메뉴 건너뛰기




Volumn 10, Issue 1, 2016, Pages 161-173

Coarse-Graining of Volumes for Modeling of Structure and Dynamics in Electron Microscopy: Algorithm to Automatically Control Accuracy of Approximation

Author keywords

Coarse graining; dynamics; electron microscopy (EM); Gaussian functions; macromolecular complexes; modeling; radial basis functions; structure

Indexed keywords

ALGORITHMS; DYNAMICS; ELECTRON MICROSCOPY; HIGH RESOLUTION TRANSMISSION ELECTRON MICROSCOPY; MACROMOLECULES; MODELS; RADIAL BASIS FUNCTION NETWORKS; STRUCTURE (COMPOSITION); TRANSMISSION ELECTRON MICROSCOPY; WORLD WIDE WEB;

EID: 84962793736     PISSN: 19324553     EISSN: None     Source Type: Journal    
DOI: 10.1109/JSTSP.2015.2489186     Document Type: Article
Times cited : (32)

References (34)
  • 1
    • 0344983360 scopus 로고    scopus 로고
    • FEMME database: Topologic and geometric information of macromolecules
    • Oct.-Nov.
    • N. Jimenez-Lozano, M. Chagoyen, J. Cuenca-Alba, and J. M. Carazo, "FEMME database: Topologic and geometric information of macromolecules," J. Struct. Biol., vol. 144, pp. 104-113, Oct.-Nov. 2003.
    • (2003) J. Struct. Biol. , vol.144 , pp. 104-113
    • Jimenez-Lozano, N.1    Chagoyen, M.2    Cuenca-Alba, J.3    Carazo, J.M.4
  • 2
    • 0037436340 scopus 로고    scopus 로고
    • Mega-Dalton biomolecular motion captured from electron microscopy reconstructions
    • Feb.
    • P. Chacon, F. Tama, and W. Wriggers, "Mega-Dalton biomolecular motion captured from electron microscopy reconstructions," J. Mol. Biol., vol. 326, pp. 485-492, Feb. 2003.
    • (2003) J. Mol. Biol. , vol.326 , pp. 485-492
    • Chacon, P.1    Tama, F.2    Wriggers, W.3
  • 3
    • 0037173062 scopus 로고    scopus 로고
    • How to describe protein motion without amino acid sequence and atomic coordinates
    • Jun.
    • 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. Nat. Acad. Sci., vol. 99, pp. 8620-8625, Jun. 2002.
    • (2002) Proc. Nat. Acad. Sci. , vol.99 , pp. 8620-8625
    • Ming, D.1    Kong, Y.2    Lambert, M.A.3    Huang, Z.4    Ma, J.5
  • 4
    • 0034782444 scopus 로고    scopus 로고
    • HYDROMIC: Prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images
    • Oct.
    • J. Garcia de la Torre, O. Llorca, J. L. Carrascosa, and J. M. Valpuesta, "HYDROMIC: Prediction of hydrodynamic properties of rigid macromolecular structures obtained from electron microscopy images," Eur. Biophys. J., vol. 30, pp. 457-462, Oct. 2001.
    • (2001) Eur. Biophys. J. , vol.30 , pp. 457-462
    • Garcia de la Torre, J.1    Llorca, O.2    Carrascosa, J.L.3    Valpuesta, J.M.4
  • 5
    • 33845302057 scopus 로고    scopus 로고
    • Multi-resolution anchor-point registration of biomolecular assemblies and their components
    • Jan.
    • S. Birmanns and W. Wriggers, "Multi-resolution anchor-point registration of biomolecular assemblies and their components," J. Struct. Biol., vol. 157, pp. 271-280, Jan. 2007.
    • (2007) J. Struct. Biol. , vol.157 , pp. 271-280
    • Birmanns, S.1    Wriggers, W.2
  • 6
    • 0032545184 scopus 로고    scopus 로고
    • Selforganizing neural networks bridge the biomolecular resolution gap
    • Dec.
    • W. Wriggers, R. A. Milligan, K. Schulten, and J. A. McCammon, "Selforganizing neural networks bridge the biomolecular resolution gap," J. Mol. Biol., vol. 284, pp. 1247-1254, Dec. 1998.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1247-1254
    • Wriggers, W.1    Milligan, R.A.2    Schulten, K.3    McCammon, J.A.4
  • 7
    • 0035996965 scopus 로고    scopus 로고
    • Modeling shape and topology of low-resolution density maps of biological macromolecules
    • Aug.
    • P. A. De-Alarcon, A. Pascual-Montano, A. Gupta, and J. M. Carazo, "Modeling shape and topology of low-resolution density maps of biological macromolecules," Biophys. J., vol. 83, pp. 619-632, Aug. 2002.
    • (2002) Biophys. J. , vol.83 , pp. 619-632
    • De-Alarcon, P.A.1    Pascual-Montano, A.2    Gupta, A.3    Carazo, J.M.4
  • 8
    • 58149293674 scopus 로고    scopus 로고
    • Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a Gaussian mixture model
    • Nov.
    • T. Kawabata, "Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a Gaussian mixture model," Biophys. J., vol. 95, pp. 4643-4658, Nov. 2008.
    • (2008) Biophys. J. , vol.95 , pp. 4643-4658
    • Kawabata, T.1
  • 9
    • 0347753596 scopus 로고    scopus 로고
    • Mixed levels of coarsegraining of large proteins using elastic network model succeeds in extracting the slowest motions
    • O. Kurkcuoglu, R. L. Jernigan, and P. Doruker, "Mixed levels of coarsegraining of large proteins using elastic network model succeeds in extracting the slowest motions," Polymer, vol. 45, pp. 649-657, 2004.
    • (2004) Polymer , vol.45 , pp. 649-657
    • Kurkcuoglu, O.1    Jernigan, R.L.2    Doruker, P.3
  • 10
    • 0036382958 scopus 로고    scopus 로고
    • Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory
    • Aug.
    • 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., vol. 321, pp. 297-305, Aug. 2002.
    • (2002) J. Mol. Biol. , vol.321 , pp. 297-305
    • Tama, F.1    Wriggers, W.2    Brooks, C.L.3
  • 11
    • 84896727281 scopus 로고    scopus 로고
    • Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes
    • Mar.
    • Q. Jin, C. O. Sorzano, J. M. de la Rosa-Trevin, J. R. Bilbao-Castro, R. Nunez-Ramirez, O. Llorca, F. Tama, and S. Jonic, "Iterative elastic 3D-to-2D alignment method using normal modes for studying structural dynamics of large macromolecular complexes," Structure, vol. 22, pp. 496-506, Mar. 2014.
    • (2014) Structure , vol.22 , pp. 496-506
    • Jin, Q.1    Sorzano, C.O.2    De La Rosa-Trevin, J.M.3    Bilbao-Castro, J.R.4    Nunez-Ramirez, R.5    Llorca, O.6    Tama, F.7    Jonic, S.8
  • 12
    • 79957762477 scopus 로고    scopus 로고
    • Nonuniform sampling and recovery of multidimensional bandlimited functions by Gaussian radial-basis functions
    • B. A. Bailey, T. Schlumprecht, and N. Sivakumar, "Nonuniform sampling and recovery of multidimensional bandlimited functions by Gaussian radial-basis functions," J. Fourier Anal. Applicat., vol. 17, pp. 519-533, 2011.
    • (2011) J. Fourier Anal. Applicat. , vol.17 , pp. 519-533
    • Bailey, B.A.1    Schlumprecht, T.2    Sivakumar, N.3
  • 14
    • 84927636805 scopus 로고    scopus 로고
    • Hybrid electron microscopy normal mode analysis graphical interface and protocol
    • Nov.
    • C. O. Sorzano, J. M. de la Rosa-Trevin, F. Tama, and S. Jonic, "Hybrid electron microscopy normal mode analysis graphical interface and protocol," J. Struct. Biol., vol. 188, pp. 134-141, Nov. 2014.
    • (2014) J. Struct. Biol. , vol.188 , pp. 134-141
    • Sorzano, C.O.1    De La Rosa-Trevin, J.M.2    Tama, F.3    Jonic, S.4
  • 15
    • 0028748949 scopus 로고
    • Growing cell structures-A self-organizing network for unsupervised and supervised learning
    • B. Fritzke, "Growing cell structures-A self-organizing network for unsupervised and supervised learning," Neural Netw., vol. 7, pp. 1441-1460, 1994.
    • (1994) Neural Netw. , vol.7 , pp. 1441-1460
    • Fritzke, B.1
  • 17
    • 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 Crystallographica Sec. A, vol. 52, pp. 257-276, 1996.
    • (1996) Acta Crystallographica Sec. A , vol.52 , pp. 257-276
    • Peng, L.M.1    Ren, G.2    Dudarev, S.L.3    Whelan, M.J.4
  • 20
    • 80051471655 scopus 로고    scopus 로고
    • Simulation of transmission electron microscope images of biological specimens
    • Sep.
    • H. Rullgard, L. G. Ofverstedt, S. Masich, B. Daneholt, and O. Oktem, "Simulation of transmission electron microscope images of biological specimens," J. Microsc., vol. 243, pp. 234-256, Sep. 2011.
    • (2011) J. Microsc. , vol.243 , pp. 234-256
    • Rullgard, H.1    Ofverstedt, L.G.2    Masich, S.3    Daneholt, B.4    Oktem, O.5
  • 21
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Aug.
    • M. M. Tirion, "Large amplitude elastic motions in proteins from a single-parameter, atomic analysis," Phys. Rev. Lett., vol. 77, pp. 1905-1908, Aug. 1996.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 23
    • 69249187438 scopus 로고    scopus 로고
    • Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion
    • Aug.
    • J. N. Stember and W. Wriggers, "Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion," J. Chem. Phys., vol. 131, p. 074112, Aug. 2009.
    • (2009) J. Chem. Phys. , vol.131 , pp. 074112
    • Stember, J.N.1    Wriggers, W.2
  • 24
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
    • Feb.
    • C. W. Muller, G. J. Schlauderer, J. Reinstein, and G. E. Schulz, "Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding," Structure, vol. 4, pp. 147-156, Feb. 1996.
    • (1996) Structure , vol.4 , pp. 147-156
    • Muller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4
  • 25
    • 0026544877 scopus 로고
    • Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state
    • Mar.
    • C. W. Muller and G. E. Schulz, "Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state," J. Mol. Biol., vol. 224, pp. 159-177, Mar. 1992.
    • (1992) J. Mol. Biol. , vol.224 , pp. 159-177
    • Muller, C.W.1    Schulz, G.E.2
  • 26
    • 2342518038 scopus 로고    scopus 로고
    • On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
    • May
    • M. Delarue and P. Dumas, "On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models," Proc. Nat. Acad. Sci. USA, vol. 101, pp. 6957-6962, May 2004.
    • (2004) Proc. Nat. Acad. Sci. USA , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 27
    • 33748351384 scopus 로고    scopus 로고
    • NORMA: A tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps
    • Sep.
    • 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., vol. 62, Sep. 2006, 1098-100.
    • (2006) Acta Crystallogr D Biol. Crystallogr. , vol.62 , pp. 1098-1100
    • Suhre, K.1    Navaza, J.2    Sanejouand, Y.H.3
  • 28
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Jan.
    • F. Tama and Y. H. Sanejouand, "Conformational change of proteins arising from normal mode calculations," Protein Eng., vol. 14, pp. 1-6, Jan. 2001.
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 29
    • 4344685227 scopus 로고    scopus 로고
    • Global ribosome motions revealed with elastic network model
    • Sep.
    • Y. Wang, A. J. Rader, I. Bahar, and R. L. Jernigan, "Global ribosome motions revealed with elastic network model," J. Struct. Biol., vol. 147, pp. 302-314, Sep. 2004.
    • (2004) J. Struct. Biol. , vol.147 , pp. 302-314
    • Wang, Y.1    Rader, A.J.2    Bahar, I.3    Jernigan, R.L.4
  • 30
    • 69249112231 scopus 로고    scopus 로고
    • Structures of the ribosome in intermediate states of ratcheting
    • Aug.
    • W. Zhang, J. A. Dunkle, and J. H. Cate, "Structures of the ribosome in intermediate states of ratcheting," Science, vol. 325, pp. 1014-1017, Aug. 2009.
    • (2009) Science , vol.325 , pp. 1014-1017
    • Zhang, W.1    Dunkle, J.A.2    Cate, J.H.3
  • 31
    • 0032780181 scopus 로고    scopus 로고
    • Situs: A package for docking crystal structures into low-resolution maps from electron microscopy
    • Apr.-May
    • 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., vol. 125, pp. 185-195, Apr.-May 1999.
    • (1999) J. Struct. Biol. , vol.125 , pp. 185-195
    • Wriggers, W.1    Milligan, R.A.2    McCammon, J.A.3
  • 32
    • 79953216748 scopus 로고    scopus 로고
    • Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation
    • Mar.
    • 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. Nat. Acad. Sci. USA, vol. 108, pp. 4817-4821, Mar. 2011.
    • (2011) Proc. Nat. Acad. Sci. USA , vol.108 , pp. 4817-4821
    • Fu, J.1    Munro, J.B.2    Blanchard, S.C.3    Frank, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.