Modeling of assemblies using varied data

Computational modeling of assemblies

Computational modeling of assemblies by satisfaction of restraints. Zoom Image

Computational modeling of assemblies by satisfaction of restraints.

Maximum integration of spatial information at different granularities is essential to determine the architectures of membrane-associated complexes, where the structural knowledge is generally scarce. We develop a methodology for modeling complexes, which integrates primarily low-resolution spatial information, such as CET maps and various types of proteomics data.

We are developing and applying methods for modeling protein complexes based on varied input data. Major input data are the sequences of the modeled proteins, homolog structures of probable domain boundaries, cryo-EM maps, and protein-protein interactions.

Related Publications:

  1. Förster F, Villa E,
    Integration of cryo-EM with atomic and protein-protein interaction data
    Meth. Enzymol. 483:47-72 (2010) PubMed
  2. Förster F,  Lasker K, Beck F, Nickell S, Sali A, Baumeister W., 
    An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome.
    Biochem. Biophys. Res. Commun. 388:228-233 (2009). PubMed
  3. Förster F, Webb B, Tsuruta H, Agard DA, Sali A,
    Integration of small angle X-ray scattering data and modeling for structure determination of multidomain proteins and complexes.
    J.Mol.Biol., 382:1089-1106 (2008). PubMed
  4. Alber F, Förster F, Korkin K, Topf M, Sali A,
    Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.
    Annu. Rev. Biochem., 77:443-477 (2008). PubMed

Additional Interests

Small-angle X-ray scattering of macromolecular complexes in solution is a method for obtaining structural insights into those proteins or assemblies that are not amenable to higher information techniques such as X-ray crystallography, NMR spectroscopy, or cryo-EM. We pursue integration of SAXS data in conjuction with other data to obtain structural insights into multi-domain proteins.



Further reading:

  1. Förster F, Webb B, Tsuruta H, Agard DA, Sali A,
    Integration of small angle X-ray scattering data and modeling for structure determination of multidomain proteins and complexes.
    J.Mol.Biol., 382:1089-1106 (2008). PubMed
  2. Krukenberg KA, Förster F., Rice LM, Sali A, Agard DA,
    novel conformation of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90.
    Structure, 16:755-65 (2008). PubMed
 
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