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Article ; Online: Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases.

Nagata, Takuya / Shinya, Shoko / Ohnuma, Takayuki / Fukamizo, Tamo

2021 Volume 11, Issue 1, Page(s) 2494

Abstract: GH19 and GH22 glycoside hydrolases belonging to the lysozyme superfamily have a related structure/function. A highly conserved tryptophan residue, Trp103, located in the binding groove of a GH19 chitinase from moss Bryum coronatum (BcChi-A) appears to ... ...

Abstract	GH19 and GH22 glycoside hydrolases belonging to the lysozyme superfamily have a related structure/function. A highly conserved tryptophan residue, Trp103, located in the binding groove of a GH19 chitinase from moss Bryum coronatum (BcChi-A) appears to have a function similar to that of well-known Trp62 in GH22 lysozymes. Here, we found that mutation of Trp103 to phenylalanine (W103F) or alanine (W103A) strongly reduced the enzymatic activity of BcChi-A. NMR experiments and the X-ray crystal structure suggested a hydrogen bond between the Trp103 side chain and the -2 sugar. Chitooligosaccharide binding experiments using NMR indicated that the W103F mutation reduced the sugar-binding abilities of nearby amino acid residues (Tyr105/Asn106) in addition to Trp103. This appeared to be derived from enhanced aromatic stacking of Phe103 with Tyr105 induced by disruption of the Trp103 hydrogen bond with the -2 sugar. Since the stacking with Tyr105 was unlikely in W103A, Tyr105/Asn106 of W103A was not so affected as in W103F. However, the W103A mutation appeared to reduce the catalytic potency, resulting in the lowest enzymatic activity in W103A. We concluded that Trp103 does not only interact with the sugar, but also controls other amino acids responsible for substrate binding and catalysis. Trp103 (GH19) and Trp62 (GH22) with such a multi-functionality may be advantageous for enzyme action and conserved in the divergent evolution in the lysozyme superfamily.
MeSH term(s)	Amino Acid Substitution ; Binding Sites ; Bryopsida/enzymology ; Bryopsida/genetics ; Chitin/analogs & derivatives ; Chitin/chemistry ; Chitinases/chemistry ; Chitinases/genetics ; Mutation, Missense ; Plant Proteins/chemistry ; Plant Proteins/genetics ; Tryptophan/chemistry ; Tryptophan/genetics
Chemical Substances	Plant Proteins ; oligochitosan ; Chitin (1398-61-4) ; Tryptophan (8DUH1N11BX) ; Chitinases (EC 3.2.1.14)
Language	English
Publishing date	2021-01-28
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/s41598-021-81903-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: [Proteins capturing the tail of chitosan].

Shinya, Shoko / Fukamizo, Tamo

Seikagaku. The Journal of Japanese Biochemical Society

2018 Volume 88, Issue 5, Page(s) 664–668

MeSH term(s)	Chitosan/chemistry ; Chitosan/metabolism ; Proteins/chemistry ; Proteins/metabolism
Chemical Substances	Proteins ; Chitosan (9012-76-4)
Language	Japanese
Publishing date	2018-04-06
Publishing country	Japan
Document type	Journal Article ; Review
ZDB-ID	282319-6
ISSN	0037-1017
ISSN	0037-1017
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Article ; Online: Interaction between chitosan and its related enzymes: A review.

Shinya, Shoko / Fukamizo, Tamo

International journal of biological macromolecules

2017 Volume 104, Issue Pt B, Page(s) 1422–1435

Abstract: Chitosan-related enzymes including chitosanases, exo-β-glucosaminidases, and enzymes having chitosan-binding modules recognize ligands through electrostatic interactions between the acidic amino acids in proteins and amino groups of chitosan ... ...

Abstract	Chitosan-related enzymes including chitosanases, exo-β-glucosaminidases, and enzymes having chitosan-binding modules recognize ligands through electrostatic interactions between the acidic amino acids in proteins and amino groups of chitosan polysaccharides. However, in GH8 chitosanases, several aromatic residues are also involved in substrate recognition through stacking interactions, and these enzymes consequently hydrolyze β-1,4-glucan as well as chitosan. The binding grooves of these chitosanases are extended and opened at both ends of the grooves, so that the enzymes can clamp a long chitosan polysaccharide. The association/dissociation of positively charged glucosamine residues to/from the binding pocket of a GH2 exo-β-glucosaminidase controls the p K
Language	English
Publishing date	2017-11
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2017.02.040
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Article: Interaction between chitosan and its related enzymes: A review

Shinya, Shoko / Tamo Fukamizo

International journal of biological macromolecules. 2017,

2017

Abstract: Chitosan-related enzymes including chitosanases, exo-Î²-glucosaminidases, and enzymes having chitosan-binding modules recognize ligands through electrostatic interactions between the acidic amino acids in proteins and amino groups of chitosan ... ...

Abstract	Chitosan-related enzymes including chitosanases, exo-Î²-glucosaminidases, and enzymes having chitosan-binding modules recognize ligands through electrostatic interactions between the acidic amino acids in proteins and amino groups of chitosan polysaccharides. However, in GH8 chitosanases, several aromatic residues are also involved in substrate recognition through stacking interactions, and these enzymes consequently hydrolyze Î²-1,4-glucan as well as chitosan. The binding grooves of these chitosanases are extended and opened at both ends of the grooves, so that the enzymes can clamp a long chitosan polysaccharide. The association/dissociation of positively charged glucosamine residues to/from the binding pocket of a GH2 exo-Î²-glucosaminidase controls the p Ka of the catalytic acid, thereby maintaining the high catalytic potency of the enzyme. In contrast to chitosanases, chitosan-binding modules only accommodate a couple of glucosamine residues, predominantly recognizing the non-reducing end glucosamine residue of chitosan by electrostatic interactions and a hydrogen-bonding network. These structural findings on chitosan-related enzymes may contribute to future applications for the efficient conversion of the chitin/chitosan biomass.
Keywords	amino acids ; biomass ; chitin ; chitosan ; dissociation ; electrostatic interactions ; enzymes ; glucosamine ; hydrogen bonding ; ligands ; proteins
Language	English
Size	p. .
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2017.02.040
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Article ; Online: Hydrogen bonds connecting the N-terminal region and the DE loop stabilize the monomeric structure of transthyretin.

Inada, Yuki / Ono, Yuichiro / Okazaki, Kyo / Yamashita, Takuma / Kawaguchi, Tomoyuki / Kawano, Shingo / Kobashigawa, Yoshihiro / Shinya, Shoko / Kojima, Chojiro / Shuto, Tsuyoshi / Kai, Hirofumi / Morioka, Hiroshi / Sato, Takashi

Journal of biochemistry

2023 Volume 174, Issue 4, Page(s) 355–370

Abstract: Transthyretin (TTR) is a homo-tetrameric serum protein associated with sporadic and hereditary systemic amyloidosis. TTR amyloid formation proceeds by the dissociation of the TTR tetramer and the subsequent partial unfolding of the TTR monomer into an ... ...

Abstract	Transthyretin (TTR) is a homo-tetrameric serum protein associated with sporadic and hereditary systemic amyloidosis. TTR amyloid formation proceeds by the dissociation of the TTR tetramer and the subsequent partial unfolding of the TTR monomer into an aggregation-prone conformation. Although TTR kinetic stabilizers suppress tetramer dissociation, a strategy for stabilizing monomers has not yet been developed. Here, we show that an N-terminal C10S mutation increases the thermodynamic stability of the TTR monomer by forming new hydrogen bond networks through the side chain hydroxyl group of Ser10. Nuclear magnetic resonance spectrometry and molecular dynamics simulation revealed that the Ser10 hydroxyl group forms hydrogen bonds with the main chain amide group of either Gly57 or Thr59 on the DE loop. These hydrogen bonds prevent the dissociation of edge strands in the DAGH and CBEF β-sheets during the unfolding of the TTR monomer by stabilizing the interaction between β-strands A and D and the quasi-helical structure in the DE loop. We propose that introducing hydrogen bonds to connect the N-terminal region to the DE loop reduces the amyloidogenic potential of TTR by stabilizing the monomer.
MeSH term(s)	Protein Conformation ; Hydrogen Bonding ; Prealbumin/chemistry ; Prealbumin/genetics ; Prealbumin/metabolism ; Molecular Dynamics Simulation ; Amyloid/chemistry ; Amyloid/metabolism
Chemical Substances	Prealbumin ; Amyloid
Language	English
Publishing date	2023-07-01
Publishing country	England
Document type	Journal Article
ZDB-ID	218073-x
ISSN	1756-2651 ; 0021-924X
ISSN (online)	1756-2651
ISSN	0021-924X
DOI	10.1093/jb/mvad049
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Article ; Online: Biochemical and biotechnological trends in chitin, chitosan, and related enzymes produced by Paenibacillus IK-5 Strain.

Kusaoke, Hideo / Shinya, Shoko / Fukamizo, Tamo / Kimoto, Hisashi

International journal of biological macromolecules

2017 Volume 104, Issue Pt B, Page(s) 1633–1640

Abstract: We review studies on biochemical characterization of the structures and functions of chitinase, chitosanase, and chitobiase produced by cells of the bacterium, Paenibacillus sp. IK-5. The IK-5 chitinases comprise two GH18 chitinases (ChiA and ChiB), an ... ...

Abstract	We review studies on biochemical characterization of the structures and functions of chitinase, chitosanase, and chitobiase produced by cells of the bacterium, Paenibacillus sp. IK-5. The IK-5 chitinases comprise two GH18 chitinases (ChiA and ChiB), an auxiliary activity family 10 (AA10) chitin oxydehydrolase (ChiC), and a GH19 chitinase (ChiD). The IK-5 chitosanase (ChiE) has a glycosyl hydrolase family 8 (GH8) catalytic domain at the amino-terminus and two discoidin domains (DD) at the carboxyl-terminus. The IK-5 cells also produce chitobiase, containing carbohydrate hydrolase H-20 and S-layer homology domains. Together, these ChiA∼ChiE proteins form a huge complex, designated the "chitinasome". The DD domains bind specifically and tightly to chitosan, suggesting that they are chitosan-specific carbohydrate-binding modules (CBM32); indeed, CBM32 modules have been confirmed to bind to chitosan oligosaccharides (GlcN)
Language	English
Publishing date	2017-11
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2017.04.118
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Article ; Online: Multifunctional chemical inhibitors of the florigen activation complex discovered by structure-based high-throughput screening.

Taoka, Ken-Ichiro / Kawahara, Ikumi / Shinya, Shoko / Harada, Ken-Ichi / Yamashita, Eiki / Shimatani, Zenpei / Furuita, Kyoko / Muranaka, Tomoaki / Oyama, Tokitaka / Terada, Rie / Nakagawa, Atsushi / Fujiwara, Toshimichi / Tsuji, Hiroyuki / Kojima, Chojiro

The Plant journal : for cell and molecular biology

2022 Volume 112, Issue 6, Page(s) 1337–1349

Abstract: Structure-based high-throughput screening of chemical compounds that target protein-protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At ...

Abstract	Structure-based high-throughput screening of chemical compounds that target protein-protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At present, there are no examples of using high-throughput screening to identify chemicals that target plant transcriptional complexes, some of which are responsible for regulating multiple physiological functions. Florigen, a protein encoded by FLOWERING LOCUS T (FT), was initially identified as a molecule that promotes flowering and has since been shown to regulate flowering and other developmental phenomena such as tuber formation in potato (Solanum tuberosum). FT functions as a component of the florigen activation complex (FAC) with a 14-3-3 scaffold protein and FD, a bZIP transcription factor that activates downstream gene expression. Although 14-3-3 is an important component of FAC, little is known about the function of the 14-3-3 protein itself. Here, we report the results of a high-throughput in vitro fluorescence resonance energy transfer (FRET) screening of chemical libraries that enabled us to identify small molecules capable of inhibiting FAC formation. These molecules abrogate the in vitro interaction between the 14-3-3 protein and the OsFD1 peptide, a rice (Oryza sativa) FD, by directly binding to the 14-3-3 protein. Treatment with S4, a specific hit molecule, strongly inhibited FAC activity and flowering in duckweed, tuber formation in potato, and branching in rice in a dose-dependent manner. Our results demonstrate that the high-throughput screening approach based on the three-dimensional structure of PPIs is suitable in plants. In this study, we have proposed good candidate compounds for future modification to obtain inhibitors of florigen-dependent processes through inhibition of FAC formation.
MeSH term(s)	Florigen/metabolism ; Plant Proteins/metabolism ; 14-3-3 Proteins/genetics ; 14-3-3 Proteins/metabolism ; High-Throughput Screening Assays ; Oryza/metabolism ; Gene Expression Regulation, Plant ; Flowers/genetics
Chemical Substances	Florigen ; Plant Proteins ; 14-3-3 Proteins
Language	English
Publishing date	2022-11-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.16008
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Article ; Online: Multifunctional chemical inhibitors of the florigen activation complex discovered by structure‐based high‐throughput screening

Taoka, Ken‐ichiro / Kawahara, Ikumi / Shinya, Shoko / Harada, Ken‐ichi / Yamashita, Eiki / Shimatani, Zenpei / Furuita, Kyoko / Muranaka, Tomoaki / Oyama, Tokitaka / Terada, Rie / Nakagawa, Atsushi / Fujiwara, Toshimichi / Tsuji, Hiroyuki / Kojima, Chojiro

The Plant Journal. 2022 Dec., v. 112, no. 6 p.1337-1349

2022

Abstract: Structure‐based high‐throughput screening of chemical compounds that target protein–protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At ...

Abstract	Structure‐based high‐throughput screening of chemical compounds that target protein–protein interactions (PPIs) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At present, there are no examples of using high‐throughput screening to identify chemicals that target plant transcriptional complexes, some of which are responsible for regulating multiple physiological functions. Florigen, a protein encoded by FLOWERING LOCUS T (FT), was initially identified as a molecule that promotes flowering and has since been shown to regulate flowering and other developmental phenomena such as tuber formation in potato (Solanum tuberosum). FT functions as a component of the florigen activation complex (FAC) with a 14‐3‐3 scaffold protein and FD, a bZIP transcription factor that activates downstream gene expression. Although 14‐3‐3 is an important component of FAC, little is known about the function of the 14‐3‐3 protein itself. Here, we report the results of a high‐throughput in vitro fluorescence resonance energy transfer (FRET) screening of chemical libraries that enabled us to identify small molecules capable of inhibiting FAC formation. These molecules abrogate the in vitro interaction between the 14‐3‐3 protein and the OsFD1 peptide, a rice (Oryza sativa) FD, by directly binding to the 14‐3‐3 protein. Treatment with S4, a specific hit molecule, strongly inhibited FAC activity and flowering in duckweed, tuber formation in potato, and branching in rice in a dose‐dependent manner. Our results demonstrate that the high‐throughput screening approach based on the three‐dimensional structure of PPIs is suitable in plants. In this study, we have proposed good candidate compounds for future modification to obtain inhibitors of florigen‐dependent processes through inhibition of FAC formation.
Keywords	Araceae ; Oryza sativa ; Solanum tuberosum ; dose response ; energy transfer ; florigen ; fluorescence ; gene expression ; loci ; peptides ; plant development ; potatoes ; rice ; scaffolding proteins ; transcription (genetics) ; transcription factors
Language	English
Dates of publication	2022-12
Size	p. 1337-1349.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.16008
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Article ; Online: Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks.

Kobayashi, Naohiro / Hattori, Yoshikazu / Nagata, Takashi / Shinya, Shoko / Güntert, Peter / Kojima, Chojiro / Fujiwara, Toshimichi

Bioinformatics (Oxford, England)

2018 Volume 34, Issue 24, Page(s) 4300–4301

Abstract: Motivation: Multi-dimensional NMR spectra are generally used for NMR signal assignment and structure analysis. There are several programs that can achieve highly automated NMR signal assignments and structure analysis. On the other hand, NMR spectra ... ...

Abstract	Motivation: Multi-dimensional NMR spectra are generally used for NMR signal assignment and structure analysis. There are several programs that can achieve highly automated NMR signal assignments and structure analysis. On the other hand, NMR spectra tend to have a large number of noise peaks even for data acquired with good sample and machine conditions, and it is still difficult to eliminate these noise peaks. Results: We have developed a method to eliminate noise peaks using convolutional neural networks, implemented in the program package Filt_Robot. The filtering accuracy of Filt_Robot was around 90-95% when applied to 2D and 3D NMR spectra, and the numbers of resulting non-noise peaks were close to those in corresponding manually prepared peaks lists. The filtering can strongly enhance automated NMR spectra analysis. Availability and implementation: The full package of the program, documents and example data are available from http://bmrbdep.pdbj.org/en/nmr_tool_box/Filt_Robot.html. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Magnetic Resonance Spectroscopy ; Neural Networks (Computer) ; Proteins ; Software
Chemical Substances	Proteins
Language	English
Publishing date	2018-07-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bty581
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Article: Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study

Bala, Siqin / Ishikawa, Marie / Kobayashi, Naohiro / Kohda, Daisuke / Kojima, Chojiro / Miyashita, Osamu / Shimada, Atsushi / Shinya, Shoko / Srivastava, Arpita / Tama, Florence

Biochimica et biophysica acta. 2020 Feb., v. 1864, no. 2

2020

Abstract: In protein crystals, flexible loops are frequently deformed by crystal contacts, whereas in solution, the large motions result in the poor convergence of such flexible loops in NMR structure determinations. We need an experimental technique to ... ...

Abstract	In protein crystals, flexible loops are frequently deformed by crystal contacts, whereas in solution, the large motions result in the poor convergence of such flexible loops in NMR structure determinations. We need an experimental technique to characterize the structural and dynamic properties of intrinsically flexible loops of protein molecules.We designed an intended crystal contact-free space (CCFS) in protein crystals, and arranged the flexible loop of interest in the CCFS. The yeast Tim 21 protein was chosen as the model protein, because one of the loops (loop 2) is distorted by crystal contacts in the conventional crystal.Yeast Tim21 was fused to the MBP protein by a rigid α-helical linker. The space created between the two proteins was used as the CCFS. The linker length provides adjustable freedom to arrange loop 2 in the CCFS. We re-determined the NMR structure of yeast Tim21, and conducted MD simulations for comparison. Multidimensional scaling was used to visualize the conformational similarity of loop 2. We found that the crystal contact-free conformation of loop 2 is located close to the center of the ensembles of the loop 2 conformations in the NMR and MD structures.Loop 2 of yeast Tim21 in the CCFS adopts a representative, dominant conformation in solution.No single powerful technique is available for the characterization of flexible structures in protein molecules. NMR analyses and MD simulations provide useful, but incomplete information. CCFS crystallography offers a third route to this goal.
Keywords	case studies ; crystallography ; crystals ; models ; multidimensional scaling ; nuclear magnetic resonance spectroscopy ; proteins ; yeasts
Language	English
Dates of publication	2020-02
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	840755-1
ISSN	0304-4165
ISSN	0304-4165
DOI	10.1016/j.bbagen.2019.129418
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