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Article Cite This: ACS Omega 2018, 3, 15442−15454
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Characterizing the Binding Interactions between DNA-Binding Proteins, XPA and XPE: A Molecular Dynamics Approach Sushmita Pradhan, Pundarikaksha Das, and Venkata Satish Kumar Mattaparthi* Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784 028, Assam, India
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ABSTRACT: The scaffold nature of Xeroderma pigmentosum complementation group A (XPA) protein makes it an important member of nucleotide excision repair (NER) that removes bulky DNA lesions with the help of various protein− protein interactions (PPI) and DNA−protein interactions. However, many structural insights of XPA’s interaction and the binding patterns with other NER proteins are yet to be understood. Here, we have studied one such crucial PPI of XPA with another NER protein, Xeroderma pigmentosum complementation group A (XPE), by using the previously identified binding site of XPA (residues 185−226) in the Assisted Model Building With Energy Refinement force-fieldmediated dynamic system. We studied the relationship between XPA185−226−XPE complex using three different docked models. The major residues observed in all of the models that were responsible for the PPI of this complex were Arg20, Arg47, Asp51, and Leu57 from XPE and the residues Leu191, Gln192, Val193, Trp194, Glu198, Glu202, Glu205, Arg207, Glu209, Gln216, and Phe219 from XPE185−226. During the simulation study, the orientation of XPA was also noted to be changed by almost 180° in models 1 and 3, which remain unchanged in model 2, indicating that XPA interacts with XPE with its N-terminal end facing downward and C-terminal end facing upward. The same was concurrent with the binding of DNA-binding domain region of XPA (aa98−239) with XPE. The N-terminal of XPE was stretched for accommodating XPA. Using the per-residue energy decomposition analysis for the interface residues of all models, the binding affinity between these proteins were found to be dependent on R20, R47, and L57 of XPE and the residues L191, V193, W194, E198, E202, E205, R207, and F219 of XPA. The net binding free energy of the XPA185−226−XPE protein complex was found to be −48.3718 kcal mol−1 for model 1, −49.09 kcal mol−1 for model 2, and −56.51 kcal mol−1 for model 3. The highly conserved XPA, 19−21 consisting of 273 residues,22 with its disordered N- and C-terminals, has been reported to bind and interact with many proteins of NER as well as with the damaged DNA.23−25 The DNA-interacting region of XPA was mapped initially to the globular DNAbinding domain (DBD), which spans between 98 and 219 amino acid residues,26,27 but since the earlier DBD lacked a significant amount of positive residues for the strong bonding with the negatively charged DNA, the DBD of XPA has been now redefined between 98 and 239 amino acid residues.28−30 To date, only a small number of the XPA’s protein−protein interactions (PPI) with other NER proteins have been explored. Some of the well-documented PPIs of XPA are with (i) helicase, transcription factor II H (TFIIH) complex,3,11,31 (ii) GG-NER damage verifier, Xeroderma pigmentosum complementation group C (XPC) protein,32−34 (iii) excision-repair cross-complementing group 1 endonu-
1. INTRODUCTION DNA is always under constant threats and attacks from entities of endogenous or exogenous nature, which makes DNA repair response a crucial mechanism in all living beings. Nucleotide excision repair (NER) is one such DNA repair pathway that addresses bulky DNA damages, such as cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4PP), and helix-distorting platinum (Pt) cross-links, which are inflicted upon DNA by various mutagens.1−3 This process is mediated in a multistep fashion by the coordinated interaction of more than 20 different proteins, which is mainly overseen and systematized by Xeroderma pigmentosum complementation group A (XPA) protein, earning itself a title of “scaffolding protein”. XPA functions as a primary damage recognition protein in both global genome NER (GG-NER) and transcription-coupled NER (TC-NER).3−7 As a result, any alteration in the XPA gene or in the protein function leads to classical Xeroderma pigmentosum (XP) disease that is characterized by extreme sun sensitivity, neurological damages, and is often linked with skin cancers.4,6,8−18 © 2018 American Chemical Society
Received: July 27, 2018 Accepted: November 1, 2018 Published: November 13, 2018 15442
DOI: 10.1021/acsomega.8b01793 ACS Omega 2018, 3, 15442−15454
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Table 1. MolProbity Summary Statistics for the modeled XPA185−226 Proteina all-atom contacts protein geometry
peptide omegas
clashscore, all atoms 1.36 99th percentile* (N = 1784, all resolutions) clashscore is the number of serious steric overlaps (>0.4 Å) per 1000 atoms poor rotamers 0 0.00% goal: 98% Ramachandran outliers 0 0.00% goal: 98% MolProbity score∧ 0.87 100th percentile* (N = 27675, 0−99 Å) Cβ deviations >0.25 Å 0 0.00% goal: 0 bad bonds 0/360 0.00% goal: 0% bad angles 1/474 0.21% goal:
