Modeling Protein Structures Based on Density Maps at Intermediate Resolutions

  • Jianpeng Ma


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.


Secondary Structural Element Deconvolution Method Native Topology Sheet Density MoFe Protein 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  • Jianpeng Ma

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