Flexible fitting to cryo-electron microscopy maps with coarse-grained elastic network models

References

• Chiu W, Baker ML, Jiang W, et al. Electron cryomicroscopy of biological machines at subnanometer resolution. Structure. 2005;13:363–372 . [cited 2005 Mar 16].10.1016/j.str.2004.12.016
   PubMed Web of Science ®Google Scholar
• Fabiola F, Chapman MS. Fitting of high-resolution structures into electron microscopy reconstruction images. Structure. 2005;13:389–400 . [cited 2005 Mar 16].10.1016/j.str.2005.01.007
   PubMed Web of Science ®Google Scholar
• Lindert S, Stewart PL, Meiler J. Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr Opin Struct Biol. 2009;19:218–225 . [cited 2009 Apr 3].10.1016/j.sbi.2009.02.010
   PubMed Web of Science ®Google Scholar
• Esquivel-Rodriguez J, Kihara D. Computational methods for constructing protein structure models from 3D electron microscopy maps. J Struct Biol. 2013;184:93–102 . [cited 2013 Jun 26].10.1016/j.jsb.2013.06.008
   PubMed Web of Science ®Google Scholar
• Wriggers W, Birmanns S. Using situs for flexible and rigid-body fitting of multiresolution single-molecule data. J Struct Biol. 2001;133:193–202 . [cited 2001 Jul 27].10.1006/jsbi.2000.4350
   PubMed Web of Science ®Google Scholar
• Noda K, Nakamura M, Nishida R, et al. Atomic model construction of protein complexes from electron micrographs and visualization of their 3D structure using a virtual reality system. J Plasma Phys. 2006;72:1037–1040.10.1017/S0022377806005174
   Web of Science ®Google Scholar
• Caulfield TR, Harvey SC. Conformational fitting of atomic models to cryogenic-electron microscopy maps using Maxwell’s demon molecular dynamics. Biophys J. 2007:368A–A.
   Web of Science ®Google Scholar
• Trabuco LG, Villa E, Mitra K, et al. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure. 2008;16:673–683.10.1016/j.str.2008.03.005
   PubMed Web of Science ®Google Scholar
• Orzechowski M, Tama F. Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations. Biophys J. 2008;95:5692–5705 . [cited 2008 Oct 14].10.1529/biophysj.108.139451
   PubMed Web of Science ®Google Scholar
• Hsin J, Gumbart J, Trabuco LG, et al. Protein-induced membrane curvature investigated through molecular dynamics flexible fitting. Biophys J. 2009;97:321–329 . [cited 2009 Jul 8].10.1016/j.bpj.2009.04.031
   PubMed Web of Science ®Google Scholar
• Trabuco LG, Villa E, Schreiner E, et al. Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods. 2009;49:174–180.10.1016/j.ymeth.2009.04.005
   PubMed Web of Science ®Google Scholar
• Chan KY, Gumbart J, McGreevy R, et al. Symmetry-restrained flexible fitting for symmetric EM maps. Structure. 2011;19:1211–1218 . [cited 2011 Sep 07].10.1016/j.str.2011.07.017
   PubMed Web of Science ®Google Scholar
• Trabuco LG, Schreiner E, Gumbart J, et al. Applications of the molecular dynamics flexible fitting method. J Struct Biol. 2011;173:420–427 . [cited 2010 Oct 12].10.1016/j.jsb.2010.09.024
   PubMed Web of Science ®Google Scholar
• Chan KY, Trabuco LG, Schreiner E, et al. Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method. Biopolymers. 2012;97:678–686 . [cited 2012 Jun 15].10.1002/bip.22042
   PubMed Web of Science ®Google Scholar
• Maragliano L, Fischer A, Vanden-Eijnden E, et al. String method in collective variables: minimum free energy paths and isocommittor surfaces. J Chem Phys. 2006;125:024106 . [cited 2006 Jun 20].10.1063/1.2212942
   PubMed Web of Science ®Google Scholar
• Maragliano L, Vanden-Eijnden E. Single-sweep methods for free energy calculations. J Chem Phys. 2008;128:184110 . [cited 2008 Jun 06].10.1063/1.2907241
   PubMed Web of Science ®Google Scholar
• Vashisth H, Skiniotis G, Brooks CL 3rd. Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps. J Phys Chem B. 2013;117:3738–3746 . [cited 2013 Mar 20].10.1021/jp3126297
   PubMed Web of Science ®Google Scholar
• Wu X, Damjanovic A, Brooks BR. Efficient and unbiased sampling of biomolecular systems in the canonical ensemble: a review of self-guided langevin dynamics. Adv Chem Phys. 2012;150:255–326 . [cited 2012 Jan 31].
   PubMed Web of Science ®Google Scholar
• Wu X, Subramaniam S, Case DA, et al. Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps. J Struct Biol. 2013;183:429–440 . [cited 2013 Jul 24].10.1016/j.jsb.2013.07.006
   PubMed Web of Science ®Google Scholar
• Tama F, Miyashita O, Brooks CL. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J Mol Biol. 2004;337:985–999.10.1016/j.jmb.2004.01.048
   PubMed Web of Science ®Google Scholar
• Tama F, Miyashita O, Brooks CL 3rd. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J Struct Biol. 2004;147:315–326 . [cited 2004 Sep 29].10.1016/j.jsb.2004.03.002
   PubMed Web of Science ®Google Scholar
• Delarue M, Dumas P. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc Nat Acad Sci. 2004;101:6957–6962 . [cited 2004 Apr 21].10.1073/pnas.0400301101
   PubMed Web of Science ®Google Scholar
• Hinsen K, Reuter N, Navaza J, et al. Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophys J. 2005;88:818–827 . [cited 2004 Nov 16].10.1529/biophysj.104.050716
   PubMed Web of Science ®Google Scholar
• Suhre K, Navaza JJ, Sanejouand YH. NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps. Acta Crystallogr Sect D Biol Crystallogr. 2006;62:1098–1100 . [cited 2006 Aug 25].10.1107/S090744490602244X
   PubMedGoogle Scholar
• Schroder GF, Brunger AT, Levitt M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure. 2007;15:1630–1641 . [cited 2007 Dec 13].10.1016/j.str.2007.09.021
   PubMed Web of Science ®Google Scholar
• Zheng W. Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization. Biophys J. 2011;100:478–488 . [cited 2011 Jan 20].10.1016/j.bpj.2010.12.3680
   PubMedGoogle Scholar
• Lopez-Blanco JR, Chacon P. iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates. J Struct Biol. 2013;184:261–270 . [cited 2013 Sep 04].10.1016/j.jsb.2013.08.010
   PubMed Web of Science ®Google Scholar
• Brooks B, Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Nat Acad Sci. 1983;80:6571–6575 . [cited 1983 Nov 01].10.1073/pnas.80.21.6571
   PubMed Web of Science ®Google Scholar
• Go N, Noguti T, Nishikawa T. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Nat Acad Sci. 1983;80:3696–3700 . [cited 1983 Jun 01].10.1073/pnas.80.12.3696
   PubMed Web of Science ®Google Scholar
• Tirion MM. Large amplitude elastic motions in proteins from a single-parameter. Phys Rev Lett. 1996;77:1905–1908 . [cited 1996 Aug 26].10.1103/PhysRevLett.77.1905
   PubMed Web of Science ®Google Scholar
• Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des. 1997;2:173–181 . [cited 1997 Jan 01].10.1016/S1359-0278(97)00024-2
   PubMedGoogle Scholar
• Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng Des Sel. 2001;14:1–6.10.1093/protein/14.1.1
   Google Scholar
• Tama F, Gadea FX, Marques O, et al. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins Struct Funct Genet. 2000;41:1–7.10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Humphrey W, Dalke A, Schulten K. VMD - Visual Molecular Dynamics. J Molec Graphics. 1996;14:33–38.
   PubMedGoogle Scholar
• Braig K, Adams PD, Brunger AT. Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution. Nat Struct Mol Biol. 1995;2:1083–1094 . [cited 1995 Dec 01].10.1038/nsb1295-1083
   Google Scholar
• Clare DK, Bakkes PJ, van Heerikhuizen H, et al. An expanded protein folding cage in the GroEL–gp31 complex. J Mol Biol. 2006;358:905–911 . [cited 2006 Mar 22].10.1016/j.jmb.2006.02.033
   PubMed Web of Science ®Google Scholar
• Ludtke SJ, Jakana J, Song JL, et al. A 11.5 A single particle reconstruction of GroEL using EMAN. J Mol Biol. 2001;314:253–262 . [cited 2001 Nov 24].10.1006/jmbi.2001.5133
   PubMed Web of Science ®Google Scholar
• Clare DK, Bakkes PJ, van Heerikhuizen H, et al. Chaperonin complex with a newly folded protein encapsulated in the folding chamber. Nature. 2009;457:107–110 . [cited 2009 Jan 06].10.1038/nature07479
   PubMed Web of Science ®Google Scholar
• Li D, Liu MS, Ji B. Mapping the dynamics landscape of conformational transitions in enzyme: the adenylate kinase case. Biophys J. 2015;109:647–660.10.1016/j.bpj.2015.06.059
   PubMed Web of Science ®Google Scholar
• Zheng W, Tekpinar M. High-resolution modeling of protein structures based on flexible fitting of low-resolution structural data. Advan Protein Chem Struct Biol. 2014;96:267–284.10.1016/bs.apcsb.2014.06.004
   PubMed Web of Science ®Google Scholar
• Formoso E, Limongelli V, Parrinello M. Energetics and structural characterization of the large-scale functional motion of adenylate kinase. Sci Rep. 2015;5:31366.10.1038/srep08425
   Web of Science ®Google Scholar
• Ahmed A, Tama F. Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data. J Struct Biol. 2013;182:67–77 . [cited 2013 Feb 19].10.1016/j.jsb.2013.02.002
   PubMed Web of Science ®Google Scholar
• Xu Z, Horwich AL, Sigler PB. The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature. 1997;388:741–750 . [cited 1997 Aug 21].10.1038/41944
   PubMed Web of Science ®Google Scholar
• Hayward S, Berendsen HJ. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins Struct Funct Genet. 1998;30:144–154 . [cited 1998 Mar 07].10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Hayward S, Lee RA. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model. 2002;21:181–183.10.1016/S1093-3263(02)00140-7
   PubMed Web of Science ®Google Scholar
• Miyashita O, Kobayashi C, Mori T, et al. Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations. J Comput Chem. 2017;38:1447–1461.10.1002/jcc.v38.16
   PubMed Web of Science ®Google Scholar
• Singharoy A, Teo I, McGreevy R, et al. Molecular dynamics-based refinement and validation for sub-5 A cryo-electron microscopy maps. Elife. 2016;5:e16105.
   PubMed Web of Science ®Google Scholar
• Ahmed A, Whitford PC, Sanbonmatsu KY, et al. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data. J Struct Biol. 2012;177:561–570 . [cited 2011 Oct 25]. .10.1016/j.jsb.2011.10.002
   PubMed Web of Science ®Google Scholar