Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

Journal of Molecular Biology

Volumn 392, Issue 1, 2009, Pages 181-190

  DiMaio, Frank ^a   Tyka, Michael D ^a   Baker, Matthew L ^b   Chiu, Wah ^b   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

comparative modeling; cryoEM; density fitting; Rosetta; structure prediction

Indexed keywords

CAPSID PROTEIN; CHAPERONIN;

ACCURACY; AMINO ACID COMPOSITION; ARTICLE; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; DENSITY; EXPERIMENTAL MODEL; MATHEMATICAL ANALYSIS; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE;

EID: 68949187842     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.07.008     Document Type: Article

References (27)

1. Jiang W., Baker M.L., Ludtke S.J., and Chiu W. Bridging the information gap: computational tools for intermediate resolution structure interpretation. J. Mol. Biol. 308 (2001) 1033-1044
2. Cowtan K. Modified phased translation functions and their application to molecular fragment location. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 (1998) 750-756
3. Abeysinghe S., Ju T., Baker M.L., and Chiu W. Shape modeling and matching in identifying 3D protein structures. Comput.-Aided Des. 40 (2008) 708-720
4. Topf M., Baker M.L., Marti-Renoma M.A., Chiu W., and Sali A. Refinement of protein structures by iterative comparative modeling and cryoEM density fitting. J. Mol. Biol. 357 (2006) 1655-1668
5. Trabuco L.G., Villa E., Mitra K., Frank J., and Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16 (2008) 673-683
6. Orzechowski M., and Tama F. Flexible fitting of high-resolution X-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations. Biophys. J. 95 (2008) 5692-5705
7. Schröder G., Brunger A., and Levitt M. Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution. Structure 15 (2007) 1630-1641
8. Tama F., Miyashita O., and Brooks III C.L. 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
9. Jolley C.C., Wells S.A., Fromme P., and Thorpe M.F. Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations. Biophys. J. 94 (2008) 1613-1621
10. Velazquez-Muriel J.A., Valle M., Santamaría-Pang A., Kakadiaris I.A., and Carazo J.M. Flexible fitting in 3D-EM guided by the structural variability of protein superfamilies. Structure 14 (2006) 1115-1126
11. Topf M., Lasker K., Webb B., Wolfson H., Chiu W., and Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure 16 (2008) 295-307
12. Bradley P., Misura K.M., and Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 309 (2005) 1868-1871
13. Rohl C.A. Protein structure estimation using RosettaNMR. Methods Enzymol. 394 (2005) 244-260
14. John B., and Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res. 31 (2003) 3982-3992
15. Zhou H., Baker M.L., Jiang W., Dougherty M., Jakana J., Dong G., et al. Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat. Struct. Biol. 8 (2001) 868-873
16. Nakagawa A., Miyazaki N., Taka J., Naitow H., Ogawa A., Fujimoto Z., et al. The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins. Structure 11 (2003) 1227-1238
17. McGuffin L.J., and Jones D.T. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19 (2003) 874-881
18. Grimes J., Basak A.K., Roy P., and Stuart D. The crystal structure of bluetongue virus VP7. Nature 373 (1995) 167-170
19. Ludtke S.J., Baker M.L., Chen D.H., Song J.L., Chuang D.T., and Chiu W. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16 (2008) 441-448
20. Baker M.L., Ju T., and Chiu W. Identification of secondary structure elements in intermediate-resolution density maps. Structure 15 (2007) 7-19
21. Bryson K., McGuffin L.J., Marsden R.L., Ward J.J., Sodhi J.S., and Jones D.T. Protein structure prediction servers at University College London. Nucleic Acids Res. 33 (2005) W36-W38
22. Abe H., Braun W., Noguti T., and Gō N. Rapid calculation of first and second derivatives of conformational energy with respect to dihedral angles for proteins general recurrent equations. Comput. Chem. 8 (1984) 239-247
23. Bradley P., and Baker D. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 65 (2006) 922-929
24. Canutescu A., and Dunbrack Jr. R. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci. 12 (2003) 963-972
25. Kuhlman B., and Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA 97 (2000) 10383-10388
26. Dunbrack Jr. R., and Karplus M. Backbone-dependent rotamer library for proteins: application to side-chain prediction. J. Mol. Biol. 230 (1993) 543-574
27. Wu G.A., Coutsias E.A., and Dill K. Iterative assembly of helical proteins by optimal hydrophobic packing. Structure 16 (2008) 1257-1266