160
Views
2
CrossRef citations to date
0
Altmetric
Research Articles

Delineating the folding perturbations and molecular mechanisms of Thr-Ala 642 mutation in Rab-GTPase activating protein Akt substrate of 160kDa and its impact on the aetiology of diabetes

, , , &
Pages 409-420 | Received 30 Oct 2019, Accepted 23 Dec 2019, Published online: 18 Feb 2020

References

  • Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., … Sunyaev, S. R. (2010). A method and server for predicting damaging missense mutations. Nature Methods, 7(4), 248–249. doi:10.1038/nmeth0410-248
  • Amberger, J. S., Bocchini, C. A., Scott, A. F., & Hamosh, A. (2019). OMIM.org: Leveraging knowledge across phenotype-gene relationships. Nucleic Acids Research, 47(D1), D1038–D1043. doi:10.1093/nar/gky1151
  • Bartlett, G. J., Newberry, R. W., VanVeller, B., Raines, R. T., & Woolfson, D. N. (2013). Interplay of hydrogen bonds and n→π* interactions in proteins. Journal of the American Chemical Society, 135(49), 18682–18688. doi:10.1021/ja4106122
  • Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27(3), 343–350. doi:10.1093/bioinformatics/btq662
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. doi:10.1093/nar/28.1.235
  • Bhardwaj, V., & Purohit, R. (2019). Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway. Journal of Biomolecular Structure and Dynamics, 30, 1–12. doi:10.1080/07391102.2019.1621210
  • Capriotti, E., Fariselli, P., & Casadio, R. (2005). I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Research, 33, W306–310. doi:10.1093/nar/gki375
  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. doi:10.1002/pro.5560020916
  • Dingerdissen, H. M., Torcivia-Rodriguez, J., Hu, Y., Chang, T.-C., Mazumder, R., & Kahsay, R. (2018). BioMuta and BioXpress: Mutation and expression knowledge bases for cancer biomarker discovery. Nucleic Acids Research, 46(D1), D1128–D1136. doi:10.1093/nar/gkx907
  • Dosztányi, Z., Csizmok, V., Tompa, P., & Simon, I. (2005). IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics (Oxford, England), 21(16), 3433–3434. doi:10.1093/bioinformatics/bti541
  • Dosztányi, Z., Csizmók, V., Tompa, P., & Simon, I. (2005). The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. Journal of Molecular Biology, 347(4), 827–839. doi:10.1016/j.jmb.2005.01.071
  • Dyson, H. J., Wright, P. E., & Scheraga, H. A. (2006). The role of hydrophobic interactions in initiation and propagation of protein folding. Proceedings of the National Academy of Sciences, 103(35), 13057–13061. doi:10.1073/pnas.0605504103
  • El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., … Finn, R. D. (2019). The Pfam protein families database in 2019. Nucleic Acids Research, 47(D1), D427–D432. doi:10.1093/nar/gky995
  • Eswar, N., & Ramakrishnan, C. (2000). Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. Protein Engineering, Design and Selection, 13(4), 227–238. doi:10.1093/protein/13.4.227
  • Geraghty, K. M., Chen, S., Harthill, J. E., Ibrahim, A. F., Toth, R., Morrice, N. A., … MacKintosh, C. (2007). Regulation of multisite phosphorylation and 14-3-3 binding of AS160 in response to IGF-1, EGF, PMA and AICAR. Biochemical Journal, 407(2), 231–241. doi:10.1042/BJ20070649
  • Hecht, M., Bromberg, Y., & Rost, B. (2015). Better prediction of functional effects for sequence variants. BMC Genomics., 16(Supple 8), S1.doi:10.1186/1471-2164-16-S8-S1
  • Jafari, E., Gheysarzadeh, A., Mahnam, K., Shahmohammadi, R., Ansari, A., Bakhtyari, H., & Mofid, M. R. (2018). In silico interaction of insulin-like growth factor binding protein 3 with insulin-like growth factor 1. Research in Pharmaceutical Sciences, 13(4), 332–342. doi:10.4103/1735-5362.235160
  • Karaca, E., & Bonvin, A. M. J. J. (2013). Advances in integrative modeling of biomolecular complexes. Methods (San Diego, Calif.), 59(3), 372–381. doi:10.1016/j.ymeth.2012.12.004
  • Kortemme, T., Kim, D. E., & Baker, D. (2004). Computational alanine scanning of protein-protein interfaces. Science Signaling, 2004(219), pl2. doi:10.1126/stke.2192004pl2
  • Kumar, P., Henikoff, S., & Ng, P. C. (2009). Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols, 4(7), 1073–1081. doi:10.1038/nprot.2009.86
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. doi:10.1107/S0021889892009944
  • Mackenzie, R. W., & Elliott, B. T. (2014). Akt/PKB activation and insulin signaling: A novel insulin signaling pathway in the treatment of type 2 diabetes. Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy, 7, 55–64. 10.2147/DMSO.S48260.
  • Margreitter, C., Petrov, D., & Zagrovic, B. (2013). Vienna-PTM web server: A toolkit for MD simulations of protein post-translational modifications. Nucleic Acids Research, 41(W1), W422–426. Web Server issue),. doi:10.1093/nar/gkt416
  • Mîinea, C. P., Sano, H., Kane, S., Sano, E., Fukuda, M., Peränen, J., … Lienhard, G. E. (2005). AS160, the Akt substrate regulating GLUT4 translocation, has a functional Rab GTPase-activating protein domain. Biochemical Journal, 391(1), 87–93. doi:10.1042/BJ20050887
  • Petrov, D., Margreitter, C., Grandits, M., Oostenbrink, C., & Zagrovic, B. (2013). A systematic framework for molecular dynamics simulations of protein post-translational modifications. PLoS Computational Biology, 9(7), e1003154. doi:10.1371/journal.pcbi.1003154
  • 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. doi:10.1002/jcc.20084
  • Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., … Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29(7), 845–854. doi:10.1093/bioinformatics/btt055
  • Rajendran, V., Gopalakrishnan, C., & Purohit, R. (2016). Impact of point mutation P29S in RAC1 on tumorigenesis. Tumor Biology, 37(11), 15293–15304. doi:10.1007/s13277-016-5329-y
  • Raghuraman, P., Sudan, R. J. J., Kumari, J. L. J., & Sudandiradoss, C. (2017). Casting the critical regions in nucleotide binding oligomerization domain 2 protein: A signature mediated structural dynamics approach. Journal of Biomolecular Structure and Dynamics, 35(15), 3297–3315. doi:10.1080/07391102.2016.1254116
  • Raghuraman, P., & Sudandiradoss, C. (2018). R516Q mutation in Melanoma differentiation-associated protein 5 (MDA5) and its pathogenic role towards rare Singleton-Merten syndrome; a signature associated molecular dynamics study. Journal of Biomolecular Structure and Dynamics, 0(0), 1–16. doi:10.1080/07391102.2018.1439770
  • Rajendran, V., Gopalakrishnan, C., & Sethumadhavan, R. (2018). Pathological role of a point mutation (T315I) in BCR-ABL1 protein-A computational insight. Journal of Cellular Biochemistry, 119(1), 918–925. doi:10.1002/jcb.26257
  • Rajendran, V., & Sethumadhavan, R. (2014). Drug resistance mechanism of PncA in Mycobacterium tuberculosis. Journal of Biomolecular Structure and Dynamics, 32(2), 209–221. doi:10.1080/07391102.2012.759885
  • Ramm, G., Larance, M., Guilhaus, M., & James, D. E. (2006). A role for 14-3-3 in insulin-stimulated GLUT4 translocation through its interaction with the RabGAP AS160. Journal of Biological Chemistry, 281(39), 29174–29180. doi:10.1074/jbc.M603274200
  • Raveendran, A. V., Chacko, E. C., & Pappachan, J. M. (2018). Non-pharmacological Treatment Options in the Management of Diabetes Mellitus. European Endocrinology, 14(2), 31–39. doi:10.17925/EE.2018.14.2.31
  • Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5(4), 725–738. doi:10.1038/nprot.2010.5
  • Sang, P., Du, X., Yang, L.-Q., Meng, Z.-H., & Liu, S.-Q. (2017). Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: A comparative molecular dynamics simulation study and the underlying mechanisms. RSC Advances, 7(46), 28580–28590. doi:10.1039/C6RA23230B
  • Sigrist, C. J. A., de Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., … Xenarios, I. (2013). New and continuing developments at PROSITE. Nucleic Acids Research, 41(D1), D344–347. doi:10.1093/nar/gks1067
  • 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), W452–457. doi:10.1093/nar/gks539
  • Sriroopreddy, R., Raghuraman, P., & Sudandiradoss, C. (2019). Structural debilitation of mutation G322D associated with MSH2 and their role in triple negative breast cancer. Journal of Biomolecular Structure and Dynamics, 38(3), 771–780. doi:10.1080/07391102.2019.1587512
  • Tan, S.-X., Ng, Y., Burchfield, J. G., Ramm, G., Lambright, D. G., Stöckli, J., & James, D. E. (2012). The Rab GTPase-activating protein TBC1D4/AS160 contains an atypical phosphotyrosine-binding domain that interacts with plasma membrane phospholipids to facilitate GLUT4 trafficking in adipocytes. Molecular and Cellular Biology, 32(24), 4946–4959. doi:10.1128/MCB.00761-12
  • Thiel, P., Röglin, L., Meissner, N., Hennig, S., Kohlbacher, O., & Ottmann, C. (2013). Virtual screening and experimental validation reveal novel small-molecule inhibitors of 14-3-3 protein-protein interactions. Chemical Communications, 49(76), 8468–8470. doi:10.1039/c3cc44612c
  • Tina, K. G., Bhadra, R., & Srinivasan, N. (2007). PIC: Protein interactions calculator. Nucleic Acids Research, 35, W473–476. doi:10.1093/nar/gkm423
  • UniProt Consortium. (2018). UniProt: The universal protein knowledgebase. Nucleic Acids Research, 46(5), 2699. 10.1093/nar/gky092.
  • Uversky, V. N., Oldfield, C. J., & Dunker, A. K. (2008). Intrinsically disordered proteins in human diseases: Introducing the D2 concept. Annual Review of Biophysics, 37(1), 215–246. doi:10.1146/annurev.biophys.37.032807.125924
  • van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., … Bonvin, A. M. J. J. (2016). The HADDOCK2.2 Web Server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. doi:10.1016/j.jmb.2015.09.014
  • Wallner, B., & Elofsson, A. (2003). Can correct protein models be identified? Protein Science, 12(5), 1073–1086. doi:10.1110/ps.0236803
  • Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, W407–410. doi:10.1093/nar/gkm290
  • Wilker, E., & Yaffe, M. B. (2004). 14-3-3 Proteins–a focus on cancer and human disease. Journal of Molecular and Cellular Cardiology, 37(3), 633–642. doi:10.1016/j.yjmcc.2004.04.015
  • Wu, S., Skolnick, J., & Zhang, Y. (2007). Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biology, 5(1), 17. doi:10.1186/1741-7007-5-17
  • Yang, J., & Zhang, Y.(2015). Protein Structure and Function Prediction Using I‐TASSER. Current Protocols in Bioinformatics, 52(1). doi:10.1002/0471250953.bi0508s52
  • Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9(1), 40. doi:10.1186/1471-2105-9-40

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.