Deciphering the structural and functional impact of missense mutations in Egr1-DNA interacting interface: an integrative computational approach

References

• Abbehausen, C. (2019). Zinc finger domains as therapeutic targets for metal-based compounds - an update. Metallomics: Integrated Biometal Science, 11(1), 15–28. https://doi.org/10.1039/c8mt00262b
   PubMed Web of Science ®Google Scholar
• Adzhubei, I., Jordan, D. M., & Sunyaev, S. R. (2013). Predicting functional effect of human missense mutations using PolyPhen-2. Current Protocols in Human Genetics, Chapter 7, Unit7.20. https://doi.org/10.1002/0471142905.hg0720s76
   PubMedGoogle Scholar
• Agrahari, A. K., Kumar, A., Shiva, R., Zayed, H., & Doss, C. G. P. (2018). Substitution impact of highly conserved arginine residue at position 75 in GJB1 gene in association with X-linked Charcot-Marie-tooth disease: A computational study. Journal of Theoretical Biology, 437, 305–317. https://doi.org/10.1016/j.jtbi.2017.10.028
   PubMed Web of Science ®Google Scholar
• Agrahari, A. K., Muskan, M., George Priya Doss, C., Siva, R., & Zayed, H. (2018). Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: A molecular modeling and dynamics approach. Metabolic Brain Disease, 33(5), 1443–1457. https://doi.org/10.1007/s11011-018-0251-1
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Bird, A. J., McCall, K., Kramer, M., Blankman, E., Winge, D. R., & Eide, D. J. (2003) .Zinc fingers can act as Zn2+ sensors to regulate transcriptional activation domain function + sensors to regulate transcriptional activation domain function. The EMBO Journal, 22(19), 5137–5146. https://doi.org/10.1093/emboj/cdg484
   PubMed Web of Science ®Google Scholar
• Carman, J. A., & Monroe, J. G. (1995). The EGR1 protein contains a discrete transcriptional regulatory domain whose deletion results in a truncated protein that blocks EGR1-induced transcription. DNA and Cell Biology, 14(7), 581–589. https://doi.org/10.1089/dna.1995.14.581
   PubMed Web of Science ®Google Scholar
• Cassandri, M., Smirnov, A., Novelli, F., Pitolli, C., Agostini, M., Malewicz, M., Melino, G., & Raschellà, G. (2017). Zinc-finger proteins in health and disease. Cell Death Discovery, 3, 17071. https://doi.org/10.1038/cddiscovery.2017.71
   PubMed Web of Science ®Google Scholar
• Crosby, S. D., Puetz, J. J., Simburger, K. S., Fahrner, T. J., & Milbrandt, J. (1991). The early response gene NGFI-C encodes a zinc finger transcriptional activator and is a member of the GCGGGGGCG (GSG) element-binding protein family. Molecular and Cellular Biology, 11(8), 3835–3841. https://doi.org/10.1128/mcb.11.8.3835-3841.1991
   PubMed Web of Science ®Google Scholar
• Cunningham, F., Achuthan, P., Akanni, W., Allen, J., Amode, M. R., Armean, I. M., Bennett, R., Bhai, J., Billis, K., Boddu, S., Cummins, C., Davidson, C., Dodiya, K. J., Gall, A., Girón, C. G., Gil, L., Grego, T., Haggerty, L., Haskell, E., … Flicek, P. (2019). Ensembl 2019. Nucleic Acids Research, 47(D1), D745–D751. https://doi.org/10.1093/nar/gky1113
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Doncheva, N. T., Klein, K., Domingues, F. S., & Albrecht, M. (2011). Analyzing and visualizing residue networks of protein structures. Trends in Biochemical Sciences, 36(4), 179–182. https://doi.org/10.1016/j.tibs.2011.01.002
   PubMed Web of Science ®Google Scholar
• Duclot, F., & Kabbaj, M. (2017). The role of early growth response 1 (EGR1) in brain plasticity and neuropsychiatric disorders. Frontiers in Behavioral Neuroscience, 11, 35. https://doi.org/10.3389/fnbeh.2017.00035
   PubMed Web of Science ®Google Scholar
• Emerson, R. O., & Thomas, J. H. (2009). Adaptive evolution in zinc finger transcription factors. PLoS Genetics, 5(1), e1000325. https://doi.org/10.1371/journal.pgen.1000325
   PubMed Web of Science ®Google Scholar
• Eom, K. S., Cheong, J. S., & Lee, S. J. (2016). Structural analyses of zinc finger domains for specific interactions with DNA. Journal of Microbiology and Biotechnology, 26(12), 2019–2029. https://doi.org/10.4014/jmb.1609.09021
   PubMed Web of Science ®Google Scholar
• Fedotova, A. A., Bonchuk, A. N., Mogila, V. A., & Georgiev, P. G. (2017). C2H2 zinc finger proteins: The largest but poorly explored family of higher eukaryotic transcription factors. Acta Naturae, 9(2), 47–58. https://doi.org/10.32607/20758251-2017-9-2-47-58
   PubMed Web of Science ®Google Scholar
• Garton, M., Najafabadi, H. S., Schmitges, F. W., Radovani, E., Hughes, T. R., & Kim, P. M. (2015). A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity. Nucleic Acids Research, 43(19), 9147–9157. https://doi.org/10.1093/nar/gkv919
   PubMed Web of Science ®Google Scholar
• Gashler, A., & Sukhatme, V. P. (1995). Early growth response protein 1 (Egr-1): Prototype of a zinc-finger family of transcription factors. Progress in Nucleic Acid Research and Molecular Biology, 50, 191–224. https://doi.org/10.1016/s0079-6603(08)60815-6
   PubMed Web of Science ®Google Scholar
• Godwin, R. C., Melvin, R. L., Gmeiner, W. H., & Salsbury, F. R. (2017). Binding site configurations probe the structure and dynamics of the zinc finger of NEMO (NF-κB essential modulator). Biochemistry, 56(4), 623–633. https://doi.org/10.1021/acs.biochem.6b00755
   PubMed Web of Science ®Google Scholar
• Hamilton, T. B., Borel, F., & Romaniuk, P. J. (1998). Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1. Biochemistry, 37(7), 2051–2058. https://doi.org/10.1021/bi9717993
   PubMed Web of Science ®Google Scholar
• Hashimoto, H., Olanrewaju, Y. O., Zheng, Y., Wilson, G. G., Zhang, X., & Cheng, X. (2014). Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Genes & Development, 28(20), 2304–2313. https://doi.org/10.1101/gad.250746.114
   Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Im, W., Beglov, D., & Roux, B. (1998). Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Computer Physics Communications, 111(1–3), 59–75. https://doi.org/10.1016/S0010-4655(98)00016-2
   Web of Science ®Google Scholar
• Jayaraj, J. M., Krishnasamy, G., Lee, J.-K., & Muthusamy, K. (2019). In silico identification and screening of CYP24A1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis. Journal of Biomolecular Structure & Dynamics, 37(7), 1700–1714. https://doi.org/10.1080/07391102.2018.1464958
   PubMed Web of Science ®Google Scholar
• Jo, S., Vargyas, M., Vasko-Szedlar, J., Roux, B., & Im, W. (2008). PBEQ-solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Research, 36(Web Server issue), W270–W275. https://doi.org/10.1093/nar/gkn314
   PubMedGoogle Scholar
• Kemme, C. A., Luu, R. H., Chen, C., Pletka, C. C., Pettitt, B. M., & Iwahara, J. (2019). Mobility of histidine side chains analyzed with 15N NMR relaxation and cross-correlation data: Insight into zinc-finger-DNA interactions. The Journal of Physical Chemistry B, 123(17), 3706–3710. https://doi.org/10.1021/acs.jpcb.9b03132
   PubMed Web of Science ®Google Scholar
• Kirubakaran, P., Kothandan, G., Cho, S. J., & Muthusamy, K. (2014). Molecular insights on TNKS1/TNKS2 and inhibitor-IWR1 interactions. Molecular bioSystems, 10(2), 281–293. https://doi.org/10.1039/c3mb70305c
   PubMedGoogle Scholar
• Kluska, K., Adamczyk, J., & Krężel, A. (2018). Metal binding properties, stability and reactivity of zinc fingers. Coordination Chemistry Reviews, 367, 18–64. https://doi.org/10.1016/j.ccr.2018.04.009
   Web of Science ®Google Scholar
• Li, B., Krishnan, V. G., Mort, M. E., Xin, F., Kamati, K. K., Cooper, D. N., Mooney, S. D., & Radivojac, P. (2009). Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics (Oxford, England), 25(21), 2744–2750. https://doi.org/10.1093/bioinformatics/btp528
   PubMed Web of Science ®Google Scholar
• Li, W., Zhang, J., Wang, J., & Wang, W. (2008). Metal-coupled folding of Cys2His2 zinc-finger. Journal of the American Chemical Society, 130(3), 892–900. https://doi.org/10.1021/ja075302g
   PubMed Web of Science ®Google Scholar
• López-Ferrando, V., Gazzo, A., La Cruz, X., de Orozco, M., & Gelpí, J. L. (2017). PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update. Nucleic Acids Research, 45(W1), W222–W228. https://doi.org/10.1093/nar/gkx313
   PubMed Web of Science ®Google Scholar
• Luscombe, N. M., Laskowski, R. A., & Thornton, J. M. (1997). NUCPLOT: A program to generate schematic diagrams of protein-nucleic acid interactions. Nucleic Acids Research, 25(24), 4940–4945. https://doi.org/10.1093/nar/25.24.4940
   PubMed Web of Science ®Google Scholar
• Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2010). Relation between free energy landscapes of proteins and dynamics. Journal of Chemical Theory and Computation, 6(2), 583–595. https://doi.org/10.1021/ct9005745
   PubMed Web of Science ®Google Scholar
• Nagarajan, H., Narayanaswamy, S., & Vetrivel, U. (2020). Mutational landscape screening of methylene tetrahydrofolate reductase to predict homocystinuria associated variants: An integrative computational approach. Mutation Research, 819–820, 111687. https://doi.org/10.1016/j.mrfmmm.2020.111687
   PubMed Web of Science ®Google Scholar
• Nagarajan, H., & Vetrivel, U. (2018). Demystifying the pH dependent conformational changes of human heparanase pertaining to structure-function relationships: An in silico approach. Journal of Computer-Aided Molecular Design, 32(8), 821–840. https://doi.org/10.1007/s10822-018-0131-0
   PubMed Web of Science ®Google Scholar
• Nagarajan, H., & Vetrivel, U. (2020). Microsecond scale sampling of Egr-1 conformational landscape to decipher the impact of its disorder regions on structure–function relationship. Molecular Simulation, 46(16), 1255–1264. https://doi.org/10.1080/08927022.2020.1815731
   Web of Science ®Google Scholar
• Namuswe, F., & Berg, J. M. (2012). Secondary interactions involving zinc-bound ligands: Roles in structural stabilization and macromolecular interactions. Journal of Inorganic Biochemistry, 111, 146–149. https://doi.org/10.1016/j.jinorgbio.2011.10.018
   PubMed Web of Science ®Google Scholar
• Nixon, J. C., Rajaiya, J., & Webb, C. F. (2004). Mutations in the DNA-binding domain of the transcription factor Bright act as dominant negative proteins and interfere with immunoglobulin transactivation. The Journal of Biological Chemistry, 279(50), 52465–52472. https://doi.org/10.1074/jbc.M403028200
   PubMed Web of Science ®Google Scholar
• O’Donovan, K. J., Tourtellotte, W. G., Millbrandt, J., & Baraban, J. M. (1999). The EGR family of transcription-regulatory factors: Progress at the interface of molecular and systems neuroscience. Trends in Neurosciences, 22(4), 167–173. https://doi.org/10.1016/S0166-2236(98)01343-5
   PubMed Web of Science ®Google Scholar
• Pace, N. J., & Weerapana, E. (2014). Zinc-binding cysteines: Diverse functions and structural motifs. Biomolecules, 4(2), 419–434. https://doi.org/10.3390/biom4020419
   PubMedGoogle Scholar
• Pagel, J.-I., & Deindl, E. (2012). Disease progression mediated by EGR-1 associated signaling in response to oxidative stress. International Journal of Molecular Sciences, 13(10), 13104–13117. https://doi.org/10.3390/ijms131013104
   PubMed Web of Science ®Google Scholar
• Pérez, A., Marchán, I., Svozil, D., Sponer, J., Cheatham, T. E., Laughton, C. A., & Orozco, M. (2007). Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophysical Journal, 92(11), 3817–3829. https://doi.org/10.1529/biophysj.106.097782
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Piovesan, D., Minervini, G., & Tosatto, S. C. E. (2016). The RING 2.0 web server for high quality residue interaction networks. Nucleic Acids Research, 44(W1), W367–W374. https://doi.org/10.1093/nar/gkw315
   PubMed Web of Science ®Google Scholar
• Ravasi, T., Huber, T., Zavolan, M., Forrest, A., Gaasterland, T., Grimmond, S., & Hume, D. A. (2003). Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome Research, 13(6B), 1430–1442. https://doi.org/10.1101/gr.949803
   PubMed Web of Science ®Google Scholar
• Russo, M. W., Matheny, C., & Milbrandt, J. (1993). Transcriptional activity of the zinc finger protein NGFI-A is influenced by its interaction with a cellular factor. Molecular and Cellular Biology, 13(11), 6858–6865. https://doi.org/10.1128/mcb.13.11.6858-6865.1993
   PubMed Web of Science ®Google Scholar
• Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/10.1093/nar/gkv315
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504. https://doi.org/10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Sherry, S. T., Ward, M. H., Kholodov, M., Baker, J., Phan, L., Smigielski, E. M., & Sirotkin, K. (2001). dbSNP: The NCBI database of genetic variation. Nucleic Acids Research, 29(1), 308–311. https://doi.org/10.1093/nar/29.1.308
   PubMed Web of Science ®Google Scholar
• Sim, N.-L., Kumar, P., Hu, J., Henikoff, S., Schneider, G., & Ng, P. C. (2012). SIFT web server: Predicting effects of amino acid substitutions on proteins. Nucleic Acids Research, 40(Web Server issue), W452–W457. https://doi.org/10.1093/nar/gks539
   PubMedGoogle Scholar
• Tang, H., & Thomas, P. D. (2016). PANTHER-PSEP: Predicting disease-causing genetic variants using position-specific evolutionary preservation. Bioinformatics (Oxford, England), 32(14), 2230–2232. https://doi.org/10.1093/bioinformatics/btw222
   PubMed Web of Science ®Google Scholar
• Végran, F., Rebucci, M., Chevrier, S., Cadouot, M., Boidot, R., & Lizard-Nacol, S. (2013). Only missense mutations affecting the DNA binding domain of p53 influence outcomes in patients with breast carcinoma. PloS One, 8(1), e55103. https://doi.org/10.1371/journal.pone.0055103
   PubMed Web of Science ®Google Scholar
• Wolfe, S. A., Nekludova, L., & Pabo, C. O. (2000). DNA recognition by Cys2His2 zinc finger proteins. Annual Review of Biophysics and Biomolecular Structure, 29, 183–212. https://doi.org/10.1146/annurev.biophys.29.1.183
   PubMedGoogle Scholar
• Xiao, Z., Guo, L., Zhang, Y., Cui, L., Dai, Y., Lan, Z., Zhang, Q., Wang, S., Liu, W. (2020). Structural analysis of missense mutations occurring in the DNA-binding domain of HSF4 associated with congenital cataracts. Journal of Structural Biology, X, 4, 100015.
   PubMedGoogle Scholar
• Yella, V. R., Bhimsaria, D., Ghoshdastidar, D., Rodríguez-Martínez, J. A., Ansari, A. Z., & Bansal, M. (2018). Flexibility and structure of flanking DNA impact transcription factor affinity for its core motif. Nucleic Acids Research, 46(22), 11883–11897. https://doi.org/10.1093/nar/gky1057
   PubMed Web of Science ®Google Scholar
• Yoneda, Y., Saitsu, H., Touyama, M., Makita, Y., Miyamoto, A., Hamada, K., Kurotaki, N., Tomita, H., Nishiyama, K., Tsurusaki, Y., Doi, H., Miyake, N., Ogata, K., Naritomi, K., & Matsumoto, N. (2012). Missense mutations in the DNA-binding/dimerization domain of NFIX cause Sotos-like features. Journal of Human Genetics, 57(3), 207–211. https://doi.org/10.1038/jhg.2012.7
   PubMed Web of Science ®Google Scholar