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Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition pp 91–158Cite as

Lesion Recognition by XPC (Rad4) Protein

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Abstract

DNA contains the blueprint for the proper development, functioning, and reproduction of every organism. DNA in cells is continuously being damaged by a wide variety of environmental sources such as UV rays, pollutants, cigarette smoke, and food toxins [1]. The lesions, if not repaired, can hamper critical cellular functions such as replication and transcription and lead to cell death or turn into genomic instability (mutagenesis) [1–5]. Nucleotide excision repair (NER) is a highly versatile and sophisticated repair pathway that has been conserved from yeast to humans to counter these diverse lesions and keep the genome integrity. NER removes primarily bulky, helix distorting damages induced by environmental sources that include intra-strand crosslinks such as (6–4) photo product and cyclobutane pyrimidine dimer (CPD) generated by UV light, a variety of adducts formed by environmental pollutants such as polycylic aromatic hydrocarbons (PAH) (induced by components in cigarette smoke) or aromatic amines, interstrand crosslinks created by chemotherapeutic agents such as cisplatin, and endogenous metabolites including reactive oxygen species ([1, 6, 7]. NER in human cell is a complex biochemical process that requires several proteins [7–15]).

Statement of Authorship

Major part of Chap. 4 contains materials from the following two papers: “Kinetic gating mechanism of DNA damage recognition by Rad4/XPC,”, published in Nature Communications, Jan. 2015 (1) and “Twist-open mechanism of DNA damage recognition by Rad4/XPC nucleotide excision repair complex,” accepted for publication in PNAS, Feb. 2016 (2).

(1) Xuejing Chen*, Yogambigai Velmurugu*, Guanqun Zheng, Beom Seok Park, Yoonjung Shim, Youngchang Kim, Lili Liu, Bennett Van Houten, Chuan He, Anjum Ansari and Jung-Hyun Min, Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat. Commun. 6, 5849 (2015).

(2) Yogambigai Velmurugu*, Xuejing Chen*, Phillip Slogoff-Sevilla, Jung-Hyun Min, and Anjum Ansari, Twist-open mechanism of DNA damage recognition by Rad4/XPC nucleotide excision repair complex. Accepted for publication in Proc. Natl. Acad. Sci. (2016).

*Co-first authors

Author contributions for publication (1): X. C. carried out protein engineering and purifications, protein–DNA crosslinking and crystallization experiments with contributions from B. P. and Y. S. G. Z. and C. H. synthesized modified oligonucleotides for crosslinking experiments. X. C., Y. K., and J. H. M. collected and analyzed crystallographic data. J. H. M and Y. K. did model building and refinement. Y. V. and A. A. designed the fluorescence measurements on complexes with 2AP-labeled DNA substrates with contributions from X. C. and J. H. M. Y. V. carried out the equilibrium and T-jump experiments and analyzed the relaxation traces to obtain the DNA-opening times. L. L. and B. V. H. carried out the AFM studies. A. A. and J. M. wrote the manuscript with contributions from all authors.

Author contributions for publication (2): X. C. carried out protein engineering and purifications of Rad4 protein and its mutants. Y. V. and A. A. designed the fluorescence measurements on complexes with tCo-tCnitro-labeled DNA substrates with contributions from X. C. and J. H. M. Y. V., X. C., and P. S-S. carried out the equilibrium temperature scan measurements. X. C. measured the melting temperatures of all DNA constructs reported in this chapter, and also measured the binding affinities of the different DNA constructs in complex with wild-type and mutant Rad4 proteins. Y. V. carried out all the T-jump experiments and analyzed the relaxation traces to obtain the DNA dynamics in the presence of Rad4. A. A. and J. M. wrote the manuscript with contributions from all authors.

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    Yogambigai Velmurugu

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Velmurugu, Y. (2017). Lesion Recognition by XPC (Rad4) Protein. In: Dynamics and Mechanism of DNA-Bending Proteins in Binding Site Recognition. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-319-45129-9_4

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