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Articles

Structural insights into Rab21 GTPase activation mechanism by molecular dynamics simulations

, , , , , , , & ORCID Icon show all
Pages 179-189 | Received 29 Oct 2016, Accepted 15 Jul 2017, Published online: 31 Jul 2017

References

  • Seabra MC, Mules EH, Hume AN. Rab GTPases, intracellular traffic and disease. Trends Mol Med. 2002;8:23–30.10.1016/S1471-4914(01)02227-4
  • Stenmark H. Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol. 2009;10:513–525.10.1038/nrm2728
  • Wandinger-Ness A, Zerial M. Rab proteins and the compartmentalization of the endosomal system. Cold Spring Harb Perspect Biol.. 2014; 6(11):a022616. 10.1101/cshperspect.a022616
  • Pfeffer SR. Rab GTPase regulation of membrane identity. Curr Opin Cell Biol. 2013;25:414–419.10.1016/j.ceb.2013.04.002
  • Amir M, Dar MA, Wahiduzzaman, et al. Purification and characterization of RGA2, a Rho2 GTPase-activating protein from Tinospora cordifolia. 3. Biotech. 2016;6:85.
  • Amir M, Wahiduzzaman, Dar MA, et al. Purification and characterization of Ras related protein, Rab5a from Tinospora cordifolia. Int J Biol Macromol. 2016;82:471–479.10.1016/j.ijbiomac.2015.10.077
  • Pfeffer SR. Structural clues to Rab GTPase functional diversity. J Biol Chem. 2005;280:15485–15488.10.1074/jbc.R500003200
  • Stenmark H. Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol. 2009;10:513–525.10.1038/nrm2728
  • Eathiraj S, Pan X, Ritacco C, et al. Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Nature. 2005;436:415–419.10.1038/nature03798
  • Yang MJ, Zhang X. Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation. Proteins. 2011;79:1774–1785.10.1002/prot.23000
  • Blümer J, Rey J, Dehmelt L, et al. RabGEFs are a major determinant for specific Rab membrane targeting. J. Cell Biol. 2013;200:287–300.10.1083/jcb.201209113
  • Gabe Lee MT, Mishra A, Lambright DG. Structural mechanisms for regulation of membrane traffic by Rab GTPases. Traffic. 2009;10:1377–1389.10.1111/tra.2009.10.issue-10
  • Pellinen T, Arjonen A, Vuoriluoto K, et al. Small GTPase Rab21 regulates cell adhesion and controls endosomal traffic of β1-integrins. J. Cell Biol. 2006;173:767–780.10.1083/jcb.200509019
  • Cheng KW, Lahad JP, Gray JW, et al. Emerging role of RAB GTPases in cancer and human disease. Can Res. 2005;65:2516–2519.10.1158/0008-5472.CAN-05-0573
  • Lin Chua CE, Tang BL. α-synuclein and Parkinson’s disease: the first roadblock. J Cell Mol Med. 2006;10:828–837.10.2755/jcmm010.004.04
  • Di Pietro SM, Dell’Angelica EC. The cell biology of Hermansky-Pudlak syndrome: recent advances. Traffic. 2005;6:525–533.10.1111/j.1600-0854.2005.00299.x
  • Khan P, Shandilya A, Jayaram B, et al. Effect of pH on the stability of hemochromatosis factor E: a combined spectroscopic and molecular dynamics simulation-based study. J Biomol Struct Dyn. 2017;35:1582–1598.10.1080/07391102.2016.1189359
  • Hoda N, Naz H, Jameel E, et al. Curcumin specifically binds to the human calcium-calmodulin-dependent protein kinase IV: fluorescence and molecular dynamics simulation studies. J Biomol Struct Dyn. 2016;34:572–584.10.1080/07391102.2015.1046934
  • Khan FI, Shahbaaz M, Bisetty K, et al. Large scale analysis of the mutational landscape in β-glucuronidase: a major player of mucopolysaccharidosis type VII. Gene. 2016;576:36–44.10.1016/j.gene.2015.09.062
  • Naz F, Singh P, Islam A, et al. Human microtubule affinity-regulating kinase 4 is stable at extremes of pH. J Biomol Struct Dyn. 2016;34:1241–1251.10.1080/07391102.2015.1074942
  • Anwer K, Rahman S, Sonani RR, et al. Probing pH sensitivity of αC-phycoerythrin and its natural truncant: a comparative study. Int J Biol Macromol. 2016;86:18–27.10.1016/j.ijbiomac.2016.01.046
  • Anwer K, Sonani R, Madamwar D, et al. Role of N-terminal residues on folding and stability of C-phycoerythrin: simulation and urea-induced denaturation studies. J Biomol Struct Dyn. 2015;33:121–133.10.1080/07391102.2013.855144
  • Haque MA, Zaidi S, Ubaid-ullah S, et al. In vitro and in silico studies of urea-induced denaturation of yeast iso-1-cytochrome c and its deletants at pH 6.0 and 25 °C. J Biomol Struct Dyn. 2015;33:1493–1502.10.1080/07391102.2014.958760
  • Idrees D, Prakash A, Haque MA, et al. GdnHCl-induced unfolding intermediate in the mitochondrial carbonic anhydrase VA. Int J Biol Macromol. 2016;91:1151–1160.10.1016/j.ijbiomac.2016.06.080
  • Khan P, Prakash A, Haque MA, et al. Structural basis of urea-induced unfolding: unraveling the folding pathway of hemochromatosis factor E. Int J Biol Macromol. 2016;91:1051–1061.10.1016/j.ijbiomac.2016.06.055
  • Yang M, Zhang X, Han K. Molecular dynamics simulation of SRP GTPases: towards an understanding of the complex formation from equilibrium fluctuations. Proteins. 2010;78:2222–2237.10.1002/prot.v78:10
  • Yang MJ, Pang XQ, Zhang X, et al. Molecular dynamics simulation reveals preorganization of the chloroplast FtsY towards complex formation induced by GTP binding. J Struct Biol. 2011;173:57–66.10.1016/j.jsb.2010.07.013
  • Willard L, Ranjan A, Zhang H, et al. VADAR: a web server for quantitative evaluation of protein structure quality. Nucleic Acids Res. 2003;31:3316–3319.10.1093/nar/gkg565
  • Cristobal S, Zemla A, Fischer D, et al. A study of quality measures for protein threading models. BMC Bioinformatics. 2001;2:1–15.
  • Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30:2785–2791.10.1002/jcc.v30:16
  • Neudert G, Klebe G. DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes. J Chem Inf Model. 2011;51:2731–2745.10.1021/ci200274q
  • Vanommeslaeghe K, Hatcher E, Acharya C, et al. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010;31:671–690.
  • Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins. 2003;52:80–87.10.1002/(ISSN)1097-0134
  • Devika NT, Amresh P, Hassan MI, et al. Molecular modeling and simulation of the human eNOS reductase domain, an enzyme involved in the release of vascular nitric oxide. J Mol Model. 2014;20:213.10.1007/s00894-014-2470-7
  • Khan FI, Aamir M, Wei DQ, et al. Molecular mechanism of Ras-related protein Rab-5A and effect of mutations in the catalytically active phosphate-binding loop. J Biomol Struct Dyn. 2017;35:105–118.10.1080/07391102.2015.1134346
  • Khan FI, Wei DQ, Gu KR, et al. Current updates on computer aided protein modeling and designing. Int J Biol Macromol. 2016;85:48–62.10.1016/j.ijbiomac.2015.12.072
  • Kumari S, Idrees D, Mishra CB, et al. Design and synthesis of a novel class of carbonic anhydrase-IX inhibitor 1-(3-(phenyl/4-fluorophenyl)-7-imino-3H-[1,2,3]triazolo[4,5d]pyrimidin 6(7H)yl)urea. J Mol Graph Model. 2016;64:101–109.10.1016/j.jmgm.2016.01.006
  • Pronk S, Pall S, Schulz R, et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013;29:845–854.10.1093/bioinformatics/btt055
  • Oostenbrink C, Villa A, Mark AE, et al. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem. 2004;25:1656–1676.10.1002/(ISSN)1096-987X
  • Schüttelkopf AW, van Aalten DM. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr. 2004;60:1355–1363.10.1107/S0907444904011679
  • Frisch MJ, Trucks GW, Schlegel HB, et al. Gaussian 09. Wallingford, CT: Gaussian, Inc.; 2009.
  • Zielkiewicz J. Structural properties of water: comparison of the SPC, SPCE, TIP4P, and TIP5P models of water. J. Chem. Phys. 2005;123:104501.10.1063/1.2018637
  • Khan FI, Nizami B, Anwer R, et al. Structure prediction and functional analyses of a thermostable lipase obtained from Shewanella putrefaciens. J Biomol Struct Dyn. 2017;35:2123–2135.
  • Naz F, Shahbaaz M, Bisetty K, et al. Designing new kinase inhibitor derivatives as therapeutics against common complex diseases: structural basis of microtubule affinity-regulating kinase 4 (MARK4) inhibition. OMICS. 2015;19:700–711.10.1089/omi.2015.0111
  • Naz H, Shahbaaz M, Haque MA, et al. Urea-induced denaturation of human calcium/calmodulin-dependent protein kinase IV: a combined spectroscopic and MD simulation studies. J Biomol Struct Dyn. 2017;35:463–475.10.1080/07391102.2016.1150203
  • Kumari R, Kumar R, Lynn A. g_mmpbsa – a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model. 2014;54:1951–1962.10.1021/ci500020 m
  • Eathiraj S, Pan X, Ritacco CJ, et al. Structural basis of family-wide Rab GTPase recognition by rabenosyn-5. Nature. 2005;436:415–419.10.1038/nature03798
  • Simpson JC, Griffiths G, Wessling-Resnick M, et al. A role for the small GTPase Rab21 in the early endocytic pathway. J Cell Sci. 2004;117:6297–6311.10.1242/jcs.01560
  • Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Engineering. 1995;8:127–134.10.1093/protein/8.2.127
  • Naz F, Shahbaaz M, Khan S, et al. PKR-inhibitor binds efficiently with human microtubule affinity-regulating kinase 4. J Mol Graph Model. 2015;62:245–252.10.1016/j.jmgm.2015.10.009
  • Naz H, Shahbaaz M, Bisetty K, et al. Effect of pH on the structure, function, and stability of human calcium/calmodulin-dependent protein kinase IV: combined spectroscopic and MD simulation studies. Biochem. Cell Biol. 2016;94:221–228.
  • Shahbaaz M, Rahman S, Khan P, et al. Classification and structural analyses of mutational landscapes in hemochromatosis factor E protein: a protein defective in the hereditary hemochromatosis. Gene Reports. 2017;6:93–102.10.1016/j.genrep.2016.12.007
  • Hassan I, Ahmad F. Structural diversity of class I MHC-like molecules and its implications in binding specificities. Adv Protein Chem Struct Biol. 2011;83:223–270.10.1016/B978-0-12-381262-9.00006-9
  • Hassan MI, Aijaz A, Ahmad F. Structural and functional analysis of human prostatic acid phosphatase. Expert Rev Anticancer Ther. 2010;10:1055–1068.10.1586/era.10.46
  • Hassan MI, Saxena A, Ahmad F. Structure and function of von Willebrand factor. Blood Coagul Fibrinolysis. 2012;23:11–22.10.1097/MBC.0b013e32834cb35d
  • Hassan MI, Toor A, Ahmad F. Progastriscin: structure, function, and its role in tumor progression. J Mol Cell Biol. 2010;2:118–127.10.1093/jmcb/mjq001
  • Hassan MI, Waheed A, Grubb JH, et al. High resolution crystal structure of human beta-glucuronidase reveals structural basis of lysosome targeting. PLoS One. 2013;8:e79687.10.1371/journal.pone.0079687
  • Naiyer A, Hassan MI, Islam A, et al. Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques. J Biomol Struct Dyn. 2015;33:2267–2284.10.1080/07391102.2014.999354
  • Shahbaaz M, Bisetty K, Ahmad F, et al. Towards new drug targets? Function prediction of putative proteins of Neisseria meningitidis MC58 and their virulence characterization. OMICS. 2015;19:416–434.10.1089/omi.2015.0032
  • Shahbaaz M, Bisetty K, Ahmad F, et al. In silico approaches for the identification of virulence candidates amongst hypothetical proteins of Mycoplasma pneumoniae 309. Comp. Biol. Chem. 2015; 59(Part A):67–80.10.1016/j.compbiolchem.2015.09.007
  • Kamal MZ, Mohammad TAS, Krishnamoorthy G, et al. Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant. PLoS One. 2012;7:e35188.10.1371/journal.pone.0035188
  • Marsh JA, Teichmann SA. Relative solvent accessible surface area predicts protein conformational changes upon binding. Structure. 2011;19:859–867.10.1016/j.str.2011.03.010
  • Ali SA, Hassan MI, Islam A, et al. A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states. Curr Protein Pept Sci. 2014;15:456–476.10.2174/1389203715666140327114232
  • Delprato A, Lambright DG. Structural basis for Rab GTPase activation by VPS9 domain exchange factors. Nat. Struct. Mol. Biol. 2007;14:406–412.10.1038/nsmb1232

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