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Quantifying the relationship of protein burying depth and sequence
1Institute for Molecular Bioscience and ARC Centre in Bioinformatics, The University of Queensland, Brisbane, Australia. z.yuan@imb.uq.edu.au
Proteins
|August 21, 2007
Summary
Protein burying depth (BD) predicts residue burial extent using sequence information. This method accurately identifies deeply buried residues, aiding protein structure and folding studies.
Area of Science:
- Structural biology
- Computational biology
- Biophysics
Background:
- Protein burying depth (BD) quantifies residue burial, offering insights beyond solvent accessible surface area.
- BD is crucial for understanding protein interior structure, folding nuclei, and deep-level structural organization.
Purpose of the Study:
- To analyze the relationship between protein residue burying depth and local sequence characteristics.
- To develop predictive models for residue burying depth using sequence information.
- To investigate the influence of molecular size on prediction accuracy.
Main Methods:
- Nonlinear functions were estimated using support vector machines to model the sequence-depth relationship.
- Cross-validation tests were employed to assess the accuracy of the developed functions.
- Correlation coefficients were calculated to quantify the agreement between predicted and observed depths.
Main Results:
- A strong correlation was found between residue BD and its local sequence environment.
- Incorporating molecular size improved the correlation coefficient from 0.60 to 0.65.
- Approximately 50% of the deepest 10% residues were correctly predicted.
Conclusions:
- Residue burying extent can be predicted to some degree using local sequence information.
- The developed methods show promise for advancing the investigation of protein structures and folding mechanisms.
