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Oktaviani NA, Malay AD, Matsugami A, Hayashi F, Numata K. Unusual p Ka Values Mediate the Self-Assembly of Spider Dragline Silk Proteins. Biomacromolecules 2023; 24:1604-1616. [PMID: 36990448 PMCID: PMC10091414 DOI: 10.1021/acs.biomac.2c01344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/17/2023] [Indexed: 03/31/2023]
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 Trichonephila clavipes and determined the experimental pKa values of conserved residues involved in dimerization using NMR. Surprisingly, we found that the Asp40 located on an acidic cluster protonates at an unusually high pH (∼6.5-7.1), suggesting the first step in the pH response. Then, protonation of Glu119 and Glu79 follows, with pKas above their intrinsic values, contributing toward stable dimer formation. We propose that exploiting the atypical pKa values is a strategy to achieve tight spatiotemporal control of spider silk self-assembly.
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Affiliation(s)
- Nur Alia Oktaviani
- Biomacromolecules
Research Team, RIKEN Center for the Sustainable
Resource Sciences, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ali D. Malay
- Biomacromolecules
Research Team, RIKEN Center for the Sustainable
Resource Sciences, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akimasa Matsugami
- Advanced
NMR Application and Platform Team, NMR Research and Collaboration
Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Fumiaki Hayashi
- Advanced
NMR Application and Platform Team, NMR Research and Collaboration
Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiji Numata
- Biomacromolecules
Research Team, RIKEN Center for the Sustainable
Resource Sciences, 2-1
Hirosawa, Wako, Saitama 351-0198, Japan
- Department
of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyotodaigaku,
Katsura, Kyoto 615-8510, Japan
- Institute
for Advanced Bioscience, Keio University, 403-1 Nihonkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
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Cheng JE, Su P, Zhang ZH, Zheng LM, Wang ZY, Hamid MR, Dai JP, Du XH, Chen LJ, Zhai ZY, Kong XT, Liu Y, Zhang DY. Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods. PLoS One 2022; 17:e0262517. [PMID: 35834536 PMCID: PMC9282544 DOI: 10.1371/journal.pone.0262517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022] Open
Abstract
Photosynthetic bacteria are beneficial to plants, but knowledge of photosynthetic bacterial community dynamics in field crops during different growth stages is scarce. The factors controlling the changes in the photosynthetic bacterial community during plant growth require further investigation. In this study, 35 microbial community samples were collected from the seedling, flowering, and mature stages of tomato, cucumber, and soybean plants. 35 microbial community samples were assessed using Illumina sequencing of the photosynthetic reaction center subunit M (pufM) gene. The results revealed significant alpha diversity and community structure differences among the three crops at the different growth stages. Proteobacteria was the dominant bacterial phylum, and Methylobacterium, Roseateles, and Thiorhodococcus were the dominant genera at all growth stages. PCoA revealed clear differences in the structure of the microbial populations isolated from leaf samples collected from different crops at different growth stages. In addition, a dissimilarity test revealed significant differences in the photosynthetic bacterial community among crops and growth stages (P<0.05). The photosynthetic bacterial communities changed during crop growth. OTUs assigned to Methylobacterium were present in varying abundances among different sample types, which we speculated was related to the function of different Methylobacterium species in promoting plant growth development and enhancing plant photosynthetic efficiency. In conclusion, the dynamics observed in this study provide new research ideas for the detailed assessments of the relationship between photosynthetic bacteria and different growth stages of plants.
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Affiliation(s)
- Ju-E Cheng
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Pin Su
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zhan-Hong Zhang
- Hunan Vegetable Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Li-Min Zheng
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhong-Yong Wang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Muhammad Rizwan Hamid
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Jian-Ping Dai
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Xiao-Hua Du
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Li-Jie Chen
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhong-Ying Zhai
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Xiao-Ting Kong
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Yong Liu
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - De-Yong Zhang
- Hunan Hybrid Rice Research Center, Changsha, China
- * E-mail:
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Koeppe B, Tolstoy PM, Guo J, Denisov GS, Limbach HH. Combined NMR and UV-Vis Spectroscopic Studies of Models for the Hydrogen Bond System in the Active Site of Photoactive Yellow Protein: H-Bond Cooperativity and Medium Effects. J Phys Chem B 2021; 125:5874-5884. [PMID: 34060830 DOI: 10.1021/acs.jpcb.0c09923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intramolecular hydrogen bonds in aprotic media were studied by combined (simultaneous) NMR and UV-vis spectroscopy. The species under investigation were anionic and featured single or coupled H-bonds between, for example, carboxylic groups and phenolic oxygen atoms (COO···H···OC)-, among phenolic oxygen atoms (CO···H···OC)-, and hydrogen bond chains between a carboxylic group and two phenolic oxygen atoms (COO···H···(OC)···H···OC)-. The last anion may be regarded as a small molecule model for the hydrogen bond system in the active site of wild-type photoactive yellow protein (PYP) while the others mimic the corresponding H-bonds in site-selective mutants. Proton positions in isolated hydrogen bonds and hydrogen bond chains were assessed by calculations for vacuum conditions and spectroscopically for the two media, CD2Cl2 and the liquefied gas mixture CDClF2/CDF3 at low temperatures. NMR parameters allow for the estimation of time-averaged H-bond geometries, and optical spectra give additional information about geometry distributions. Comparison of the results from the various systems revealed the effects of the formation of hydrogen bond chains and changes of medium conditions on the geometry of individual H-bonds. In particular, the proton in a hydrogen bond to a carboxylic group shifts from the phenolic oxygen atom in the system COO-···H-OC to the carboxylic group in COO-H···(OC)-···H-OC as a result of hydrogen bond formation to the additional phenolic donor. Increase in medium polarity may, however, induce the conversion of a structure of a type COO-H···(OC)-···H-OC to the type COO-···H-(OC)···H-OC. Application of these results obtained from the model systems to PYP suggests that both cooperative effects within the hydrogen bond chain and a low-polarity protein environment are prerequisites for the stabilization of negative charge on the cofactor and hence for the spectral tuning of the photoreceptor.
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Affiliation(s)
- Benjamin Koeppe
- J. Heyrovský Institute of Physical Chemistry, Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Peter M Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 St. Petersburg, Russia
| | - Jing Guo
- Department of Radiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Gleb S Denisov
- Department of Physics, St. Petersburg State University, 198504 St. Petersburg, Russian Federation
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Thomson B, Both J, Wu Y, Parrish RM, Martínez TJ, Boxer SG. Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation. J Phys Chem B 2019; 123:4844-4849. [PMID: 31117606 PMCID: PMC7061054 DOI: 10.1021/acs.jpcb.9b01571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p Ka of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.
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Affiliation(s)
| | | | | | - Robert M. Parrish
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Todd J. Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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