Symmetry-restrained flexible fitting for symmetric em maps

Structure

Volumn 19, Issue 9, 2011, Pages 1211-1218

  Chan, Kwok Yan ^a,b   Gumbart, James ^a,b   McGreevy, Ryan ^b   Watermeyer, Jean M ^c   Sewell, B Trevor ^c   Schulten, Klaus ^a,b  

^a United States of America   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN; NITRILASE; PROTEIN MM CPN; UNCLASSIFIED DRUG;

ANALYTIC METHOD; ARTICLE; CONFORMATION; CRYOELECTRON MICROSCOPY; MOLECULAR DYNAMICS; MOLECULAR DYNAMICS FLEXIBLE FITTING; PRIORITY JOURNAL; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

ALGORITHMS; AMINOHYDROLASES; BACTERIAL PROTEINS; CHAPERONIN 10; CHAPERONIN 60; CRYOELECTRON MICROSCOPY; DATA INTERPRETATION, STATISTICAL; GROUP II CHAPERONINS; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION;

EID: 80052442678     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2011.07.017     Document Type: Article

References (51)

1. X. Agirrezabala, J. Lei, J.L. Brunelle, R.F. Ortiz-Meoz, R. Green, and J. Frank Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome Mol. Cell 32 2008 190 197
2. I. André, P. Bradley, C. Wang, and D. Baker Prediction of the structure of symmetrical protein assemblies Proc. Natl. Acad. Sci. USA 104 2007 17656 17661 (Pubitemid 350210890)
3. I. André, C.E.M. Strauss, D.B. Kaplan, P. Bradley, and D. Baker Emergence of symmetry in homooligomeric biological assemblies Proc. Natl. Acad. Sci. USA 105 2008 16148 16152
4. A. Anishkin, A.L. Milac, and H.R. Guy Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels Proteins 78 2010 932 949
5. T.L. Blundell, and N. Srinivasan Symmetry, stability, and dynamics of multidomain and multicomponent protein systems Proc. Natl. Acad. Sci. USA 93 1996 14243 14248 (Pubitemid 26418947)
6. M.S. Chapman Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function Acta Crystallogr. A51 1995 69 80
7. C. Chaudhry, G.W. Farr, M.J. Todd, H.S. Rye, A.T. Brunger, P.D. Adams, A.L. Horwich, and P.B. Sigler Role of the γ-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics EMBO J. 22 2003 4877 4887 (Pubitemid 37222010)
8. L.F. Chen, E. Blanc, M.S. Chapman, and K.A. Taylor Real space refinement of acto-myosin structures from sectioned muscle J. Struct. Biol. 133 2001 221 232
9. + conduction and selectivity Science 280 1998 69 77 (Pubitemid 28169082)
10. E.H. Egelman A robust algorithm for the reconstruction of helical filaments using single-particle methods Ultramicroscopy 85 2000 225 234
11. J. Frauenfeld, J. Gumbart, E.O. Sluis, S. Funes, M. Gartmann, B. Beatrix, T. Mielke, O. Berninghausen, T. Becker, K. Schulten, and R. Beckmann Cryo-EM structure of the ribosome-SecYE complex in the membrane environment Nat. Struct. Mol. Biol. 18 2011 614 621
12. H. Frauenfelder, S.G. Sligar, and P.G. Wolynes The energy landscapes and motions of proteins Science 254 1991 1598 1603 (Pubitemid 21917496)
13. D.S. Goodsell, and A.J. Olson Structural symmetry and protein function Annu. Rev. Biophys. Biomol. Struct. 29 2000 105 153 (Pubitemid 30599590)
14. H. Grubmüller, H. Heller, A. Windemuth, and K. Schulten Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions Mol. Simul. 6 1991 121 142
15. T.X. Hoang, A. Trovato, F. Seno, J.R. Banavar, and A. Maritan Geometry and symmetry presculpt the free-energy landscape of proteins Proc. Natl. Acad. Sci. USA 101 2004 7960 7964 (Pubitemid 38698036)
16. J.M. Hogle Poliovirus cell entry: common structural themes in viral cell entry pathways Annu. Rev. Microbiol. 56 2002 677 702 (Pubitemid 35217471)
17. J.M. Hogle, M. Chow, and D.J. Filman Three-dimensional structure of poliovirus at 2.9 resolution Science 229 1985 1358 1365 (Pubitemid 16222374)
18. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-28 (Pubitemid 26152973)
19. D. Jandhyala, M. Berman, P.R. Meyers, B.T. Sewell, R.C. Willson, and M.J. Benedik CynD, the cyanide dihydratase from Bacillus pumilus: gene cloning and structural studies Appl. Environ. Microbiol. 69 2003 4794 4805 (Pubitemid 36992943)
20. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
21. S.J. Ludtke, P.R. Baldwin, and W. Chiu EMAN: semiautomated software for high-resolution single-particle reconstructions J. Struct. Biol. 128 1999 82 97 (Pubitemid 30013436)
22. A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, and S. Ha All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616 (Pubitemid 128576688)
23. A.D. Mackerell Jr., M. Feig, and C.L. Brooks 3rd Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25 2004 1400 1415
24. H. Nymeyer, A.E. García, and J.N. Onuchic Folding funnels and frustration in off-lattice minimalist protein landscapes Proc. Natl. Acad. Sci. USA 95 1998 5921 5928 (Pubitemid 28248940)
25. J.H. Pereira, C.Y. Ralston, N.R. Douglas, D. Meyer, K.M. Knee, D.R. Goulet, J.A. King, J. Frydman, and P.D. Adams Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle J. Biol. Chem. 285 2010 27958 27966
26. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kalé, and K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802 (Pubitemid 43078511)
27. P. Qian, C.N. Hunter, and P.A. Bullough The 8.5 projection structure of the core RC-LH1-PufX dimer of Rhodobacter sphaeroides J. Mol. Biol. 349 2005 948 960 (Pubitemid 40779618)
28. N.A. Ranson, D.K. Clare, G.W. Farr, D. Houldershaw, A.L. Horwich, and H.R. Saibil Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes Nat. Struct. Mol. Biol. 13 2006 147 152 (Pubitemid 43214718)
29. A.M. Roseman, S. Chen, H. White, K. Braig, and H.R. Saibil The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL Cell 87 1996 241 251 (Pubitemid 26359002)
30. G.F. Schröder, A.T. Brunger, and M. Levitt Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution Structure 15 2007 1630 1641 (Pubitemid 350213409)
31. B. Seidelt, C.A. Innis, D.N. Wilson, M. Gartmann, J.-P. Armache, E. Villa, L.G. Trabuco, T. Becker, T. Mielke, and K. Schulten Structural insight into nascent polypeptide chain-mediated translational stalling Science 326 2009 1412 1415
32. K. Suhre, J. Navaza, and Y.H. Sanejouand NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps Acta Crystallogr. D Biol. Crystallogr. 62 2006 1098 1100 (Pubitemid 44337384)
33. F. Tama, O. Miyashita, and C.L. Brooks 3rd Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis J. Mol. Biol. 337 2004 985 999 (Pubitemid 38368939)
34. F. Tama, O. Miyashita, and C.L. Brooks 3rd Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM J. Struct. Biol. 147 2004 315 326 (Pubitemid 39140738)
35. R.N. Thuku, B.W. Weber, A. Varsani, and B.T. Sewell Post-translational cleavage of recombinantly expressed nitrilase from Rhodococcus rhodochrous J1 yields a stable, active helical form FEBS J. 274 2007 2099 2108 (Pubitemid 46588007)
36. R.N. Thuku, D. Brady, M.J. Benedik, and B.T. Sewell Microbial nitrilases: versatile, spiral forming, industrial enzymes J. Appl. Microbiol. 106 2009 703 727
37. M. Topf, M.L. Baker, M.A. Marti-Renom, W. Chiu, and A. Sali Refinement of protein structures by iterative comparative modeling and CryoEM density fitting J. Mol. Biol. 357 2006 1655 1668
38. L.G. Trabuco, E. Villa, K. Mitra, J. Frank, and K. Schulten Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics Structure 16 2008 673 683 (Pubitemid 351615021)
39. L.G. Trabuco, E. Villa, E. Schreiner, C.B. Harrison, and K. Schulten Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography Methods 49 2009 174 180
40. L.G. Trabuco, E. Schreiner, J. Gumbart, J. Hsin, E. Villa, and K. Schulten Applications of the molecular dynamics flexible fitting method J. Struct. Biol. 173 2011 420 427
41. M. Tuckerman, B.J. Berne, and G.J. Martyna Reversible multiple time scale molecular dynamics J. Chem. Phys. 97 1992 1990 2001
42. M. van Heel, G. Harauz, E.V. Orlova, R. Schmidt, and M. Schatz A new generation of the IMAGIC image processing system J. Struct. Biol. 116 1996 17 24 (Pubitemid 26093118)
43. N. Volkmann, D. Hanein, G. Ouyang, K.M. Trybus, D.J. DeRosier, and S. Lowey Evidence for cleft closure in actomyosin upon ADP release Nat. Struct. Biol. 7 2000 1147 1155
44. P.G. Wolynes Symmetry and the energy landscapes of biomolecules Proc. Natl. Acad. Sci. USA 93 1996 14249 14255 (Pubitemid 26418948)
45. J.D. Woodward, B.W. Weber, M.P. Scheffer, M.J. Benedik, A. Hoenger, and B.T. Sewell Helical structure of unidirectionally shadowed metal replicas of cyanide hydratase from Gloeocercospora sorghi J. Struct. Biol. 161 2008 111 119
46. W. Wriggers, and P. Chacón Modeling tricks and fitting techniques for multiresolution structures Structure 9 2001 779 788 (Pubitemid 32913496)
47. W. Wriggers, R.A. Milligan, and J.A. McCammon Situs: a package for docking crystal structures into low-resolution maps from electron microscopy J. Struct. Biol. 125 1999 185 195 (Pubitemid 29402603)
48. 7 chaperonin complex Nature 388 1997 741 750 (Pubitemid 27375147)
49. J. Zhang, M.L. Baker, G.F. Schröder, N.R. Douglas, S. Reissmann, J. Jakana, M. Dougherty, C.J. Fu, M. Levitt, and S.J. Ludtke Mechanism of folding chamber closure in a group II chaperonin Nature 463 2010 379 383
50. X. Zhang, L. Jin, Q. Fang, W.H. Hui, and Z.H. Zhou 3.3 cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry Cell 141 2010 472 482
51. J. Zhu, L. Cheng, Q. Fang, Z.H. Zhou, and B. Honig Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement J. Mol. Biol. 397 2010 835 851