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Characterization and sequence prediction of structural variations in α-helix
Ashish V Tendulkar1, Pramod P Wangikar
1Department of Computer Science and Engineering, Indian Institute of Technology Madras, Chennai 600 036, India. ashishvt@gmail.com
BMC Bioinformatics
|February 24, 2011
Summary
This study identifies amino acid sequence features that cause distortions in alpha-helices. A support vector machine (SVM) model accurately predicts regular versus non-regular alpha-helices based on sequence data.
Area of Science:
- Biophysics
- Computational Biology
- Protein Structure
Background:
- Alpha-helix structure is influenced by sequence-specific and context-dependent factors leading to distortions.
- Understanding these sequence-structure relationships allows for prediction of alpha-helix variations from amino acid sequences.
Purpose of the Study:
- To discriminate between regular and non-regular alpha-helices using only their amino acid sequences.
- To identify specific amino acid propensities contributing to alpha-helix structural distortions.
Main Methods:
- Trained a support vector machine (SVM) with a dot product kernel.
- Utilized overall and position-specific amino acid propensities for sequence representation.
- Characterized structural distortions in five alpha-helix subclasses.
Main Results:
- Identified increased propensities of proline, histidine, serine, aspartic acid, and aromatic amino acids as key factors in regular alpha-helix distortions.
- Determined N-terminus preferences for neutral/acidic polar amino acids and C-terminus preferences for basic polar amino acids in regular alpha-helices.
- Observed proline's role in both regular alpha-helix first turns and kinked/curved subclasses.
- Achieved 80.97% precision and 88.05% recall in discriminating regular from non-regular alpha-helices using SVM.
Conclusions:
- The SVM's performance validates the strong correlation between alpha-helix sequence features and structural variations.
- Findings are valuable for computational design and prediction of structural perturbations in alpha-helices based solely on sequence.
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