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Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC

The ultraviolet (UV) radiation-induced DNA lesions play a causal role in many prevalent genetic skin-related diseases and cancers. The damage sensing protein Rad4/XPC specifically recognizes and repairs these lesions with high fidelity and safeguards genome integrity. Despite considerable progress,...

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Autores principales: Panigrahi, Abhinandan, Vemuri, Hemanth, Aggarwal, Madhur, Pitta, Kartheek, Krishnan, Marimuthu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049735/
https://www.ncbi.nlm.nih.gov/pubmed/32047903
http://dx.doi.org/10.1093/nar/gkaa078
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author Panigrahi, Abhinandan
Vemuri, Hemanth
Aggarwal, Madhur
Pitta, Kartheek
Krishnan, Marimuthu
author_facet Panigrahi, Abhinandan
Vemuri, Hemanth
Aggarwal, Madhur
Pitta, Kartheek
Krishnan, Marimuthu
author_sort Panigrahi, Abhinandan
collection PubMed
description The ultraviolet (UV) radiation-induced DNA lesions play a causal role in many prevalent genetic skin-related diseases and cancers. The damage sensing protein Rad4/XPC specifically recognizes and repairs these lesions with high fidelity and safeguards genome integrity. Despite considerable progress, the mechanistic details of the mode of action of Rad4/XPC in damage recognition remain obscure. The present study investigates the mechanism, energetics, dynamics, and the molecular basis for the sequence specificity of mismatch recognition by Rad4/XPC. We dissect the following three key molecular events that occur as Rad4/XPC tries to recognize and bind to DNA lesions/mismatches: (a) the association of Rad4/XPC with the damaged/mismatched DNA, (b) the insertion of a lesion-sensing β-hairpin of Rad4/XPC into the damage/mismatch site and (c) the flipping of a pair of nucleotide bases at the damage/mismatch site. Using suitable reaction coordinates, the free energy surfaces for these events are determined using molecular dynamics (MD) and umbrella sampling simulations on three mismatched (CCC/CCC, TTT/TTT and TAT/TAT mismatches) Rad4-DNA complexes. The study identifies the key determinants of the sequence-dependent specificity of Rad4 for the mismatches and explores the ramifications of specificity in the aforementioned events. The results unravel the molecular basis for the high specificity of Rad4 towards CCC/CCC mismatch and lower specificity for the TAT/TAT mismatch. A strong correlation between the depth of β-hairpin insertion into the DNA duplex and the degree of coupling between the hairpin insertion and the flipping of bases is also observed. The interplay of the conformational flexibility of mismatched bases, the depth of β-hairpin insertion, Rad4-DNA association energetics and the Rad4 specificity explored here complement recent experimental FRET studies on Rad4-DNA complexes.
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spelling pubmed-70497352020-03-10 Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC Panigrahi, Abhinandan Vemuri, Hemanth Aggarwal, Madhur Pitta, Kartheek Krishnan, Marimuthu Nucleic Acids Res Chemical Biology and Nucleic Acid Chemistry The ultraviolet (UV) radiation-induced DNA lesions play a causal role in many prevalent genetic skin-related diseases and cancers. The damage sensing protein Rad4/XPC specifically recognizes and repairs these lesions with high fidelity and safeguards genome integrity. Despite considerable progress, the mechanistic details of the mode of action of Rad4/XPC in damage recognition remain obscure. The present study investigates the mechanism, energetics, dynamics, and the molecular basis for the sequence specificity of mismatch recognition by Rad4/XPC. We dissect the following three key molecular events that occur as Rad4/XPC tries to recognize and bind to DNA lesions/mismatches: (a) the association of Rad4/XPC with the damaged/mismatched DNA, (b) the insertion of a lesion-sensing β-hairpin of Rad4/XPC into the damage/mismatch site and (c) the flipping of a pair of nucleotide bases at the damage/mismatch site. Using suitable reaction coordinates, the free energy surfaces for these events are determined using molecular dynamics (MD) and umbrella sampling simulations on three mismatched (CCC/CCC, TTT/TTT and TAT/TAT mismatches) Rad4-DNA complexes. The study identifies the key determinants of the sequence-dependent specificity of Rad4 for the mismatches and explores the ramifications of specificity in the aforementioned events. The results unravel the molecular basis for the high specificity of Rad4 towards CCC/CCC mismatch and lower specificity for the TAT/TAT mismatch. A strong correlation between the depth of β-hairpin insertion into the DNA duplex and the degree of coupling between the hairpin insertion and the flipping of bases is also observed. The interplay of the conformational flexibility of mismatched bases, the depth of β-hairpin insertion, Rad4-DNA association energetics and the Rad4 specificity explored here complement recent experimental FRET studies on Rad4-DNA complexes. Oxford University Press 2020-03-18 2020-02-12 /pmc/articles/PMC7049735/ /pubmed/32047903 http://dx.doi.org/10.1093/nar/gkaa078 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Chemical Biology and Nucleic Acid Chemistry
Panigrahi, Abhinandan
Vemuri, Hemanth
Aggarwal, Madhur
Pitta, Kartheek
Krishnan, Marimuthu
Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC
title Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC
title_full Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC
title_fullStr Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC
title_full_unstemmed Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC
title_short Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC
title_sort sequence specificity, energetics and mechanism of mismatch recognition by dna damage sensing protein rad4/xpc
topic Chemical Biology and Nucleic Acid Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049735/
https://www.ncbi.nlm.nih.gov/pubmed/32047903
http://dx.doi.org/10.1093/nar/gkaa078
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