetitive domains that dominate the length of the protein chains and structural features within the spun fibers has not been clarified. Here we determine the conformation and dynamics of the soluble precursor of the repetitive domain of spider silk using solution-state NMR, far-UV circular dichroism and vibrational circular dichroism. The soluble repetitive domain contains two major populations: ~65% random coil and ~24% polyproline type II helix (PPII helix). The PPII helix conformation in the glycine-rich region is proposed as a soluble prefibrillar region that subsequently undergoes intramolecular interactions. These findings unravel the mechanism underlying the initial step of β-sheet formation, which is an extremely rapid process during spider silk assembly.
MeSH term(s)	Animals ; Circular Dichroism ; Magnetic Resonance Spectroscopy ; Protein Conformation, beta-Strand/physiology ; Silk/chemistry ; Spiders/metabolism ; Stress, Mechanical ; Tensile Strength/physiology
Chemical Substances	Silk
Language	English
Publishing date	2018-05-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-018-04570-5
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