Abstract

The overall project will determine the structure of proteins from Mycoplasma genitalium and Mycoplasma pneumoniae. These structures will enhance the database of protein folds, and will be interpreted to suggest possible functions for the proteins. This component of the overall project will apply solution NMR methods to determine structures of small proteins from these organisms using multinuclear multidimensional methods. Sets of experiments will be designed which are optimized for assignment of resonances from proteins with specific linewidths. Methods for automated analysis of data (determination of backbone and sidechain assignments, and assignment of NOE crosspeaks) will be implemented, and extended to optimize throughput. Proteins homologous to M.g. and M.p. but from thermophilic organisms will be evaluated fro NMR work. Data collection at higher temperature is improved due to decreased linewidths, enhancing data quality and hence the ability to automate analysis. The interpretation of structures determined in terms of fold classification and function will be done in collaboration with other members of the project. NMR will also be applied to evaluation of proteins for crystallography, attempting to identify flexible regions, and comains which may hinder crystallography, attempting to identify flexible regions, and domains which may hinder crystallization.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center (P50)
Project #
1P50GM062412-01
Application #
6368933
Study Section
Special Emphasis Panel (ZGM1-BT-5 (01))
Project Start
2000-09-30
Project End
2005-08-31
Budget Start
Budget End
Support Year
1
Fiscal Year
2000
Total Cost
$1,094,372
Indirect Cost

  Institution

Name
University of California Berkeley
Department
Type
DUNS #
094878337
City
Berkeley
State
CA
Country
United States
Zip Code
94704

  Publications

Jun, Se-Ran; Sims, Gregory E; Wu, Guohong A et al. (2010) Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution. Proc Natl Acad Sci U S A 107:133-8
Lee, Jonas; Kim, Sung-Hou (2009) High-throughput T7 LIC vector for introducing C-terminal poly-histidine tags with variable lengths without extra sequences. Protein Expr Purif 63:58-61
Wu, Guohong Albert; Jun, Se-Ran; Sims, Gregory E et al. (2009) Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method. Proc Natl Acad Sci U S A 106:12826-31
Pereira, Jose Henrique; Kim, Sung-Hou (2009) Structure of human Brn-5 transcription factor in complex with CRH gene promoter. J Struct Biol 167:159-65
Sims, Gregory E; Jun, Se-Ran; Wu, Guohong Albert et al. (2009) Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc Natl Acad Sci U S A 106:17077-82
Sims, Gregory E; Jun, Se-Ran; Wu, Guohong A et al. (2009) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc Natl Acad Sci U S A 106:2677-82
Pereira, Jose Henrique; Ha, Sung Chul; Kim, Sung-Hou (2008) Crystallization and preliminary X-ray analysis of human Brn-5 transcription factor in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 64:175-8
Dahl, Christiane; Schulte, Andrea; Stockdreher, Yvonne et al. (2008) Structural and molecular genetic insight into a widespread sulfur oxidation pathway. J Mol Biol 384:1287-300
Shin, Dong Hae (2008) Preliminary structural studies on MPN423 expressed from an orthologous ORFan of Mycoplasma pneumoniae. Protein Pept Lett 15:753-5
Zwart, Peter H; Afonine, Pavel V; Grosse-Kunstleve, Ralf W et al. (2008) Automated structure solution with the PHENIX suite. Methods Mol Biol 426:419-35

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