Molecular dynamics of protein complexes from four-dimensional cryo-electron microscopy

Journal of Structural Biology

Volumn 147, Issue 3, 2004, Pages 291-301

  Heymann, J Bernard ^a   Conway, James F ^b   Steven, Alasdair C ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b INSTITUT DE BIOLOGIE STRUCTURALE   (France)

Author keywords

Conformational change; Image classification; Molecular dynamics; Molecular movie; Multiple particle analysis; Single particle analysis

Indexed keywords

ARTICLE; BACTERIOPHAGE; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; ENVIRONMENT; HERPES SIMPLEX VIRUS; MATURATION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; TIME SERIES ANALYSIS; VIRUS CAPSID;

BACTERIOPHAGES; CAPSID PROTEINS; CRYOELECTRON MICROSCOPY; HERPESVIRUS 1, HUMAN; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN PRECURSORS;

DNA VIRUSES; SIMPLEXVIRUS;

EID: 4344664583     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2004.02.006     Document Type: Article

References (30)

1. Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell. 92:1998;291-294
2. Aldroubi A., Trus B.L., Unser M., Booy F.P., Steven A.C. Magnification mismatches between micrographs: corrective procedures and implications for structural analysis. Ultramicroscopy. 46:1992;175-188
3. Baker T.S., Cheng R.H. A model-based approach for determining orientations of biological macromolecules imaged by cryoelectron microscopy. J. Struct. Biol. 116:1996;120-130
4. Baumeister W., Steven A.C. Macromolecular electron microscopy in the era of structural genomics. Trends Biochem. Sci. 25:2000;624-631
5. Berriman J., Unwin N. Analysis of transient structures by cryo-microscopy combined with rapid mixing of spray droplets. Ultramicroscopy. 56:1994;241-252
6. Cerritelli M.E., Conway J.F., Cheng N., Trus B.L., Steven A.C. Molecular mechanisms in bacteriophage T7 procapsid assembly, maturation, and DNA containment. Adv. Protein Chem. 64:2003;301-323
7. Conway J.F., Duda R.L., Cheng N., Hendrix R.W., Steven A.C. Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system. J. Mol. Biol. 253:1995;86-99
8. Duda R.L., Hempel J., Michel H., Shabanowitz J., Hunt D., Hendrix R.W. Structural transitions during bacteriophage HK97 head assembly. J. Mol. Biol. 247:1995;618-635
9. Frank J. Single-particle imaging of macromolecules by cryo-electron microscopy. Annu. Rev. Biophys. Biomol. Struct. 31:2002;303-319
10. Frank J., Wagenknecht T., McEwen B.F., Marko M., Hsieh C.E., Mannella C.A. Three-dimensional imaging of biological complexity. J. Struct. Biol. 138:2002;85-91
11. Hendrix R.W., Duda R.L. Bacteriophage HK97 head assembly: a protein ballet. Adv. Virus Res. 50:1998;235-288
12. Heymann J.B., Cheng N., Newcomb W.W., Trus B.L., Brown J.C., Steven A.C. Dynamics of herpes simplex virus capsid maturation visualized by time-lapse cryo-electron microscopy. Nat. Struct. Biol. 10:2003;334-341
13. Homa F.L., Brown J.C. Capsid assembly and DNA packaging in herpes simplex virus. Rev. Med. Virol. 7:1997;107-122
14. Jontes J.D., Wilson-Kubalek E.M., Milligan R.A. A 32 degree tail swing in brush border myosin I on ADP release. Nature. 378:1995;751-753
15. Kasas S., Dumas G., Dietler G., Catsicas S., Adrian M. Vitrification of cryoelectron microscopy specimens revealed by high-speed photographic imaging. J. Microsc. (Oxford). 211:2003;48-53
16. Lata R., Conway J.F., Cheng N., Duda R.L., Hendrix R.W., Wikoff W.R., Johnson J.E., Tsuruta H., Steven A.C. Maturation dynamics of a viral capsid: visualization of transitional intermediate states. Cell. 100:2000;253-263
17. Newcomb W.W., Homa F.L., Thomsen D.R., Booy F.P., Trus B.L., Steven A.C., Spencer J.V., Brown J.C. Assembly of the herpes simplex virus capsid: characterization of intermediates observed during cell-free capsid formation. J. Mol. Biol. 263:1996;432-446
18. Newcomb W.W., Homa F.L., Thomsen D.R., Trus B.L., Cheng N., Steven A., Booy F., Brown J.C. Assembly of the herpes simplex virus procapsid from purified components and identification of small complexes containing the major capsid and scaffolding proteins. J. Virol. 73:1999;4239-4250
19. Newcomb W.W., Juhas R.M., Thomsen D.R., Homa F.L., Burch A.D., Weller S.K., Brown J.C. The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid. J. Virol. 75:2001;10923-10932
20. Nitsch M., Walz J., Typke D., Klumpp M., Essen L.O., Baumeister W. Group II chaperonin in an open conformation examined by electron tomography. Nat. Struct. Biol. 5:1998;855-857
21. Preston V.G., Coates J.A., Rixon F.J. Identification and characterization of a herpes simplex virus gene product required for encapsidation of virus DNA. J. Virol. 45:1983;1056-1064
22. Ruprecht J., Nield J. Determining the structure of biological macromolecules by transmission electron microscopy, single particle analysis and 3D reconstruction. Prog. Biophys. Mol. Biol. 75:2001;121-164
23. Sali A., Glaeser R., Earnest T., Baumeister W. From words to literature in structural proteomics. Nature. 422:2003;216-225
24. Steven A.C., Carrascosa J.L. Proteolytic cleavage and structural transformation: their relationship in bacteriophage T4 capsid maturation. J. Supramol. Struct. 10:1979;1-11
25. Steven A.C., Spear P.G. Herpesvirus capsid assembly and envelopment. Chiu W., Burnett R.M., Garcea R.L. Structural Biology of Viruses. 1997;312-351 Oxford University Press, New York
26. Subramaniam S., Henderson R. Electron crystallography of bacteriorhodopsin with millisecond time resolution. J. Struct. Biol. 128:1999;19-25
27. Trus B.L., Booy F.P., Newcomb W.W., Brown J.C., Homa F.L., Thomsen D.R., Steven A.C. The herpes simplex virus procapsid: structure, conformational changes upon maturation, and roles of the triplex proteins VP19c and VP23 in assembly. J. Mol. Biol. 263:1996;447-462
28. White H.D., Thirumurugan K., Walker M.L., Trinick J. A second generation apparatus for time-resolved electron cryo-microscopy using stepper motors and electrospray. J. Struct. Biol. 144:2003;246-252
29. Wikoff W.R., Liljas L., Duda R.L., Tsuruta H., Hendrix R.W., Johnson J.E. Topologically linked protein rings in the bacteriophage HK97 capsid. Science. 289:2000;2129-2133
30. Zhou Z.H., Liao W., Cheng R.H., Lawson J.E., McCarthy D.B., Reed L.J., Stoops J.K. Direct evidence for the size and conformational variability of the pyruvate dehydrogenase complex revealed by three-dimensional electron microscopy. The "breathing" core and its functional relationship to protein dynamics. J. Biol. Chem. 276:2001;21704-21713