Molecular dynamics approach to identification of new OGG1 cancer-associated somatic variants with impaired activity

• Published in: The Journal of biological chemistry Vol. 296; p. 100229
• Main Authors: Popov, Aleksandr V., Endutkin, Anton V., Yatsenko, Darya D., Yudkina, Anna V., Barmatov, Alexander E., Makasheva, Kristina A., Raspopova, Darya Yu, Diatlova, Evgeniia A., Zharkov, Dmitry O.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-01-2021; American Society for Biochemistry and Molecular Biology
• Subjects: DNA damage; DNA glycosylases; DNA repair; genetic polymorphism; molecular dynamics; OGG1; personalized medicine; protein function prediction; structure–function; DNA damage; OGG1; molecular dynamics; DNA repair; BER; personalized medicine; AP; PCA; THF; COSMIC; protein function prediction; oxoG; MD; DNA glycosylases; genetic polymorphism; oxodG; structure–function; structure-function; cancer
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.RA120.014455

DNA of living cells is always exposed to damaging factors. To counteract the consequences of DNA lesions, cells have evolved several DNA repair systems, among which base excision repair is one of the most important systems. Many currently used antitumor drugs act by damaging DNA, and DNA repair often interferes with chemotherapy and radiotherapy in cancer cells. Tumors are usually extremely genetically heterogeneous, often bearing mutations in DNA repair genes. Thus, knowledge of the functionality of cancer-related variants of proteins involved in DNA damage response and repair is of great interest for personalization of cancer therapy. Although computational methods to predict the variant functionality have attracted much attention, at present, they are mostly based on sequence conservation and make little use of modern capabilities in computational analysis of 3D protein structures. We have used molecular dynamics (MD) to model the structures of 20 clinically observed variants of a DNA repair enzyme, 8-oxoguanine DNA glycosylase. In parallel, we have experimentally characterized the activity, thermostability, and DNA binding in a subset of these mutant proteins. Among the analyzed variants of 8-oxoguanine DNA glycosylase, three (I145M, G202C, and V267M) were significantly functionally impaired and were successfully predicted by MD. Alone or in combination with sequence-based methods, MD may be an important functional prediction tool for cancer-related protein variants of unknown significance.