Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

Structure - Tập 16 Số 5 - Trang 673-683 - 2008
Leonardo G. Trabuco1,2, Elizabeth Villa1,2, K. Mitra3, Joachim Frank4,3, Klaus Schulten1,5
1Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
2Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
3Howard Hughes Medical Institute, Health Research Incorporated, Wadsworth Center, Empire State Plaza, Albany, NY 12201, USA
4Department of Biomedical Sciences, State University of New York, Albany, NY 12222, USA
5Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

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Tài liệu tham khảo

Alber, 2007, Determining the architectures of macromolecular assemblies, Nature, 450, 683, 10.1038/nature06404

Alberts, 1998, The cell as a collection of protein machines – preparing the next generation of biologists, Cell, 92, 291, 10.1016/S0092-8674(00)80922-8

Arkhipov, 2006, Stability and dynamics of virus capsids described by coarse-grained modeling, Structure, 14, 1767, 10.1016/j.str.2006.10.003

Brünger, 1984, Stochastic boundary conditions for molecular dynamics simulations of ST2 water, Chem. Phys. Lett., 105, 495, 10.1016/0009-2614(84)80098-6

Chapman, 1995, Restrained real-space macromolecular atomic refinement using a new resolution-dependent electron-density function, Acta Crystallogr. A, 51, 69, 10.1107/S0108767394007130

Chen, 2001, Real space refinement of acto-myosin structures from sectioned muscle, J. Struct. Biol., 133, 221, 10.1006/jsbi.2000.4321

Darnault, 2003, Ni-Zn-[Fe-S] and Ni-Ni-[Fe-S] clusters in closed and open α subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase, Nat. Struct. Biol., 10, 271, 10.1038/nsb912

Foloppe, 2000, All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data, J. Comput. Chem., 21, 86, 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G

Frank, 2002, Single-particle imaging of macromolecules by cryo-electron microscopy, Annu. Rev. Biophys. Biomol. Struct., 31, 309, 10.1146/annurev.biophys.31.082901.134202

Frank, 2003, Electron microscopy of functional ribosome complexes, Biopolymers, 68, 223, 10.1002/bip.10210

Frank, 2006

Frank, 2006, The ribosome and the mechanism of protein synthesis, Rep. Prog. Phys., 69, 1383, 10.1088/0034-4885/69/5/R03

Frenkel, 2002

Gao, 2003, Study of the structural dynamics of the E. coli 70S ribosome using real space refinement, Cell, 113, 789, 10.1016/S0092-8674(03)00427-6

Humphrey, 1996, VMD – Visual Molecular Dynamics, J. Mol. Graph., 14, 33, 10.1016/0263-7855(96)00018-5

Isralewitz, 2001, Steered molecular dynamics and mechanical functions of proteins, Curr. Opin. Struct. Biol., 11, 224, 10.1016/S0959-440X(00)00194-9

Jacobs, 2001, Protein flexibility predictions using graph theory, Proteins, 44, 150, 10.1002/prot.1081

Jolley, 2008, Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations, Biophys. J., 94, 1613, 10.1529/biophysj.107.115949

Leontis, 1998, Conserved geometrical base-pairing patters in RNA, Q. Rev. Biophys., 31, 399, 10.1017/S0033583599003479

Li, 2007, Transfer RNA in the hybrid P/E state: Correlating molecular dynamics simulations with cryo-EM data, Proc. Natl. Acad. Sci. USA, 104, 16540, 10.1073/pnas.0708094104

MacKerell, 1998, All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B, 102, 3586, 10.1021/jp973084f

Mitra, 2006, Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps, Annu. Rev. Biophys. Biomol. Struct., 35, 299, 10.1146/annurev.biophys.35.040405.101950

Mitra, 2005, Structure of the E. coli protein-conducting channel bound to a translating ribosome, Nature, 438, 318, 10.1038/nature04133

Mitra, 2006, Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements, Mol. Cell, 22, 533, 10.1016/j.molcel.2006.05.003

Phillips, 2005, Scalable molecular dynamics with NAMD, J. Comput. Chem., 26, 1781, 10.1002/jcc.20289

Roseman, 2000, Docking structures of domains into maps from cryo-electron microscopy using local correlation, Acta Crystallogr. D Biol. Crystallogr., 56, 1332, 10.1107/S0907444900010908

Rossmann, 2000, Fitting atomic models into electron-microscopy maps, Acta Crystallogr. D Biol. Crystallogr., 56, 1341, 10.1107/S0907444900009562

Saibil, 2000, Macromolecular structure determination by cryo-electron microscopy, Acta Crystallogr. D Biol. Crystallogr., 56, 1215, 10.1107/S0907444900010787

Sali, 2003, From words to literature in structural proteomics, Nature, 422, 216, 10.1038/nature01513

Schröder, 2007, Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution, Structure, 15, 1630, 10.1016/j.str.2007.09.021

Schuwirth, 2005, Structures of the bacterial ribosome at 3.5 Å resolution, Science, 310, 827, 10.1126/science.1117230

Selmer, 2006, Structure of the 70S ribosome complexed with mRNA and tRNA, Science, 313, 1935, 10.1126/science.1131127

Shih, 2007, Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations, J. Struct. Biol., 157, 579, 10.1016/j.jsb.2006.08.006

Sotomayor, 2007, Single-molecule experiments in vitro and in silico, Science, 316, 1144, 10.1126/science.1137591

Stewart, 1993, Difference imaging of adenovirus: Bridging the resolution gap between X-ray crystallography and electron microscopy, EMBO J., 12, 2589, 10.1002/j.1460-2075.1993.tb05919.x

Suhre, 2006, 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, 1098, 10.1107/S090744490602244X

Tama, 2004, Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM, J. Struct. Biol., 147, 315, 10.1016/j.jsb.2004.03.002

Topf, 2006, Refinement of protein structures by iterative comparative modeling and cryoEM density fitting, J. Mol. Biol., 357, 1655, 10.1016/j.jmb.2006.01.062

Topf, 2008, Protein structure fitting and refinement guided by cryo-EM density, Structure, 16, 295, 10.1016/j.str.2007.11.016

Valle, 2003, Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy, Nat. Struct. Biol., 10, 899, 10.1038/nsb1003

Velazquez-Muriel, 2006, Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies, Structure, 14, 1115, 10.1016/j.str.2006.05.013

Volkmann, 2000, Evidence for cleft closure in actomyosin upon ADP release, Nat. Struct. Biol., 7, 1147, 10.1038/82008

Wells, 2007, Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics, J. Chem. Phys., 127, 125101, 10.1063/1.2770738

Wriggers, 2001, Using Situs for flexible and rigid-body fitting of multiresolution single-molecule data, J. Struct. Biol., 133, 193, 10.1006/jsbi.2000.4350

Wriggers, 2001, Modeling tricks and fitting techniques for multiresolution structures, Structure, 9, 779, 10.1016/S0969-2126(01)00648-7

Wriggers, 1999, Situs: A package for docking crystal structures into low-resolution maps from electron microscopy, J. Struct. Biol., 125, 185, 10.1006/jsbi.1998.4080

Wriggers, 2000, Domain motions of EF-G bound to the 70S ribosome: Insights from a hand-shaking between multi-resolution structures, Biophys. J., 79, 1670, 10.1016/S0006-3495(00)76416-2

Yang, 2003, Tools for the automatic identification and classification of RNA base pairs, Nucleic Acids Res., 31, 3450, 10.1093/nar/gkg529

Zhang, 2003, Molecular dynamics simulations of peptides and proteins with amplified collective motions, Biophys. J., 84, 3583, 10.1016/S0006-3495(03)75090-5

Zhu, 2001, Automated identification of filaments in cryoelectron microscopy images, J. Struct. Biol., 135, 302, 10.1006/jsbi.2001.4415