Modeling Protein Structures Based on Density Maps at Intermediate Resolutions
Structural biology is now in a special era in which increasingly more complex biomolecules are being studied. For many of them, only low- or intermediateresolution density maps (6–10 Å) can be obtained by, for instance, electron cryomicroscopy (cryo-EM) (Bottcher et al., 1997; Conway et al., 1997; DeRosier and Harrison, 1997; Kuhn et al., 2002; Li et al., 2002; Mancini et al., 2000; Zhang et al., 2000; Zhou et al., 2000, 2001a,b). In certain cases, analysis in terms of intermediateresolution density maps is also inevitable in X-ray crystallography as exemplified in the lengthy process of structural determination of the 50S ribosomal subunit that incremented from 9 Å, 5 Å, to 2.4 Å (Ban et al., 1998, 1999, 2000). As a common feature in all these cases, it is usually impossible, with conventional methods, to construct reasonably accurate atomic models from density maps. However, for the purpose of structural analysis, it would still be very helpful if one can build some kind of pseudo-atomic models from the density maps because this will not only facilitate the structural determination to higher resolutions, but also assist further biochemical studies and functional interpretation. For example, significant insights into the architecture and organization of proteins can often be learned if one can roughly locate the major secondary structural elements such as α-helices and β-sheets. This rationale is supported by the fact that the knowledge of protein folds can be obtained primarily from the spatial arrangement of the secondary structural elements independent of the sequence identity of the proteins, as different sequences can have the same fold.
KeywordsSecondary Structural Element Deconvolution Method Native Topology Sheet Density MoFe Protein
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- Khan, A. R., Baker, B. M., Ghosh, P., Biddison, W. E., and Wiley, D. C. 2000. The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site. J. Immunol. 164:6398–6405.Google Scholar
- Kuhn, R. J., Zhang, W., Rossmann, M. G., Pletnev, S. V., Corver, J., Lenches, E., Jones, C. T., Mukhopadhyay, S., Chipman, P. R., Strauss, E. G., Baker, T. S., and Strauss, J. H. 2002. Structure of dengue virus: Implications for flavivirus organization, maturation, and fusion. Cell 108:717–725.CrossRefGoogle Scholar
- Mayer, S. M., Gormal, C. A., Smith, B. E., and Lawson, D. M. 2002. Crystallographic analysis of the MoFe protein of nitrogenase from a nifV mutant of Klebsiella pneumoniae identifies citrate as a ligand to the molybdenum of iron molybdenum cofactor (FeMoco). J. Biol. Chem. 277:35263–35266.CrossRefGoogle Scholar
- Miller, R. T., Jones, D. T., and Thornton, J. M. 1996. Protein fold recognition by sequence threading: Tools and assessment techniques. Faseb J. 10:171–178.Google Scholar
- Zhou, Z. H., Liao, W., Cheng, R. H., Lawson, J. E., McCarthy, D. B., Reed, L. J., and Stoops, J. K. 2001b. 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. 276:21704–21713.CrossRefGoogle Scholar