EXPANDED PROTEIN STRUCTURE REFINEMENT AND VALIDATION

Summary

Principal Investigator: Ethan Merritt
Abstract: Description: (Applicant's abstract) A major goal of the Protein Structure Initiative (Structural Genomics) is to increase the rate of new biological knowledge obtained from protein crystallography, by developing new methods to enhance the efficiency and throughput of structure determination. This proposal addresses several factors limiting the current efficiency. (1) The amount of biological information increases with increasing resolution of the X-ray structure, but full model building and refinement of the highest resolution structures is disproportionately time-consuming. (2) The amount of information from lower resolution structures is limited partly because simplified models are refined to describe these structures. (3) The utility of the database of known structures is limited partly by the reliability of those structures, and the degree to which their interpretation can be automated. This project will develop and distribute computational tools to speed the refinement, improve the quality, and validate the result of protein crystal determinations, with special emphasis on obtaining more information from the increasing number of high resolution structures. Eventual widespread application of these tools will increase the accuracy and information content of a large fraction of all future protein structural models, including those resulting from the Protein Structure Initiative. The key to this work is the use of expanded structural models that include explicit descriptions of atomic anisotropy and modes of molecular vibration. Analysis of near-atomic resolution structures refined with anisotropic displacement parameters will be used to build and maintain a database of statistical properties seen for these parameters in well-refined structures. These properties will be developed as quality control criteria for validating new protein structures. They will also be implemented as restraint targets for structure refinement at lower resolution. This approach should permit incorporation of explicit models for anisotropy into structural models refined at typical resolutions for protein crystallography (about 2A). This, in turn, will make it easier to identify key biological features such as the presence and conformation of bound ligands, and the nature of hinge and inter-domain motions.
Funding Period: 2001-03-01 - 2007-02-28
more information: NIH RePORT

Top Publications

  1. ncbi A molecular viewer for the analysis of TLS rigid-body motion in macromolecules
    Jay Painter
    Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 61:465-71. 2005
  2. pmc Cooperative hydrogen bond interactions in the streptavidin-biotin system
    David E Hyre
    Box 351721, Department of Bioengineering, University of Washington, Seattle, WA 98195 1721, USA
    Protein Sci 15:459-67. 2006
  3. pmc Structure of the conserved hypothetical protein MAL13P1.257 from Plasmodium falciparum
    Margaret A Holmes
    Structural Genomics of Pathogenic Protozoa Consortium, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:180-5. 2006
  4. ncbi Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    Jay Painter
    Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 62:439-50. 2006
  5. pmc Structure of ribose 5-phosphate isomerase from Plasmodium falciparum
    Margaret A Holmes
    Structural Genomics of Pathogenic Protozoa SGPP Consortium, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:427-31. 2006

Detail Information

Publications5

  1. ncbi A molecular viewer for the analysis of TLS rigid-body motion in macromolecules
    Jay Painter
    Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 61:465-71. 2005
    ..TLSView may also be used to prepare, analyze and validate TLS models for crystallographic refinement...
  2. pmc Cooperative hydrogen bond interactions in the streptavidin-biotin system
    David E Hyre
    Box 351721, Department of Bioengineering, University of Washington, Seattle, WA 98195 1721, USA
    Protein Sci 15:459-67. 2006
    ..Taken together, the thermodynamic and structural analyses support the conclusion that the wild-type hydrogen bond between D128-OD and biotin-N2 is thermodynamically stronger than that between S45-OG and biotin-N1...
  3. pmc Structure of the conserved hypothetical protein MAL13P1.257 from Plasmodium falciparum
    Margaret A Holmes
    Structural Genomics of Pathogenic Protozoa Consortium, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:180-5. 2006
    ..The packing of the two monomers in the asymmetric unit indicates that the biological unit may be a dimer...
  4. ncbi Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    Jay Painter
    Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, WA 98195 7742, USA
    Acta Crystallogr D Biol Crystallogr 62:439-50. 2006
    ..The models generated by TLSMD analysis can significantly improve the standard crystallographic residuals R and R(free) and can reveal intrinsic dynamic properties of the protein...
  5. pmc Structure of ribose 5-phosphate isomerase from Plasmodium falciparum
    Margaret A Holmes
    Structural Genomics of Pathogenic Protozoa SGPP Consortium, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:427-31. 2006
    ..The P. falciparum enzyme belongs to the ribose 5-phosphate isomerase A family, Pfam family PF06562 (DUF1124), and is structurally similar to other members of the family...