Abstract

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

Details

Title
Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source
Author
Gul, Mehmet 1 ; Ayan, Esra 1 ; Destan, Ebru 1 ; Johnson, J. Austin 1 ; Shafiei, Alaleh 1 ; Kepceoğlu, Abdullah 2 ; Yilmaz, Merve 1 ; Ertem, Fatma Betül 1 ; Yapici, İlkin 1 ; Tosun, Bilge 1 ; Baldir, Nilüfer 1 ; Tokay, Nurettin 1 ; Nergiz, Zeliş 3 ; Karakadioğlu, Gözde 1 ; Paydos, Seyide Seda 1 ; Kulakman, Cahine 1 ; Ferah, Cengiz Kaan 1 ; Güven, Ömür 1 ; Atalay, Necati 4 ; Akcan, Enver Kamil 5 ; Cetinok, Haluk 1 ; Arslan, Nazlı Eylül 6 ; Şabanoğlu, Kardelen 7 ; Aşci, Bengisu 1 ; Tavli, Serra 1 ; Gümüsboğa, Helin 1 ; Altuntaş, Sevde 8 ; Otsuka, Masami 9 ; Fujita, Mikako 10 ; Teki̇n, Şaban 11 ; Çi̇ftçi̇, Halilibrahim 12 ; Durdaği, Serdar 13 ; Karaca, Ezgi 14 ; Kaplan Türköz, Burcu 15 ; Kabasakal, Burak Veli 16 ; Kati, Ahmet 17 ; DeMi̇rci̇, Hasan 18 

1  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552) 
2  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Koç University, Koç University Surface Science and Technology Center (KUYTAM), Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552) 
3  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Koç University, Koç University Isbank Center for Infectious Diseases (KUISCID), Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552) 
4  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Gebze Technical University, Department of Molecular Biology and Genetics, Faculty of Science, Kocaeli, Türkiye (GRID:grid.448834.7) (ISNI:0000 0004 0595 7127); University of Health Sciences Türkiye, Experimental Medicine Application & Research Center, Istanbul, Türkiye (GRID:grid.488643.5) (ISNI:0000 0004 5894 3909) 
5  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Istanbul Technical University, Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul, Türkiye (GRID:grid.10516.33) (ISNI:0000 0001 2174 543X) 
6  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Istanbul Arel University, Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul, Türkiye (GRID:grid.440443.3) (ISNI:0000 0004 0399 4354) 
7  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Yıldız Technical University, Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Istanbul, Türkiye (GRID:grid.38575.3c) (ISNI:0000 0001 2337 3561) 
8  University of Health Sciences Türkiye, Experimental Medicine Application & Research Center, Istanbul, Türkiye (GRID:grid.488643.5) (ISNI:0000 0004 5894 3909); University of Health Sciences Türkiye, Department of Tissue Engineering, Hamidiye Institute of Health Sciences, Istanbul, Türkiye (GRID:grid.488643.5) (ISNI:0000 0004 5894 3909) 
9  Kumamoto University, Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto, Japan (GRID:grid.274841.c) (ISNI:0000 0001 0660 6749); Science Farm Ltd., Department of Drug Discovery, Kumamoto, Japan (GRID:grid.274841.c) 
10  Kumamoto University, Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto, Japan (GRID:grid.274841.c) (ISNI:0000 0001 0660 6749) 
11  The Scientific and Technological Research Council of Türkiye (TÜBİTAK) Marmara Research Center (MAM), Life Sciences, Kocaeli, Türkiye (GRID:grid.508834.2) (ISNI:0000 0004 0644 9538); University of Health Sciences Türkiye, Department of Basic Medical Sciences, Division of Medical Biology, Faculty of Medicine, Istanbul, Türkiye (GRID:grid.488643.5) (ISNI:0000 0004 5894 3909); University of Health Sciences Türkiye, Experimental Medicine Application & Research Center, Istanbul, Türkiye (GRID:grid.488643.5) (ISNI:0000 0004 5894 3909) 
12  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Kumamoto University, Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto, Japan (GRID:grid.274841.c) (ISNI:0000 0001 0660 6749); Science Farm Ltd., Department of Drug Discovery, Kumamoto, Japan (GRID:grid.274841.c) 
13  Bahcesehir University, Department of Biophysics, School of Medicine, Istanbul, Türkiye (GRID:grid.10359.3e) (ISNI:0000 0001 2331 4764) 
14  Izmir Biomedicine and Genome Center, Izmir, Türkiye (GRID:grid.21200.31) (ISNI:0000 0001 2183 9022); Dokuz Eylul University, Izmir International Biomedicine and Genome Institute, Izmir, Türkiye (GRID:grid.21200.31) (ISNI:0000 0001 2183 9022) 
15  Ege University, Department of Food Engineering, Faculty of Engineering, Izmir, Türkiye (GRID:grid.8302.9) (ISNI:0000 0001 1092 2592) 
16  Ankara University, Turkish Accelerator and Radiation Laboratory (TARLA), Ankara, Türkiye (GRID:grid.7256.6) (ISNI:0000000109409118); University of Bristol, School of Biochemistry, Bristol, UK (GRID:grid.5337.2) (ISNI:0000 0004 1936 7603) 
17  University of Health Sciences Türkiye, Experimental Medicine Application & Research Center, Istanbul, Türkiye (GRID:grid.488643.5) (ISNI:0000 0004 5894 3909); University of Health Sciences Türkiye, Department of Biotechnology, Hamidiye Institute of Health Sciences, Istanbul, Türkiye (GRID:grid.488643.5) (ISNI:0000 0004 5894 3909) 
18  Koç University, Department of Molecular Biology and Genetics, Faculty of Science, Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Koç University, Koç University Isbank Center for Infectious Diseases (KUISCID), Istanbul, Türkiye (GRID:grid.15876.3d) (ISNI:0000000106887552); Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, USA (GRID:grid.445003.6) (ISNI:0000 0001 0725 7771) 
Pages
8123
Publication year
2023
Publication date
2023
Publisher
Nature Publishing Group
e-ISSN
20452322
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41598-023-33989-0
ProQuest document ID
2815862798
Copyright
© The Author(s) 2023. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.