Effects of Peutz-Jeghers syndrome (PJS) causing missense mutations L67P, L182P, G242V and R297S on the structural dynamics of LKB1 (Liver kinase B1) protein

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
   PubMed Web of Science ®Google Scholar
• Alessi, D. R., Sakamoto, K., & Bayascas, J. R. (2006). LKB1-Dependent Signaling Pathways. Annual Review of Biochemistry, 75, 137–163. doi:10.1146/annurev.biochem.75.103004.142702
   PubMed Web of Science ®Google Scholar
• Arcangeli, C., Bizzarri, A. R., & Cannistraro, S. (2001). Molecular dynamics simulation and essential dynamics study of mutated plastocyanin: Structural, dynamical and functional effects of a disulfide bridge insertion at the protein surface. Biophysical Chemistry, 92(3), 183–199. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/1158383510.1016/S0301-4622(01)00199-5
   PubMed Web of Science ®Google Scholar
• Arnold, G. E., & Ornstein, R. L. (1997). Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: Cytochrome P450BM-3. Biophysical Journal, 73(3), 1147–1159. doi:10.1016/S0006-3495(97)78147-5
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Grigera, J. R., & Straatsma, T. P. (1987). The missing term in effective pair potentials. The Journal of Physical Chemistry, 91(24), 6269–6271. doi:10.1021/j100308a038
   Web of Science ®Google Scholar
• Berridge, M. J. (2005). Unlocking the secrets of cell signaling. Annual Review of Physiology, 67(1), 1–21. doi:10.1146/annurev.physiol.67.040103.152647
   PubMedGoogle Scholar
• Berridge, M. J. (2009). Signalling defects and disease. Cell, 6, 1–66. doi:10.1042/csb0001012
   Google Scholar
• Bhandare, V. V., & Ramaswamy, A. (2017, March). The proteinopathy of D169G and K263E mutants at the RNA Recognition Motif (RRM) domain of tar DNA-binding protein (tdp43) causing neurological disorders: A computational study. Journal of Biomolecular Structure and Dynamics, 1102, 1–19. doi:10.1080/07391102.2017.1310670
   Google Scholar
• Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., … Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), W252–W258. doi:10.1093/nar/gku340
   PubMed Web of Science ®Google Scholar
• Bjarnadottir, U., & Nielsen, J. E. (2012). Predicting the open conformations of protein kinases using molecular dynamics simulations. Biopolymers, 97(1), 65–72. doi:10.1002/bip.21704
   PubMed Web of Science ®Google Scholar
• Boudeau, J., Sapkota, G., & Alessi, D. R. (2003). LKB1, a protein kinase regulating cell proliferation and polarity. FEBS Letters, 546(1), 159–165. doi:10.1016/S0014-5793(03)00642-2
   PubMed Web of Science ®Google Scholar
• Breuhahn, K., Longerich, T., & Schirmacher, P. (2006). Dysregulation of growth factor signaling in human hepatocellular carcinoma. Oncogene, 25(27), 3787–3800. doi:10.1038/sj.onc.1209556
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. Journal of Chemical Physics, 126(1), 014101. doi:10.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Capriotti, E., Calabrese, R., & Casadio, R. (2006). Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics, 22(22), 2729–2734. doi:10.1093/bioinformatics/btl423
   PubMed Web of Science ®Google Scholar
• Capriotti, E., Fariselli, P., Rossi, I., & Casadio, R. (2008). A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics, 9(Suppl 2), S6. doi:10.1186/1471-2105-9-S2-S6
   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. doi:10.1063/1.464397
   Web of Science ®Google Scholar
• Doss, C. G. P., Rajith, B., Garwasis, N., Mathew, P. R., Raju, A. S., Apoorva, K., … Dike, I. P. (2012). Screening of mutations affecting protein stability and dynamics of FGFR1-A simulation analysis. Applied and Translational Genomics, 1, 37–43. doi:10.1016/j.atg.2012.06.002
   PubMedGoogle Scholar
• Entius, M. M., Keller, J. J., Westerman, A. M., van Rees, B. P., van Velthuysen, M. L., de Goeij, A. F., … Offerhaus, G. J. (2001). Molecular genetic alterations in hamartomatous polyps and carcinomas of patients with Peutz-Jeghers syndrome. Journal of Clinical Pathology, 54(2), 126–131. doi:10.1136/jcp.54.2.126
   PubMed Web of Science ®Google Scholar
• Giancotti, F. G. (2014). Deregulation of cell signaling in cancer. FEBS Letters, 588(16), 2558–2570. doi:10.1016/j.febslet.2014.02.005
   PubMed Web of Science ®Google Scholar
• Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18(15), 2714–2723. doi:10.1002/elps.1150181505
   PubMed Web of Science ®Google Scholar
• Guex, N., Peitsch, M. C., & Schwede, T. (2009). Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis, 30(S1), S162–S173. doi:10.1002/elps.200900140
   PubMed Web of Science ®Google Scholar
• Hess, B. (2008). P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of the American Chemical Society, 4, 116–122. doi:10.1021/CT700200B
   Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS : A linear constraint solver for molecular simulations, 18(12), 1463–1472.
   Google Scholar
• Ichiye, T., & Karplus, M. (1991). Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins: Structure, Function, and Bioinformatics, 11(3), 205–217. doi:10.1002/prot.340110305
   PubMed Web of Science ®Google Scholar
• Karplus, M., & Kuriyan, J. (2005). Molecular dynamics and protein function. Proceedings of the National Academy of Sciences of the United States of America, 102(19), 6679–6685. doi:10.1073/pnas.0408930102
   PubMed Web of Science ®Google Scholar
• Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9(9), 646–652. doi:10.1038/nsb0902-646
   PubMedGoogle Scholar
• Katajisto, P., Vaahtomeri, K., Ekman, N., Ventelä, E., Ristimäki, A., Bardeesy, N., … Makela, T. P. (2008). LKB1 signaling in mesenchymal cells required for suppression of gastrointestinal polyposis. Nature Genetics, 40(4), 455–459. doi:10.1038/ng.98
   PubMed Web of Science ®Google Scholar
• Kornev, A. P., Haste, N. M., Taylor, S. S., & Ten Eyck, L. F. (2006). Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism. Proceedings of the National Academy of Sciences of the United States of America, 103(47), 17783–17788. doi:10.1073/pnas.0607656103
   PubMed Web of Science ®Google Scholar
• Kornev, A. P., Taylor, S. S., & Ten Eyck, L. F. (2008). A helix scaffold for the assembly of active protein kinases. Proceedings of the National Academy of Sciences of the United States of America, 105(38), 14377–14382. doi:10.1073/pnas.0807988105
   PubMed Web of Science ®Google Scholar
• Krishnamoorthy, N., & Gajendrarao, P. (2017). Impact of disease-causing mutations on inter-domain interactions in cMyBP-C: A steered molecular dynamics study. Journal of Biomolecular Structure and Dynamics, 35, 1916–1922. doi:10.1080/07391102.2016.1199329
   PubMed Web of Science ®Google Scholar
• Kumar, T. D., George, P. D. C., Sneha, P., Tayubi, I. A., Siva, R., Chakraborty, C., & Magesh, R. (2017). Influence of V54M mutation in giant muscle protein titin: A computational screening and molecular dynamics approach. Journal of Biomolecular Structure and Dynamics, 35, 917–928. doi:10.1080/07391102.2016.1166456
   PubMed Web of Science ®Google Scholar
• Levitt, M. (1983). Molecular dynamics of native protein. Journal of Molecular Biology, 168, 595–617.10.1016/S0022-2836(83)80304-0
   PubMed Web of Science ®Google Scholar
• Mandal, R. S., Panda, S., & Das, S. (2017). In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein. Journal of Biomolecular Structure and Dynamics, 1–15. doi:10.1080/07391102.2017.1305295
   PubMed Web of Science ®Google Scholar
• Nagasundaram, N., Zhu, H., Liu, J., Karthick, V., George Priya Doss, C., Chakraborty, C., & Chen, L. (2015). Analysing the effect of mutation on protein function and discovering potential inhibitors of CDK4: Molecular modelling and dynamics studies. PLoS ONE, 10(8), 1–21. doi:10.1371/journal.pone.0133969
   Web of Science ®Google Scholar
• Nishi, H., Demir, E., & Panchenko, A. R. (2015). Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites. Journal of Molecular Biology, 427(2), 511–520. doi:10.1016/j.jmb.2014.11.001
   PubMed Web of Science ®Google Scholar
• Olschwang, S., Boisson, C., & Thomas, G. (2001). Peutz-Jeghers families unlinked to STK11/LKB1 gene mutations are highly predisposed to primitive biliary adenocarcinoma. Journal of Medical Genetics, 38(6), 356–360. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/1138915810.1136/jmg.38.6.356
   PubMed Web of Science ®Google Scholar
• Parrinello, M. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182. doi:10.1063/1.328693
   Web of Science ®Google Scholar
• 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. https://doi.org/10.1093/bioinformatics/btt055
   Web of Science ®Google Scholar
• Roe, D. R., & Cheatham, T. E., III. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular synamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. doi:10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Sangeetha, B., Muthukumaran, R., & Amutha, R. (2015). Structural dynamics of native and V260E mutant C-terminal domain of HIV-1 integrase. Journal of Computer-Aided Molecular Design, 29(4), 371–385. doi:10.1007/s10822-015-9830-y
   PubMed Web of Science ®Google Scholar
• Schlick, T., Collepardo-Guevara, R., Halvorsen, L. A., Jung, S., & Xiao, X. (2011). Biomolecular modeling and simulation: A field coming of age. Quarterly Reviews of Biophysics, 44(2), 191–228. doi:10.1017/S0033583510000284
   PubMed Web of Science ®Google Scholar
• Scott, W. R. P., Hu, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., … Gunsteren, W. F. Van. (1999). The GROMOS Biomolecular Simulation Program Package. The Journal of Physical Chemistry A, 103, 3596–3607.
   Web of Science ®Google Scholar
• Signalling, C., Michael, B., & Defects, S. (2009). Signalling defects and disease. Cell, 1–66. doi:10.1042/csb0001012
   Google Scholar
• Song, K., Wu, J., & Jiang, C. (2013). Dysregulation of signaling pathways and putative biomarkers in liver cancer stem cells (Review). Oncology Reports, 29(1), 3–12. doi:10.3892/or.2012.2082
   PubMed Web of Science ®Google Scholar
• Sutthibutpong, T., Rattanarojpong, T., & Khunrae, P. (2017). Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays. Journal of Biomolecular Structure and Dynamics, 1–15. doi:10.1080/07391102.2017.1404934
   PubMed Web of Science ®Google Scholar
• Swaminathan, S. (1991). Investigation of domain structure in proteins via molecular dynamics simulation: Application to HIV-1 protease dimer. Journal of the American Chemical Society, 113(7), 2717–2721. doi:10.1021/ja00007a054
   Web of Science ®Google Scholar
• Tompa, D. R., & Saraboji, K. (2017). Molecular dynamics of a far positioned SOD1 mutant V14M reveals pathogenic misfolding behavior. Journal of Biomolecular Structure and Dynamics, 1–14. doi:10.1080/07391102.2017.1407675
   PubMed Web of Science ®Google Scholar
• Vaahtomeri, K., & Mäkelä, T. P. (2011). Molecular mechanisms of tumor suppression by LKB1. FEBS Letters, 585(7), 944–951. doi:10.1016/j.febslet.2010.12.034
   PubMed Web of Science ®Google Scholar
• Wang, F., Wan, H., Hu, J., & Chang, S. (2015). Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C. Molecular BioSystems, 11(1), 223–231. doi:10.1039/C4MB00383G
   PubMed Web of Science ®Google Scholar
• Wu, W. K. K., Cho, C. H., Lee, C. W., Fan, D., Wu, K., Yu, J., & Sung, J. J. (2010). Dysregulation of cellular signaling in gastric cancer. Cancer Letters, 295, 144–153.
   PubMed Web of Science ®Google Scholar
• Zhao, F., Yang, G., Xiang, S., Gao, D., & Zeng, C. (2017). Insilico analysis of the effect of mutation on epidermal growth factor receptor in non-small- cell-lung-carcinoma : From mutational analysis to drug designing drug designing. Journal of Biomolecular Structure and Dynamics, 35, 427–434. doi:10.1080/07391102.2016.1146165
   PubMed Web of Science ®Google Scholar