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Characterization of novel proteins based on known protein structures
W A Koppensteiner1, P Lackner, M Wiederstein
1Center for Applied Molecular Engineering, Institute for Chemistry and Biochemistry, University of Salzburg, Jakob-Haringer-Strasse 3, Salzburg, A-5020, Austria.
Journal of Molecular Biology
|February 25, 2000
Summary
Discovering novel protein functions relies on comparing sequences. However, analyzing protein structures reveals many more functional relationships than sequence searches alone can detect, enhancing genomic insights.
Area of Science:
- Genomics
- Structural Biology
- Bioinformatics
Background:
- Genome sciences aim to characterize novel genes, often using sequence similarity for functional inference.
- Current sequence search techniques have limitations in predicting the structure and function of new proteins.
Purpose of the Study:
- To assess the extent of functional and structural information obtainable from known protein three-dimensional structures.
- To estimate the maximum reliable inference for novel protein sequences using structural data.
Main Methods:
- Utilized all protein structures in the Protein Data Bank known by the end of 1997.
- Characterized protein structures released in 1998 for similarity to existing structures.
- Assessed functional and structural similarity between new and known protein domains.
Main Results:
- Proteins released in 1998 showed no clear sequence similarity to known structures.
- However, 75% of these domains exhibited significant structural similarity to known folds.
- In two-thirds of cases, structural similarity correlated with related protein function.
Conclusions:
- Leveraging existing protein structure databases can provide functional insights for many new targets.
- Structural similarity offers complementary information to sequence data for inferring protein function.
- Current advanced techniques identify only about one-third of these structure-based functional relationships.