Impact of glioblastoma multiforme associated mutations on the structure and function of MAP/microtubule affinity regulating kinase 4

References

• Adzhubei, I., Jordan, D. M., & Sunyaev, S. R. (2013). Predicting functional effect of human missense mutations using PolyPhen-2. Current Protocols in Human Genetics 76(1), 7.20.1–7.20.41. doi:10.1002/0471142905.hg0720s76.
   Google Scholar
• Ahamad, S., Hassan, M. I., & Dwivedi, N. (2018). Designing of phenol-based beta-carbonic anhydrase1 inhibitors through QSAR, molecular docking, and MD simulation approach. 3 Biotech, 8(5), 256. doi:10.1007/s13205-018-1278-z
   PubMedGoogle Scholar
• Ahamad, S., Islam, A., Ahmad, F., Dwivedi, N., & Hassan, M. I. (2019). 2/3D-QSAR, molecular docking and MD simulation studies of FtsZ protein targeting benzimidazoles derivatives. Computational Biology and Chemistry, 78, 398–413. doi:10.1016/j.compbiolchem.2018.12.017
   PubMed Web of Science ®Google Scholar
• Ali, S., Khan, F. I., Mohammad, T., Lan, D., Hassan, M. I., & Wang, Y. (2019). Identification and evaluation of inhibitors of lipase from Malassezia restricta using virtual high-throughput screening and molecular dynamics studies. International Journal of Molecular Sciences, 20(4), 884. doi:10.3390/ijms20040884
   PubMed Web of Science ®Google Scholar
• Amir, M., Ahmad, S., Ahamad, S., Kumar, V., Mohammad, T., Dohare, R., Alajmi, M. F., Rehman, T., Hussain, A., Islam, A., Ahmad, F., & Hassan, M. I. (2020). Impact of Gln94Glu mutation on the structure and function of protection of telomere 1, a cause of cutaneous familial melanoma. Journal of Biomolecular Structure and Dynamics, 38(5), 1514-1524. doi:10.1080/07391102.2019.1610500.
   PubMed Web of Science ®Google Scholar
• Amir, M., Kumar, V., Mohammad, T., Dohare, R., Hussain, A., Rehman, M. T., Alam, P., Alajmi, M. F., Islam, A., Ahmad, F., & Hassan, M. I. (2019a). Investigation of deleterious effects of nsSNPs in the POT1 gene: A structural genomics-based approach to understand the mechanism of cancer development. Journal of Cellular Biochemistry, 120(6), 10281–1029410. 10.1002/jcb.28312
   PubMed Web of Science ®Google Scholar
• Amir, M., Kumar, V., Mohammad, T., Dohare, R., Rehman, M. T., Alajmi, M. F., Hussain, A., Ahmad, F., & Hassan, M. I. (2019b). Structural and functional impact of non-synonymous SNPs in the CST complex subunit TEN1: Structural genomics approach. Bioscience Reports, 39. BSR20190312. doi:10.1042/BSR20190312.
   PubMed Web of Science ®Google Scholar
• Amir, M., Mohammad, T., Kumar, V., Alajmi, M. F., Rehman, M. T., Hussain, A., Alam, P., Dohare, R., Islam, A., Ahmad, F., & Hassan, M. I. (2019c). Structural analysis and conformational dynamics of STN1 gene mutations involved in coat plus syndrome. Frontiers in Molecular Biosciences, 6(41). doi:10.3389/fmolb.2019.00041.
   PubMedGoogle Scholar
• Ancien, F., Pucci, F., Godfroid, M., & Rooman, M. (2018). Prediction and interpretation of deleterious coding variants in terms of protein structural stability. Scientific Reports, 8(1), 4480. doi:10.1038/s41598-018-22531-2
   PubMedGoogle Scholar
• Aneja, B., Khan, N. S., Khan, P., Queen, A., Hussain, A., Rehman, M. T., Alajmi, M. F., El-Seedi, H. R., Ali, S., Hassan, M. I., & Abid, M. (2019). Design and development of Isatin-triazole hydrazones as potential inhibitors of microtubule affinity-regulating kinase 4 for the therapeutic management of cell proliferation and metastasis. European Journal of Medicinal Chemistry, 163, 840–852. S0223-5234(18)31063-8 [pii]10.1016/j.ejmech.2018.12.026
   PubMed Web of Science ®Google Scholar
• Bagler, G., & Sinha, S. (2007). Assortative mixing in Protein Contact Networks and protein folding kinetics. Bioinformatics, 23(14), 1760–1767. doi:10.1093/bioinformatics/btm257
   PubMed Web of Science ®Google Scholar
• Beghini, A., Magnani, I., Roversi, G., Piepoli, T., Di Terlizzi, S., Moroni, R. F., Pollo, B., Fuhrman Conti, A. M., Cowell, J. K., Finocchiaro, G., & Larizza, L. (2003). The neural progenitor-restricted isoform of the MARK4 gene in 19q13.2 is upregulated in human gliomas and overexpressed in a subset of glioblastoma cell lines. Oncogene 22(17), 2581–2591. doi:10.1038/sj.onc.1206336
   PubMed Web of Science ®Google Scholar
• Brinda, K. V., & Vishveshwara, S. (2005). A network representation of protein structures: Implications for protein stability. Biophysical Journal, 89(6), 4159–4170. doi:10.1529/biophysj.105.064485
   PubMed Web of Science ®Google Scholar
• Choi, Y., & Chan, A. P. (2015). PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics, 31(16), 2745–2747. doi:10.1093/bioinformatics/btv195
   PubMed Web of Science ®Google Scholar
• David, C. C., & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. Methods in Molecular Biology (Clifton, N.J.), 1084, 193–226. doi:10.1007/978-1-62703-658-0_11
   PubMedGoogle Scholar
• Dehouck, Y., Kwasigroch, J. M., Gilis, D., & Rooman, M. (2011). PoPMuSiC 2.1: A web server for the estimation of protein stability changes upon mutation and sequence optimality. BMC Bioinformatics, 12(1), 151. doi:10.1186/1471-2105-12-151
   PubMedGoogle Scholar
• Fontana, L., Rovina, D., Novielli, C., Maffioli, E., Tedeschi, G., Magnani, I., & Larizza, L. (2015). Suggestive evidence on the involvement of polypyrimidine-tract binding protein in regulating alternative splicing of MAP/microtubule affinity-regulating kinase 4 in glioma. Cancer Letters, 359(1), 87–96. doi:10.1016/j.canlet.2014.12.049
   PubMed Web of Science ®Google Scholar
• Glaser, F., Pupko, T., Paz, I., Bell, R. E., Bechor-Shental, D., Martz, E., & Ben-Tal, N. (2003). ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19(1), 163–164. doi:10.1093/bioinformatics/19.1.163
   PubMed Web of Science ®Google Scholar
• Grant, B. J., Rodrigues, A. P., ElSawy, K. M., McCammon, J. A., & Caves, L. S. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22(21), 2695–2696. doi:10.1093/bioinformatics/btl461
   PubMed Web of Science ®Google Scholar
• Gulzar, M., Ali, S., Khan, F. I., Khan, P., Taneja, P., & Hassan, M. I. (2019). Binding mechanism of caffeic acid and simvastatin to the integrin linked kinase for therapeutic implications: A comparative docking and MD simulation studies. Journal of Biomolecular Structure and Dynamics, 37(16), 4327–4337. doi:10.1080/07391102.2018.1546621
   PubMed Web of Science ®Google Scholar
• Haider, S., Parkinson, G. N., & Neidle, S. (2008). Molecular dynamics and principal components analysis of human telomeric quadruplex multimers. Biophysical Journal, 95(1), 296–311. doi:10.1529/biophysj.107.120501
   PubMed Web of Science ®Google Scholar
• Hanif, F., Muzaffar, K., Perveen, K., Malhi, S. M., & Simjee Sh, U. (2017). Glioblastoma multiforme: A review of its epidemiology and pathogenesis through clinical presentation and treatment. Asian Pacific Journal of Cancer Prevention: APJCP, 18(1), 3–9. doi:10.22034/APJCP.2017.18.1.3
   PubMedGoogle Scholar
• Hoda, N., Naz, H., Jameel, E., Shandilya, A., Dey, S., Hassan, M. I., Ahmad, F., & Jayaram, B. (2016). Curcumin specifically binds to the human calcium-calmodulin-dependent protein kinase IV: Fluorescence and molecular dynamics simulation studies. Journal of Biomolecular Structure and Dynamics, 34(3), 572–584. doi:10.1080/07391102.2015.1046934
   PubMed Web of Science ®Google Scholar
• Holland, E. C. (2000). Glioblastoma multiforme: The terminator. Proceedings of the National Academy of Sciences, 97(12), 6242–6244. doi:10.1073/pnas.97.12.6242
   PubMed Web of Science ®Google Scholar
• Hunenberger, P. H., Mark, A. E., & van Gunsteren, W. F. (1995). Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. Journal of Molecular Biology, 252, 492–503. S0022-2836(85)70514-1. [pii] doi:10.1006/jmbi.1995.0514
   PubMed Web of Science ®Google Scholar
• Idrees, D., Prakash, A., Haque, M. A., Islam, A., Ahmad, F., & Hassan, M. I. (2016). Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea. Journal of Biomolecular Structure and Dynamics, 34(9), 1987–1997. doi:10.1080/07391102.2015.1100552
   PubMed Web of Science ®Google Scholar
• Idrees, D., Rahman, S., Shahbaaz, M., Haque, M. A., Islam, A., Ahmad, F., & Hassan, M. I. (2017). Estimation of thermodynamic stability of human carbonic anhydrase IX from urea-induced denaturation and MD simulation studies. International Journal of Biological Macromolecules, 105, 183–189.doi:10.1016/j.ijbiomac.2017.07.010
   PubMed Web of Science ®Google Scholar
• Kasahara, K., Fukuda, I., & Nakamura, H. (2014). A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer-DNA complex. PLoS One, 9(11), e112419.. doi:10.1371/journal.pone.0112419
   PubMed Web of Science ®Google Scholar
• Khan, F. I., Aamir, M., Wei, D. Q., Ahmad, F., & Hassan, M. I. (2017). Molecular mechanism of Ras-related protein Rab-5A and effect of mutations in the catalytically active phosphate-binding loop. Journal of Biomolecular Structure and Dynamics, 35(1), 105–118. doi:10.1080/07391102.2015.1134346
   PubMed Web of Science ®Google Scholar
• Khan, F. I., Shahbaaz, M., Bisetty, K., Waheed, A., Sly, W. S., Ahmad, F., & Hassan, M. I. (2016). Large scale analysis of the mutational landscape in beta-glucuronidase: A major player of mucopolysaccharidosis type VII. Gene, 576(1), 36–44. doi:10.1016/j.gene.2015.09.062
   PubMed Web of Science ®Google Scholar
• Khan, F. I., Wei, D. Q., Gu, K. R., Hassan, M. I., & Tabrez, S. (2016). Current updates on computer aided protein modeling and designing. International Journal of Biological Macromolecules, 85, 48–62. doi:10.1016/j.ijbiomac.2015.12.072
   PubMed Web of Science ®Google Scholar
• Khan, P., Rahman, S., Queen, A., Manzoor, S., Naz, F., Hasan, G. M., Luqman, S., Kim, J., Islam, A., Ahmad, F., & Hassan, M. I. (2017). Elucidation of dietary polyphenolics as potential inhibitor of microtubule affinity regulating kinase 4: in silico and in vitro studies. Scientific Reports, 7(1), 9470. doi:10.1038/s41598-017-09941-4
   PubMed Web of Science ®Google Scholar
• Kumar, V., Islam, A., Hassan, M. I., & Ahmad, F. (2016). Delineating the relationship between amyotrophic lateral sclerosis and frontotemporal dementia: Sequence and structure-based predictions. Biochimica et Biophysica Acta, 1862(9), 1742–1754. doi:10.1016/j.bbadis.2016.06.011
   PubMed Web of Science ®Google Scholar
• Kumar, V., Rahman, S., Choudhry, H., Zamzami, M. A., Sarwar Jamal, M., Islam, A., Ahmad, F., & Hassan, M. I. (2017). Computing disease-linked SOD1 mutations: Deciphering protein stability and patient-phenotype relations. Scientific Reports, 7(1), 4678–4610. doi:10.1038/s41598-017-04950-9
   PubMedGoogle Scholar
• Lee, J. T., & Nussbaum, R. L. (1989). An arginine to glutamine mutation in residue 109 of human ornithine transcarbamylase completely abolishes enzymatic activity in Cos1 cells. Journal of Clinical Investigation, 84(6), 1762–1766. doi:10.1172/JCI114360
   PubMed Web of Science ®Google Scholar
• Lopez-Ferrando, V., Gazzo, A., de la Cruz, X., Orozco, M., & Gelpi, J. L. (2017). PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update. Nucleic Acids Research, 45, W222–W228. doi:10.1093/nar/gkx313
   PubMed Web of Science ®Google Scholar
• Magnani, I., Novielli, C., Bellini, M., Roversi, G., Bello, L., & Larizza, L. (2009). Multiple localization of endogenous MARK4L protein in human glioma. Cellular Oncology: The Official Journal of the International Society for Cellular Oncology, 31(5), 357–370. doi:10.3233/CLO-2009-0481
   PubMed Web of Science ®Google Scholar
• Magnani, I., Novielli, C., Fontana, L., Tabano, S., Rovina, D., Moroni, R. F., Bauer, D., Mazzoleni, S., Colombo, E. A., Tedeschi, G., Monti, L., Porta, G., Bosari, S., Frassoni, C., Galli, R., Bello, L., & Larizza, L. (2011). Differential signature of the centrosomal MARK4 isoforms in glioma. Analytical Cellular Pathology, 34(6), 319–338. doi:10.1155/2011/206756
   Web of Science ®Google Scholar
• Mohammad, T., Arif, K., Alajmi, M. F., Hussain, A., Islam, A., Rehman, M. T., & Hassan, I. (2020). Identification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: Towards therapeutic management of cancer. Journal of Biomolecular Structure and Dynamics, 1–9. doi:10.1080/07391102.2020.1711810.
   PubMed Web of Science ®Google Scholar
• Naiyer, A., Hassan, M. I., Islam, A., Sundd, M., & Ahmad, F. (2015). Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques. Journal of Biomolecular Structure and Dynamics, 33(10), 2267–2284. doi:10.1080/07391102.2014.999354
   PubMed Web of Science ®Google Scholar
• Naqvi, A. A. T., Alajmi, M. F., Rehman, T., Hussain, A., & Hassan, I. (2019). Effects of Pro1266Leu mutation on structure and function of glycoprotein IB binding domain of von Willebrand factor. Journal of Cellular Biochemistry, 120(10), 17847–17857. doi:10.1002/jcb.29052
   PubMed Web of Science ®Google Scholar
• Naz, F., Anjum, F., Islam, A., Ahmad, F., & Hassan, M. I. (2013). Microtubule affinity-regulating kinase 4: Structure, function, and regulation. Cell Biochemistry and Biophysics, 67(2), 485–499. doi:10.1007/s12013-013-9550-7
   PubMed Web of Science ®Google Scholar
• Naz, H., Shahbaaz, M., Bisetty, K., Islam, A., Ahmad, F., & Hassan, M. I. (2016). Effect of pH on the structure, function, and stability of human calcium/calmodulin-dependent protein kinase IV: Combined spectroscopic and MD simulation studies. Biochemistry and Cell Biology, 94(3), 221–228. doi:10.1139/bcb-2015-0132
   PubMedGoogle Scholar
• Naz, H., Shahbaaz, M., Haque, M. A., Bisetty, K., Islam, A., Ahmad, F., & Hassan, M. I. (2017). Urea-induced denaturation of human calcium/calmodulin-dependent protein kinase IV: A combined spectroscopic and MD simulation studies. Journal of Biomolecular Structure and Dynamics, 35(3), 463–475. doi:10.1080/07391102.2016.1150203
   PubMed Web of Science ®Google Scholar
• Ohka, F., Natsume, A., & Wakabayashi, T. (2012). Current trends in targeted therapies for glioblastoma multiforme. Neurology Research International, 2012, 1–13. doi:10.1155/2012/878425
   Google Scholar
• Parthiban, V., Gromiha, M. M., & Schomburg, D. (2006). CUPSAT: Prediction of protein stability upon point mutations. Nucleic Acids Research, 34(Web Server), W239–242. doi:10.1093/nar/gkl190
   PubMedGoogle Scholar
• Parveen, I., Khan, P., Ali, S., Hassan, M. I., & Ahmed, N. (2018). Synthesis, molecular docking and inhibition studies of novel 3-N-aryl substituted-2-heteroarylchromones targeting microtubule affinity regulating kinase 4 inhibitors. European Journal of Medicinal Chemistry, 159, 166–177. doi:10.1016/j.ejmech.2018.09.030
   PubMed Web of Science ®Google Scholar
• Pejaver, V., Urresti, J., Lugo-Martinez, J., Pagel, K. A., Lin, G. N., Nam, H.-J., Mort, M., Cooper, D. N., Sebat, J., Iakoucheva, L. M., Mooney, S. D., & Radivojac, P. (2017). MutPred2: Inferring the molecular and phenotypic impact of amino acid variants. bioRxiv, 134981. doi:10.1101/134981.
   Google Scholar
• Pires, D. E., Ascher, D. B., & Blundell, T. L. (2014). DUET: A server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Research, 42(W1), W314–319. doi:10.1093/nar/gku411
   PubMed Web of Science ®Google Scholar
• Prakash, A., Idrees, D., Haque, M. A., Islam, A., Ahmad, F., & Hassan, M. I. (2017). GdmCl-induced unfolding studies of human carbonic anhydrase IX: A combined spectroscopic and MD simulation approach. Journal of Biomolecular Structure and Dynamics, 35(6), 1295–1306. doi:10.1080/07391102.2016.1179596
   PubMed Web of Science ®Google Scholar
• Quan, L., Lv, Q., & Zhang, Y. (2016). STRUM: Structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics, 32(19), 2936–2946. doi:10.1093/bioinformatics/btw361
   PubMed Web of Science ®Google Scholar
• Rodrigues, C. H., Pires, D. E., & Ascher, D. B. (2018). DynaMut: Predicting the impact of mutations on protein conformation, flexibility and stability. Nucleic Acids Research, 46(W1), W350–W355. doi:10.1093/nar/gky300
   PubMed Web of Science ®Google Scholar
• Rovina, D., Fontana, L., Monti, L., Novielli, C., Panini, N., Sirchia, S. M., Erba, E., Magnani, I., & Larizza, L. (2014). Microtubule-associated protein/microtubule affinity-regulating kinase 4 (MARK4) plays a role in cell cycle progression and cytoskeletal dynamics. European Journal of Cell Biology, 93(8–9), 355–365. doi:10.1016/j.ejcb.2014.07.004
   PubMed Web of Science ®Google Scholar
• Sack, J. S., Gao, M., Kiefer, S. E., Myers, J. E., Jr., Newitt, J. A., Wu, S., & Yan, C. (2016). Crystal structure of microtubule affinity-regulating kinase 4 catalytic domain in complex with a pyrazolopyrimidine inhibitor. Acta Crystallographica Section F Structural Biology Communications, 72(2), 129–134. doi:10.1107/S2053230X15024747
   PubMedGoogle Scholar
• Sasmita, A. O., Wong, Y. P., & Ling, A. P. K. (2018). Biomarkers and therapeutic advances in glioblastoma multiforme. Asia-Pacific Journal of Clinical Oncology, 14(1), 40–51. doi:10.1111/ajco.12756
   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(W1), W452–W457. doi:10.1093/nar/gks539
   PubMed Web of Science ®Google Scholar
• Sittel, F., Jain, A., & Stock, G. (2014). Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates. Journal of Chemical Physics, 141(1), 014111. doi:10.1063/1.4885338
   PubMed Web of Science ®Google Scholar
• Tang, H., & Thomas, P. D. (2016). PANTHER-PSEP: Predicting disease-causing genetic variants using position-specific evolutionary preservation. Bioinformatics, 32(14), 2230–2232. doi:10.1093/bioinformatics/btw222
   PubMed Web of Science ®Google Scholar
• The Cancer Genome Atlas Research Network. (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061.
   PubMed Web of Science ®Google Scholar
• Trinczek, B., Brajenovic, M., Ebneth, A., & Drewes, G. (2004). MARK4 is a novel microtubule-associated proteins/microtubule affinity-regulating kinase that binds to the cellular microtubule network and to centrosomes. Journal of Biological Chemistry, 279(7), 5915–5923. doi:10.1074/jbc.M304528200
   PubMed Web of Science ®Google Scholar
• Urbanska, K., Sokolowska, J., Szmidt, M., & Sysa, P. (2014). Glioblastoma multiforme - an overview. Współczesna Onkologia, 18, 307–312. doi:10.5114/wo.2014.4055922235
   Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. doi:10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Venselaar, H., Te Beek, T. A., Kuipers, R. K., Hekkelman, M. L., & Vriend, G. (2010). Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics, 11(1), 548. doi:10.1186/1471-2105-11-548
   PubMed Web of Science ®Google Scholar
• Voura, M., Khan, P., Thysiadis, S., Katsamakas, S., Queen, A., Hasan, G. M., Ali, S., Sarli, V., & Hassan, M. I. (2019). Probing the inhibition of microtubule affinity regulating kinase 4 by N-substituted acridones. Scientific Reports, 9(1), 1676. doi:10.1038/s41598-018-38217-8
   PubMedGoogle Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54, 5 6 1–5 6 37. 10.1002/cpbi.3
   PubMedGoogle Scholar
• Weber, C. C., & Whelan, S. (2019). Physicochemical amino acid properties better describe substitution rates in large populations. Molecular Biology and Evolution, 36(4), 679–690. doi:10.1093/molbev/msz003
   PubMed Web of Science ®Google Scholar
• Young, R. M., Jamshidi, A., Davis, G., & Sherman, J. H. (2015). Current trends in the surgical management and treatment of adult glioblastoma. Annals of Translational Medicine, 3(9), 121. doi:tm-03-09-121 [pii]10.3978/j.issn.2305-5839.2015.05.10
   PubMed Web of Science ®Google Scholar