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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Effect of low-complexity regions on protein structure determination.
Ryan M Bannen1, Craig A Bingman, George N Phillips
1Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53711, USA.
Journal of Structural and Functional Genomics
|February 28, 2008
Summary
Low-complexity protein sequences are abundant but rarely found in the Protein Data Bank. This study analyzes trends in protein structure determination targets, offering insights for selecting future research candidates.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Protein sequences with quasi-repetitive amino acid arrangements, termed low-complexity sequences, are prevalent in genomic and proteomic databases like Swiss-Prot.
- These low-complexity sequences are notably under-represented in the structure-based Protein Data Bank (PDB).
- Structural genomics initiatives have historically used the absence of low-complexity sequences as a criterion for selecting protein targets with a high likelihood of successful structure determination.
Purpose of the Study:
- To investigate trends related to low-complexity sequences in protein structure determination.
- To evaluate the utility of low-complexity sequences in the context of target selection for structural genomics.
- To provide data-driven insights for refining target selection strategies in structural biology.
Main Methods:
- Analysis of protein sequence data from the Protein Data Bank (PDB).
- Examination of data from structural genomics databases, including TargetDB and PepcDB.
- Comparative analysis of sequence characteristics and structure determination success rates.
Main Results:
- Identification of specific trends concerning the presence or absence of low-complexity sequences in proteins targeted for structure determination.
- Quantification of the under-representation of low-complexity sequences within the PDB.
- Observation of patterns in target selection by structural genomics groups concerning these sequences.
Conclusions:
- The findings offer valuable insights into the relationship between low-complexity sequences and protein structure determination.
- The study suggests that current target selection strategies may benefit from a nuanced consideration of low-complexity sequences.
- Recommendations are provided for optimizing the selection process for structural genomics projects based on sequence characteristics.
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