Understanding the role of mTOR-mLst8 binding through coarse-grained simulation approaches

References

• Conciatori F, Ciuffreda L, Bazzichetto C, et al. mTOR Cross-Talk in Cancer and Potential for Combination Therapy. Cancers [Internet]. 2018 [cited 2019 Sep 1];10. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789373/.
   Google Scholar
• Saxton RA, Sabatini DM. mTOR signaling in growth, metabolism, and disease. Cell. 2017;168:960–976.
   PubMed Web of Science ®Google Scholar
• Liu GY, Sabatini DM. mTOR at the nexus of nutrition, growth, ageing and disease. Nat Rev Mol Cell Biol. 2020;21:183–203.
   PubMed Web of Science ®Google Scholar
• Betz C, Hall MN. Where is mTOR and what is it doing there? J Cell Biol. 2013;203:563–574.
   PubMed Web of Science ®Google Scholar
• Boutouja F, Stiehm CM, Platta HW. mTOR: a cellular regulator interface in health and disease. Cells [Internet]. 2019 [cited 2019 Sep 1];8. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356367/.
   Google Scholar
• Laplante M, Sabatini DM. mTOR signaling at a glance. J Cell Sci. 2009;122:3589–3594.
   PubMed Web of Science ®Google Scholar
• Laplante M, Sabatini DM. mTOR signaling in growth control and disease. Cell. 2012;149:274–293.
   PubMed Web of Science ®Google Scholar
• Tafur L, Kefauver J, Loewith R. Structural insights into TOR signaling. Genes (Basel). 2020;11(885):1–24.
   Google Scholar
• Watanabe R, Wei L, Huang J. mTOR signaling, function, novel inhibitors, and therapeutic targets. J Nucl Med. 2011;52:497–500.
   PubMed Web of Science ®Google Scholar
• Hara K, Maruki Y, Long X, et al. Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell. 2002;110:177–189.
   PubMed Web of Science ®Google Scholar
• Kim DH, Sarbassov DD, Ali SM, et al. mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell. 2002;110:163–175.
   PubMed Web of Science ®Google Scholar
• Kim DH, Sarbassov DD, Ali SM, et al. Gbetal, a positive regulator of the rapamycin-sensitive pathway required for the nutrient-sensitive interaction between raptor and mTOR. Mol Cell. 2003;11:895–904.
   PubMed Web of Science ®Google Scholar
• Vander Haar E, Lee S-I, Bandhakavi S, et al. Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40. Nat Cell Biol. 2007;9:316–323.
   PubMed Web of Science ®Google Scholar
• Tee AR, Blenis J. mTOR, translational control and human disease. Semin Cell Dev Biol. 2005;16:29–37.
   PubMed Web of Science ®Google Scholar
• Frias MA, Thoreen CC, Jaffe JD, et al. Msin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s. Curr Biol CB. 2006;16:1865–1870.
   PubMed Web of Science ®Google Scholar
• Jacinto E, Facchinetti V, Liu D, et al. SIN1/MIP1 maintains rictor-mTOR complex integrity and regulates Akt phosphorylation and substrate specificity. Cell. 2006;127:125–137.
   PubMed Web of Science ®Google Scholar
• Pearce LR, Huang X, Boudeau J, et al. Identification of Protor as a novel Rictor-binding component of mTOR complex-2. Biochem J. 2007;405:513–522.
   PubMed Web of Science ®Google Scholar
• Sarbassov DD, Ali SM, Kim DH, et al. Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton. Curr Biol. 2004;14:1296–1302.
   PubMed Web of Science ®Google Scholar
• Yang Q, Inoki K, Ikenoue T, et al. Identification of Sin1 as an essential TORC2 component required for complex formation and kinase activity. Genes Dev. 2006;20:2820–2832.
   PubMed Web of Science ®Google Scholar
• Sarbassov DD, Guertin DA, Ali SM, et al. Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex. Science. 2005;307:1098–1101.
   PubMed Web of Science ®Google Scholar
• Yang H, Rudge DG, Koos JD, et al. mTOR kinase structure, mechanism and regulation. Nature. 2013;497:217–223.
   PubMed Web of Science ®Google Scholar
• Neer EJ, Schmidt CJ, Nambudripad R, et al. The ancient regulatory-protein family of WD-repeat proteins. Nature. 1994;371:297–300.
   PubMed Web of Science ®Google Scholar
• Guertin DA, Stevens DM, Thoreen CC, et al. Ablation in mice of the mTORC components raptor, rictor, or mLST8 reveals that mTORC2 is required for signaling to Akt-FOXO and PKC alpha but not S6K1. Dev Cell. 2006;11:859–871.
   PubMed Web of Science ®Google Scholar
• Kakumoto K, Ikeda J, Okada M, et al. mLST8 promotes mTOR-mediated tumor progression. PLoS ONE [Internet]. 2015 [cited 2019 Sep 1];10. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408021/.
   Google Scholar
• Eswar N, Webb B, Marti-Renom MA, et al. Comparative protein structure modeling using Modeller. Curr Protoc Bioinforma. 2006; Chapter 5:Unit 5.6.
   Google Scholar
• Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. 1993.
   Google Scholar
• Laskowski RA, MacArthur MW, Moss DS, et al. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993;26:283–291.
   Web of Science ®Google Scholar
• Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991;253:164–170.
   PubMed Web of Science ®Google Scholar
• Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992;356:83.
   PubMed Web of Science ®Google Scholar
• Lovell SC, Davis IW, Arendall WB, et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003;50:437–450.
   PubMed Web of Science ®Google Scholar
• Darré L, Machado MR, Brandner AF, et al. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics. J Chem Theory Comput. 2015;11:723–739.
   PubMed Web of Science ®Google Scholar
• Machado MR, Pantano S. SIRAH tools: mapping, backmapping and visualization of coarse-grained models. Bioinformatics. 2016;32:1568–1570.
   PubMed Web of Science ®Google Scholar
• Darré L, Machado MR, Dans PD, et al. Another coarse grain model for aqueous solvation: WAT FOUR? J Chem Theory Comput. 2010;6:3793–3807.
   Web of Science ®Google Scholar
• Gonzalez HC, Darré L, Pantano S. Transferable mixing of atomistic and coarse-grained water models. J Phys Chem B. 2013;117:14438–14448.
   PubMed Web of Science ®Google Scholar
• Caceres-Delpiano J, Wang L-P, Essex JW. The automated optimisation of a coarse-grained force field using free energy data [Internet]. Biophysics; 2020 [cited 2021 May 9]. Available from: http://biorxiv.org/lookup/doi/10.1101/2020.08.13.250233.
   Google Scholar
• Darré L, Tek A, Baaden M, et al. Mixing atomistic and coarse grain solvation models for MD simulations: let WT4 handle the bulk. J Chem Theory Comput. 2012;8:3880–3894.
   PubMed Web of Science ®Google Scholar
• Dolinsky TJ, Nielsen JE, McCammon JA, et al. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 2004;32:W665–W667.
   PubMed Web of Science ®Google Scholar
• Abraham MJ, Murtola T, Schulz R, et al. Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2.
   Google Scholar
• Van Der Spoel D, Lindahl E, Hess B, et al. GROMACS: fast, flexible, and free. J Comput Chem. 2005;26:1701–1718.
   PubMed Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
   Web of Science ®Google Scholar
• Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. J Chem Phys. 2007;126:014101.
   PubMed Web of Science ®Google Scholar
• Parrinello M, Rahman A. Polymorphic transitions in single crystals: A new molecular dynamics method. J Appl Phys. 1981;52:7182–7190.
   Web of Science ®Google Scholar
• Kagami LP, das Neves GM, Timmers LFSM, et al. Geo-Measures: A PyMOL plugin for protein structure ensembles analysis. Comput Biol Chem. 2020;87:107322.
   PubMed Web of Science ®Google Scholar
• Van Rossum G, Drake Jr. FL. Python reference manual. Amsterdam: Centrum voor Wiskunde en Informatica; 1995.
   Google Scholar
• Maiorov VN, Crippen GM. Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. J Mol Biol. 1994;235:625–634.
   PubMed Web of Science ®Google Scholar
• Kufareva I, Abagyan R. Methods of protein structure comparison. In: Orry AJW, Abagyan R, editors. Homol model [Internet] [cited 2021 May 22]. Totowa (NJ): Humana Press; 2011. p. 231–257. Available from: http://link.springer.com/10.1007/978-1-61779-588-6_10.
   Google Scholar
• Lobanov M, Bogatyreva NS, Galzitskaya OV. Radius of gyration as an indicator of protein structure compactness. Mol Biol. 2008;42:623–628.
   Web of Science ®Google Scholar
• Team RC. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.[WWW document]. URL Httpwww R-Proj OrgAccessed Dec 24 2013.
   Google Scholar
• Santos de Oliveira FL, Vieira Carletti J, Azevedo FFN, et al. mTOR–mLST8 interaction: hot spot identification through quantum biochemistry calculations. New J Chem. 2020;44:20982–20992.
   Web of Science ®Google Scholar