Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source “Turkish DeLight”

Necati Atalay, Enver Kamil Akcan, Mehmet Gül, Esra Ayan, Ebru Destan, Fatma Betül Ertem, Nurettin Tokay, Barış Çakilkaya, Zeliş Nergiz, Gözde Karakadioğlu, Abdullah Kepceoğlu, İlkin Yapici, Bilge Tosun, Nilüfer Baldir, Günseli Yildirim, J. Austin Johnson, Ömür Güven, Alaleh Shafiei, Nazlı Eylül Arslan, Merve YilmazCahine Kulakman, Seyide Seda Paydos, Zeynep Sena Çinal, Kardelen Şabanoğlu, Ayşegül Pazarçeviren, Ayşenur Yilmaz, Başak Canbay, Bengisu Aşci, Esra Kartal, Serra Tavli, Mehmet Çaliseki, Günce Göç, Arif Mermer, Gamze Yeşilay, Sevde Altuntaş, Hiroshi Tateishi, Masami Otsuka, Mikako Fujita, Şaban Tekin, Halilibrahim Çiftçi, Serdar Durdaği, Gizem Dinler Doğanay, Ezgi Karaca, Burcu Kaplan Türköz, Burak Veli Kabasakal, Ahmet Kati, Hasan Demirci*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)

Abstract

X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.

Original languageEnglish
JournalTurkish Journal of Biology
Volume47
Issue number1
DOIs
Publication statusPublished - 2023

Bibliographical note

Publisher Copyright:
© TÜBİTAK.

Funding

Authors would like to dedicate this manuscript to the memory of Dr Albert E. Dahlberg and Dr Nizar Turker. The authors gratefully acknowledge the use of the services and Turkish Light Source (Turkish DeLight) X-ray facility at the University of Health Sciences, Experimental Medicine Application & Research Center, Validebag Research Park. The authors gratefully acknowledge use of the services and facilities of the Koç University Isbank Infectious Disease Center (KUISCID). H.D. acknowledges support from NSF Science and Technology Center grant NSF-1231306 (Biology with X-ray Lasers, BioXFEL). A.K. acknowledges support from The Scientific and Technological Research Council of Türkiye (TÜBİTAK, 2218 - National Postdoctoral Research Fellowship Program under project number 118C476). G.G., M.Ç., and B.V.K. are funded by TÜBİTAK 2232 International Outstanding Researchers Program (Project No: 118C225). This publication has been produced benefiting from the 2232 International Fellowship for Outstanding Researchers Program, 2236 CoCirculation2 program and the 1001 Scientific and Technological Research Projects Funding Program of the TÜBİTAK (Project Nos. 118C270, 121C063 and 120Z520). However, the entire responsibility of the publication belongs to the authors of the publication. The financial support received from TÜBİTAK does not mean that the content of the publication is approved in a scientific sense by TÜBİTAK. Coordinates of the lysozyme structure has been deposited in the Protein Data Bank under accession codes 7Y6A. Authors would like to dedicate this manuscript to the memory of Dr Albert E. Dahlberg and Dr Nizar Turker. The authors gratefully acknowledge the use of the services and Turkish Light Source (Turkish DeLight) X-ray facility at the University of Health Sciences, Experimental Medicine Application & Research Center, Validebag Research Park. The authors gratefully acknowledge use of the services and facilities of the Koç University Isbank Infectious Disease Center (KUISCID). H.D. acknowledges support from NSF Science and Technology Center grant NSF-1231306 (Biology with X-ray Lasers, BioXFEL). A.K. acknowledges support from The Scientific and Technological Research Council of Türkiye (TÜBİTAK, 2218-National Postdoctoral Research Fellowship Program under project number 118C476). G.G., M.Ç., and B.V.K. are funded by TÜBİTAK 2232 International Outstanding Researchers Program (Project No: 118C225). This publication has been produced benefiting from the 2232 International Fellowship for Outstanding Researchers Program, 2236 CoCirculation2 program and the 1001 Scientific and Technological Research Projects Funding Program of the TÜBİTAK (Project Nos. 118C270, 121C063 and 120Z520). However, the entire responsibility of the publication belongs to the authors of the publication. The financial support received from TÜBİTAK does not mean that the content of the publication is approved in a scientific sense by TÜBİTAK. Coordinates of the lysozyme structure has been deposited in the Protein Data Bank under accession codes 7Y6A.

FundersFunder number
Koç University Isbank Infectious Disease Center
TÜBİTAK 2232 International Outstanding Researchers Program118C270, 118C225, 120Z520, 121C063
National Science FoundationNSF-1231306
Türkiye Bilimsel ve Teknolojik Araştırma Kurumu118C476

    Keywords

    • atomic resolution
    • drug development
    • drug repurposing
    • light source
    • structural biology
    • structural dynamics
    • X-ray crystallography

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