The impact of extremophiles on structural genomics (and vice versa)

@article{JenneyJr2007TheIO,
  title={The impact of extremophiles on structural genomics (and vice versa)},
  author={Francis E. Jenney Jr and Michael W. W. Adams},
  journal={Extremophiles},
  year={2007},
  volume={12},
  pages={39-50}
}
The advent of the complete genome sequences of various organisms in the mid-1990s raised the issue of how one could determine the function of hypothetical proteins. While insight might be obtained from a 3D structure, the chances of being able to predict such a structure is limited for the deduced amino acid sequence of any uncharacterized gene. A template for modeling is required, but there was only a low probability of finding a protein closely-related in sequence with an available structure… 
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49 Citations
Background Citations
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49 Citations

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References

SHOWING 1-10 OF 111 REFERENCES
Crystallographic analyses of hyperthermophilic proteins.
  • D. Rees
  • Biology
    Methods in enzymology
  • 2001
Developments in Structural Genomics: Protein Purification and Function Interpretation
TLDR
Three newly determined structures by the pilot structural genomics projects were shown to demonstrate how to decipher biological function from the 3-D structure of a novel protein and how to interpret the structure-function relationship and its application on drug design.
Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
TLDR
The crystal structure of one such protein, MJ0577, from a hyperthermophile, Methanococcus jannaschii, at 1.7-A resolution is reported, indicating that structure-based assignment of molecular function is a viable approach for the large-scale biochemical assignment of proteins and for discovering new motifs, a basic premise of structural genomics.
Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability.
High-throughput production of Pyrococcus furiosus proteins: considerations for metalloproteins.
TLDR
Development of the production pipeline with attention to prediction and incorporation of cofactors is described, suggesting lack of the appropriate cofactor or of the partner protein necessary to form a complex are major reasons why many recombinant proteins are insoluble.
Integrating Structure, Bioinformatics, and Enzymology to Discover Function
TLDR
The function for a protein is determined using a strategy that integrates structural and bioinformatics data with parallel experimental screening for enzymatic activity using a catalytic triad similar to that of the catalytic Triad of hydrolases.
Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline
  • S. Lesley, P. Kuhn, R. Stevens
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2002
TLDR
The design and implementation of a high-throughput structural genomics pipeline and its application to the proteome of the thermophilic bacterium Thermotoga maritima is described and successfully cloned and attempted expression of 1,376 of the predicted 1,877 genes.
A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome
TLDR
The Joint Center for Structural Genomics (JCSG), established in 2000 under the NIH/NIGMS Protein Structure Initiative, has developed and implemented an integrated high-throughput structure pipeline and applied it in a 2-tiered approach to mining the proteome of the thermophilic bacterium Thermotoga maritima.
Structural proteomics of an archaeon
TLDR
Of the first 10 structures determined, several provided clues to biochemical functions that were not detectable from sequence analysis, and in many cases these putative functions could be readily confirmed by biochemical methods, demonstrating that structural proteomics is feasible and can play a central role in functional genomics.
Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics
The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach. A total of…
...
...