메뉴 건너뛰기




Volumn 22, Issue 3, 2014, Pages 496-506

Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; DNA DIRECTED DNA POLYMERASE BETA; MACROMOLECULE;

EID: 84896727281     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.01.004     Document Type: Article
Times cited : (100)

References (38)
  • 3
    • 1242351230 scopus 로고    scopus 로고
    • Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis
    • J. Brink, S.J. Ludtke, Y. Kong, S.J. Wakil, J. Ma, and W. Chiu Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis Structure 12 2004 185 191
    • (2004) Structure , vol.12 , pp. 185-191
    • Brink, J.1    Ludtke, S.J.2    Kong, Y.3    Wakil, S.J.4    Ma, J.5    Chiu, W.6
  • 4
    • 0000216012 scopus 로고
    • Collective protein dynamics and nuclear spin relaxation
    • R. Bruschweiler Collective protein dynamics and nuclear spin relaxation J. Chem. Phys. 102 1995 3396 3403
    • (1995) J. Chem. Phys. , vol.102 , pp. 3396-3403
    • Bruschweiler, R.1
  • 5
    • 0037436340 scopus 로고    scopus 로고
    • Mega-Dalton biomolecular motion captured from electron microscopy reconstructions
    • P. Chacón, F. Tama, and W. Wriggers Mega-Dalton biomolecular motion captured from electron microscopy reconstructions J. Mol. Biol. 326 2003 485 492
    • (2003) J. Mol. Biol. , vol.326 , pp. 485-492
    • Chacón, P.1    Tama, F.2    Wriggers, W.3
  • 6
    • 2342518038 scopus 로고    scopus 로고
    • On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
    • M. Delarue, and P. Dumas On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models Proc. Natl. Acad. Sci. USA 101 2004 6957 6962
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 7
    • 41649087227 scopus 로고    scopus 로고
    • Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections
    • N. Elad, D.K. Clare, H.R. Saibil, and E.V. Orlova Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections J. Struct. Biol. 162 2008 108 120
    • (2008) J. Struct. Biol. , vol.162 , pp. 108-120
    • Elad, N.1    Clare, D.K.2    Saibil, H.R.3    Orlova, E.V.4
  • 8
    • 79953216748 scopus 로고    scopus 로고
    • Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation
    • J. Fu, J.B. Munro, S.C. Blanchard, and J. Frank Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation Proc. Natl. Acad. Sci. USA 108 2011 4817 4821
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 4817-4821
    • Fu, J.1    Munro, J.B.2    Blanchard, S.C.3    Frank, J.4
  • 9
    • 33644838451 scopus 로고    scopus 로고
    • Cryo-electron microscopy studies of human TFIID: Conformational breathing in the integration of gene regulatory cues
    • P. Grob, M.J. Cruse, C. Inouye, M. Peris, P.A. Penczek, R. Tjian, and E. Nogales Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues Structure 14 2006 511 520
    • (2006) Structure , vol.14 , pp. 511-520
    • Grob, P.1    Cruse, M.J.2    Inouye, C.3    Peris, M.4    Penczek, P.A.5    Tjian, R.6    Nogales, E.7
  • 10
    • 70350704561 scopus 로고    scopus 로고
    • Structural insights into yeast DNA polymerase delta by small angle X-ray scattering
    • R. Jain, M. Hammel, R.E. Johnson, L. Prakash, S. Prakash, and A.K. Aggarwal Structural insights into yeast DNA polymerase delta by small angle X-ray scattering J. Mol. Biol. 394 2009 377 382
    • (2009) J. Mol. Biol. , vol.394 , pp. 377-382
    • Jain, R.1    Hammel, M.2    Johnson, R.E.3    Prakash, L.4    Prakash, S.5    Aggarwal, A.K.6
  • 12
    • 67650409702 scopus 로고    scopus 로고
    • 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases
    • S. Klinge, R. Núñez-Ramírez, O. Llorca, and L. Pellegrini 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases EMBO J. 28 2009 1978 1987
    • (2009) EMBO J. , vol.28 , pp. 1978-1987
    • Klinge, S.1    Núñez-Ramírez, R.2    Llorca, O.3    Pellegrini, L.4
  • 13
    • 0020475829 scopus 로고
    • Divalent ion-dependent reversible swelling of tomato bushy stunt virus and organization of the expanded virion
    • J. Krüse, K.M. Krüse, J. Witz, C. Chauvin, B. Jacrot, and A. Tardieu Divalent ion-dependent reversible swelling of tomato bushy stunt virus and organization of the expanded virion J. Mol. Biol. 162 1982 393 414
    • (1982) J. Mol. Biol. , vol.162 , pp. 393-414
    • Krüse, J.1    Krüse, K.M.2    Witz, J.3    Chauvin, C.4    Jacrot, B.5    Tardieu, A.6
  • 14
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • D. Ming, Y. Kong, M.A. Lambert, Z. Huang, and J. Ma How to describe protein motion without amino acid sequence and atomic coordinates Proc. Natl. Acad. Sci. USA 99 2002 8620 8625
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.2    Lambert, M.A.3    Huang, Z.4    Ma, J.5
  • 17
    • 33646042904 scopus 로고    scopus 로고
    • A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation
    • P.A. Penczek, J. Frank, and C.M. Spahn A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation J. Struct. Biol. 154 2006 184 194
    • (2006) J. Struct. Biol. , vol.154 , pp. 184-194
    • Penczek, P.A.1    Frank, J.2    Spahn, C.M.3
  • 18
    • 0000416054 scopus 로고    scopus 로고
    • Robust parameterization of elastic and absorptive electron atomic scattering factors
    • L.M. Peng, G. Ren, S.L. Dudarev, and M.J. Whelan Robust parameterization of elastic and absorptive electron atomic scattering factors Acta Crystallogr. A52 1996 257 276
    • (1996) Acta Crystallogr. , vol.52 A , pp. 257-276
    • Peng, L.M.1    Ren, G.2    Dudarev, S.L.3    Whelan, M.J.4
  • 19
    • 0041711007 scopus 로고    scopus 로고
    • UOBYQA: Unconstrained optimization by quadratic approximation
    • M.J.D. Powell UOBYQA: unconstrained optimization by quadratic approximation Math. Program. 92 2002 555 582
    • (2002) Math. Program. , vol.92 , pp. 555-582
    • Powell, M.J.D.1
  • 20
    • 0000640156 scopus 로고
    • Structure of the expanded state of tomato bushy stunt virus
    • I.K. Robinson, and S.C. Harrison Structure of the expanded state of tomato bushy stunt virus Nature 297 1982 563 568
    • (1982) Nature , vol.297 , pp. 563-568
    • Robinson, I.K.1    Harrison, S.C.2
  • 25
    • 3242875210 scopus 로고    scopus 로고
    • ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    • WEB SERVER ISSUE
    • K. Suhre, and Y.H. Sanejouand ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Nucleic Acids Res. 32 Web Server issue 2004 W610 W614
    • (2004) Nucleic Acids Res. , vol.32
    • Suhre, K.1    Sanejouand, Y.H.2
  • 26
    • 33748351384 scopus 로고    scopus 로고
    • NORMA: A tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps
    • 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
    • (2006) Acta Crystallogr. D Biol. Crystallogr. , vol.62 , pp. 1098-1100
    • Suhre, K.1    Navaza, J.2    Sanejouand, Y.H.3
  • 27
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • F. Tama, and Y.H. Sanejouand Conformational change of proteins arising from normal mode calculations Protein Eng. 14 2001 1 6
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 28
    • 9644266693 scopus 로고    scopus 로고
    • Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
    • F. Tama, and C.L. Brooks 3rd Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis J. Mol. Biol. 345 2005 299 314
    • (2005) J. Mol. Biol. , vol.345 , pp. 299-314
    • Tama, F.1    Brooks III, C.L.2
  • 29
    • 33745024278 scopus 로고    scopus 로고
    • Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
    • F. Tama, and C.L. Brooks Symmetry, form, and shape: guiding principles for robustness in macromolecular machines Annu. Rev. Biophys. Biomol. Struct. 35 2006 115 133
    • (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 115-133
    • Tama, F.1    Brooks, C.L.2
  • 30
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • F. Tama, W. Wriggers, and C.L. Brooks 3rd Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory J. Mol. Biol. 321 2002 297 305
    • (2002) J. Mol. Biol. , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks III, C.L.3
  • 31
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • F. Tama, M. Valle, J. Frank, and C.L. Brooks 3rd Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proc. Natl. Acad. Sci. USA 100 2003 9319 9323
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks III, C.L.4
  • 32
    • 1642355235 scopus 로고    scopus 로고
    • Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis
    • 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
    • (2004) J. Mol. Biol. , vol.337 , pp. 985-999
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 33
    • 4344716056 scopus 로고    scopus 로고
    • Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM
    • 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
    • (2004) J. Struct. Biol. , vol.147 , pp. 315-326
    • Tama, F.1    Miyashita, O.2    Brooks III, C.L.3
  • 34
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • M.M. Tirion Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys. Rev. Lett. 77 1996 1905 1908
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 36
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosome motions revealed with elastic network model
    • Y. Wang, A.J. Rader, I. Bahar, and R.L. Jernigan Global ribosome motions revealed with elastic network model J. Struct. Biol. 147 2004 302 314
    • (2004) J. Struct. Biol. , vol.147 , pp. 302-314
    • Wang, Y.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4
  • 37
    • 0035558423 scopus 로고    scopus 로고
    • Structural dynamics, an intrinsic property of viral capsids
    • J. Witz, and F. Brown Structural dynamics, an intrinsic property of viral capsids Arch. Virol. 146 2001 2263 2274
    • (2001) Arch. Virol. , vol.146 , pp. 2263-2274
    • Witz, J.1    Brown, F.2
  • 38
    • 69249112231 scopus 로고    scopus 로고
    • Structures of the ribosome in intermediate states of ratcheting
    • W. Zhang, J.A. Dunkle, and J.H. Cate Structures of the ribosome in intermediate states of ratcheting Science 325 2009 1014 1017
    • (2009) Science , vol.325 , pp. 1014-1017
    • Zhang, W.1    Dunkle, J.A.2    Cate, J.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.