메뉴 건너뛰기




Volumn 94, Issue 5, 2008, Pages 1613-1621

Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONIN;

EID: 41449099769     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.115949     Document Type: Article
Times cited : (68)

References (39)
  • 1
    • 0030272365 scopus 로고    scopus 로고
    • Low resolution meets high: Towards a resolution continuum from cells to atoms
    • Baker, T. S., and J. E. Johnson. 1996. Low resolution meets high: towards a resolution continuum from cells to atoms. Curr. Opin. Struct. Biol. 6:585-594.
    • (1996) Curr. Opin. Struct. Biol , vol.6 , pp. 585-594
    • Baker, T.S.1    Johnson, J.E.2
  • 2
    • 0033780164 scopus 로고    scopus 로고
    • Fitting atomic models into electron-microscopy maps
    • Rossmann, M. G. 2000. Fitting atomic models into electron-microscopy maps. Acta Crystallogr. D Biol. Crystallogr. 56:1341-1349.
    • (2000) Acta Crystallogr. D Biol. Crystallogr , vol.56 , pp. 1341-1349
    • Rossmann, M.G.1
  • 3
    • 14844311200 scopus 로고    scopus 로고
    • Fitting of high-resolution structures into electron microscopy reconstruction images
    • Fabiola, F., and M. S. Chapman. 2005. Fitting of high-resolution structures into electron microscopy reconstruction images. Structure. 13:389-400.
    • (2005) Structure , vol.13 , pp. 389-400
    • Fabiola, F.1    Chapman, M.S.2
  • 4
    • 0035783173 scopus 로고    scopus 로고
    • Using situs for flexible and rigid-body fitting of multiresolution single-molecule data
    • Wriggers, W., and S. Birmanns. 2001. Using situs for flexible and rigid-body fitting of multiresolution single-molecule data. J. Struct. Biol. 133:193-202.
    • (2001) J. Struct. Biol , vol.133 , pp. 193-202
    • Wriggers, W.1    Birmanns, S.2
  • 5
    • 0344120716 scopus 로고    scopus 로고
    • Low-resolution structure refinement in electron microscopy
    • Chen, J. Z., J. Furst, M. S. Chapman, and N. Grigorieff. 2003. Low-resolution structure refinement in electron microscopy. J. Struct. Biol. 144:144-151.
    • (2003) J. Struct. Biol , vol.144 , pp. 144-151
    • Chen, J.Z.1    Furst, J.2    Chapman, M.S.3    Grigorieff, N.4
  • 7
    • 1642355235 scopus 로고    scopus 로고
    • Tama, F., O. Miyashita, and C. L. Brooks 3rd. 2004. Flexible multiscale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337: 985-999.
    • Tama, F., O. Miyashita, and C. L. Brooks 3rd. 2004. Flexible multiscale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. J. Mol. Biol. 337: 985-999.
  • 8
    • 4344716056 scopus 로고    scopus 로고
    • Tama, F., O. Miyashita, and C. L. Brooks 3rd. 2004. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 147:315-326.
    • Tama, F., O. Miyashita, and C. L. Brooks 3rd. 2004. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. J. Struct. Biol. 147:315-326.
  • 9
    • 2342518038 scopus 로고    scopus 로고
    • On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models
    • Delarue, M., and P. Dumas. 2004. On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proc. Natl. Acad. Sci. USA. 101:6957-6962.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 10
    • 17044432465 scopus 로고    scopus 로고
    • Normal mode-based fitting of atomic structure into electron density maps: Application to sarcoplasmic reticulum Ca-ATPase
    • Hinsen, K., N. Reuter, J. Navaza, D. L. Stokes, and J. J. Lacapere. 2005. Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase. Biophys. J. 88: 818-827.
    • (2005) Biophys. J , vol.88 , pp. 818-827
    • Hinsen, K.1    Reuter, N.2    Navaza, J.3    Stokes, D.L.4    Lacapere, J.J.5
  • 11
    • 0003545679 scopus 로고
    • 2nd ed. North-Holland Publishing, Amsterdam
    • Cowley, J. M. 1981. Diffraction Physics, 2nd ed. North-Holland Publishing, Amsterdam.
    • (1981) Diffraction Physics
    • Cowley, J.M.1
  • 12
    • 33644847296 scopus 로고    scopus 로고
    • Estimation of variance in single-particle reconstruction using the bootstrap technique
    • Penczek, P. A., C. Yang, J. Frank, and C. M. Spahn. 2006. Estimation of variance in single-particle reconstruction using the bootstrap technique. J. Struct. Biol. 154:168-183.
    • (2006) J. Struct. Biol , vol.154 , pp. 168-183
    • Penczek, P.A.1    Yang, C.2    Frank, J.3    Spahn, C.M.4
  • 13
    • 0029903197 scopus 로고    scopus 로고
    • Electron-crystallographic refinement of the structure of bacteriorhodopsin
    • Grigorieff, N., T. A. Ceska, K. H. Downing, J. M. Baldwin, and R. Henderson. 1996. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259:393-421.
    • (1996) J. Mol. Biol , vol.259 , pp. 393-421
    • Grigorieff, N.1    Ceska, T.A.2    Downing, K.H.3    Baldwin, J.M.4    Henderson, R.5
  • 15
    • 85031355681 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 16
    • 85031349285 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 17
    • 30044450170 scopus 로고    scopus 로고
    • Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses
    • Khayat, R., L. Tang, E. T. Larson, C. M. Lawrence, M. Young, and J. E. Johnson. 2005. Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Proc. Natl. Acad. Sci. USA. 102:18944-18949.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 18944-18949
    • Khayat, R.1    Tang, L.2    Larson, E.T.3    Lawrence, C.M.4    Young, M.5    Johnson, J.E.6
  • 19
    • 34248172479 scopus 로고    scopus 로고
    • Interpretation of electron density with stereographic roadmap projections
    • Xiao, C., and M. G. Rossmann. 2007. Interpretation of electron density with stereographic roadmap projections. J. Struct. Biol. 158: 182-187.
    • (2007) J. Struct. Biol , vol.158 , pp. 182-187
    • Xiao, C.1    Rossmann, M.G.2
  • 20
    • 27744471408 scopus 로고    scopus 로고
    • Constrained geometric simulation of diffusive motion in proteins
    • Wells, S., S. Menor, B. Hespenheide, and M. F. Thorpe. 2005. Constrained geometric simulation of diffusive motion in proteins. Phys. Biol. 2:S127-S136.
    • (2005) Phys. Biol , vol.2
    • Wells, S.1    Menor, S.2    Hespenheide, B.3    Thorpe, M.F.4
  • 21
    • 0034308140 scopus 로고    scopus 로고
    • Building-block approach for determining low-frequency normal modes of macromolecules
    • Tama, F., F. X. Gadea, O. Marques, and Y. H. Sanejouand. 2000. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins. 41:1-7.
    • (2000) Proteins , vol.41 , pp. 1-7
    • Tama, F.1    Gadea, F.X.2    Marques, O.3    Sanejouand, Y.H.4
  • 22
    • 33748448490 scopus 로고    scopus 로고
    • A natural coarse graining for simulating large biomolecular motion
    • Gohlke, H., and M. F. Thorpe. 2006. A natural coarse graining for simulating large biomolecular motion. Biophys. J. 91:2115-2120.
    • (2006) Biophys. J , vol.91 , pp. 2115-2120
    • Gohlke, H.1    Thorpe, M.F.2
  • 23
    • 0000785338 scopus 로고
    • Generic rigidity percolation: The pebble game
    • Jacobs, D. J., and M. F. Thorpe. 1995. Generic rigidity percolation: the pebble game. Phys. Rev. Lett. 75:4051-4054.
    • (1995) Phys. Rev. Lett , vol.75 , pp. 4051-4054
    • Jacobs, D.J.1    Thorpe, M.F.2
  • 25
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs, D. J., A. J. Rader, L. A. Kuhn, and M. F. Thorpe. 2001. Protein flexibility predictions using graph theory. Proteins. 44:150-165.
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 27
    • 0036888379 scopus 로고    scopus 로고
    • Identifying protein folding cores from the evolution of flexible regions during unfolding
    • Hespenheide, B. M., A. J. Rader, M. F. Thorpe, and L. A. Kuhn. 2002. Identifying protein folding cores from the evolution of flexible regions during unfolding. J. Mol. Graph. Model. 21:195-207.
    • (2002) J. Mol. Graph. Model , vol.21 , pp. 195-207
    • Hespenheide, B.M.1    Rader, A.J.2    Thorpe, M.F.3    Kuhn, L.A.4
  • 28
    • 9144263145 scopus 로고    scopus 로고
    • Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus
    • Hespenheide, B. M., D. J. Jacobs, and M. F. Thorpe. 2004. Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus. J. Phys. Condens. Matter. 16:S5055-S5064.
    • (2004) J. Phys. Condens. Matter , vol.16
    • Hespenheide, B.M.1    Jacobs, D.J.2    Thorpe, M.F.3
  • 29
    • 33745955275 scopus 로고
    • The Monte Carlo method
    • Metropolis. 1949. The Monte Carlo method. J Am Stat Assoc 44:335.
    • (1949) J Am Stat Assoc , vol.44 , pp. 335
    • Metropolis1
  • 30
    • 84977295671 scopus 로고
    • Dirac-Fock calculations of x-ray scattering factors and contributions to the mean inner potential for electron scattering
    • Rez, D., P. Rez, and I. Grant. 1994. Dirac-Fock calculations of x-ray scattering factors and contributions to the mean inner potential for electron scattering. Acta Crystallogr. A. 50:481-497.
    • (1994) Acta Crystallogr. A , vol.50 , pp. 481-497
    • Rez, D.1    Rez, P.2    Grant, I.3
  • 31
    • 0032780181 scopus 로고    scopus 로고
    • Situs: A package for docking crystal structures into low-resolution maps from electron microscopy
    • Wriggers, W., R. A. Milligan, and J. A. McCammon. 1999. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125:185-195.
    • (1999) J. Struct. Biol , vol.125 , pp. 185-195
    • Wriggers, W.1    Milligan, R.A.2    McCammon, J.A.3
  • 32
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word, J. M., S. C. Lovell, J. S. Richardson, and D. C. Richardson. 1999. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285:1735-1747.
    • (1999) J. Mol. Biol , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 34
    • 33745939477 scopus 로고    scopus 로고
    • Docking of photosystem I subunit C using a constrained geometric simulation
    • Jolley, C. C., S. A. Wells, B. M. Hespenheide, M. F. Thorpe, and P. Fromme. 2006. Docking of photosystem I subunit C using a constrained geometric simulation. J. Am. Chem. Soc. 128:8803-8812.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 8803-8812
    • Jolley, C.C.1    Wells, S.A.2    Hespenheide, B.M.3    Thorpe, M.F.4    Fromme, P.5
  • 36
    • 33746265142 scopus 로고    scopus 로고
    • GroEL-mediated protein folding: Making the impossible, possible
    • Lin, Z., and H. S. Rye. 2006. GroEL-mediated protein folding: making the impossible, possible. Crit. Rev. Biochem. Mol. Biol. 41:211-239.
    • (2006) Crit. Rev. Biochem. Mol. Biol , vol.41 , pp. 211-239
    • Lin, Z.1    Rye, H.S.2
  • 37
    • 0037418665 scopus 로고    scopus 로고
    • Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0A resolution
    • Wang, J., and D. C. Boisvert. 2003. Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0A resolution. J. Mol. Biol. 327:843-855.
    • (2003) J. Mol. Biol , vol.327 , pp. 843-855
    • Wang, J.1    Boisvert, D.C.2
  • 39
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman, D., and P. Argos. 1995. Knowledge-based protein secondary structure assignment. Proteins. 23:566-579.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.