Bottom-up design of peptide nanoshapes in water using oligomers of N-methyl-L/D-alanine

Morimoto, Jumpei; Shiratori, Yota; Yokomine, Marin; Ueda, Takumi; Nakamuro, Takayuki; Takaba, Kiyotsugu; Maki-Yonekura, Saori; Umezawa, Koji; Miyanishi, Koichiro; Fukuda, Yasuhiro; Watanabe, Takumu; Mizukami, Wataru; Takeuchi, Koh; Yonekura, Koji; Nakamura, Eiichi; Sando, Shinsuke

doi:10.26434/chemrxiv-2023-c4mw6

Cited by 2 publications

(3 citation statements)

References 33 publications

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“…A peptoid monomer named “monopeptoid” and an oligomer consisting of three residues named “tripeptoid” were synthesized. The crystal structure of monopeptoid was recently reported, while the structure of tripeptoid had not been determined yet.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds

Takaba,

Maki-Yonekura,

Inoue

et al. 2024

J. Am. Chem. Soc.

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There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to the crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to small (a few μm or less) and thin (a few hundred nm or less) crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate coupled with rotation enables highly efficient data collection. The recorded patterns can be successfully indexed using lattice parameters obtained through 3D ED. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferentially oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies of small crystals of organic compounds.

show abstract

Section: Resultsmentioning

confidence: 99%

Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds

Takaba,

Maki-Yonekura,

Inoue

et al. 2024

J. Am. Chem. Soc.

Self Cite

View full text Add to dashboard Cite

show abstract

“…A peptoid monomer named "monopeptoid" and an oligomer consisting of three residues named "tripeptoid" were synthetized. The crystal structure of monopeptoid was recently reported 37 , while the structure of tripeptoid had not been determined yet. Powder crystals of these peptoids were first observed using a cryogenic-electron microscope (cryo-EM).…”

Section: Strategy For Data Acquisition and Analysismentioning

confidence: 99%

“…Acetyl-L-alanine piperazine, N-Boc was synthesized and crystallized as described in Morimoto et al (2023) 37 , and referred to monopeptoid in this report. Tripeptoid was synthesized as follows.…”

Section: Synthesis and Crystallization Of Peptoidsmentioning

confidence: 99%

Comprehensive application of XFEL micro crystallography for novel organic compounds

Takaba,

Maki-Yonekura,

Inoue

et al. 2023

Preprint

View full text Add to dashboard Cite

There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to tiny crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate, coupled with rotation, enables highly efficient data collection. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferred-oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data, regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies on small crystals of organic compounds.

show abstract

Bottom-up design of peptide nanoshapes in water using oligomers of N-methyl-L/D-alanine

Cited by 2 publications

References 33 publications

Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds

Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds

Comprehensive application of XFEL micro crystallography for novel organic compounds

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