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Comparative analysis of threshold and tessellation methods for determining protein contacts
Jeremy Esque1, Christophe Oguey, Alexandre G de Brevern
1LPTM, CNRS UMR 8089, Université de Cergy Pontoise, Cergy-Pontoise, France. jeremy.esque@univ-paris-diderot.fr
Journal of Chemical Information and Modeling
|January 14, 2011
Summary
The Laguerre tessellation method accurately identifies protein residue contacts, outperforming traditional distance-threshold methods. This improved contact identification has significant implications for protein structure prediction and understanding protein folding.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Protein 3D structure is crucial for biological function, maintained by amino acid interactions and inter-residue contacts.
- Understanding residue contacts is fundamental for protein structure analysis, prediction, and structure-function relationship studies.
Purpose of the Study:
- To compare the classical distance-threshold method with Laguerre tessellation for determining inter-residue contacts.
- To analyze contact distributions, preferences, and the influence of various factors on contact identification.
Main Methods:
- Comparative analysis of distance-threshold and Laguerre tessellation methods.
- Examination of contact distributions based on residue properties (volume, accessibility, hydrophobicity).
- Analysis of contact preferences considering chain length, sequence proximity, and secondary structure.
Main Results:
- Both methods generally agreed, but Cα distance-based contacts showed discrepancies with all-atom tessellation.
- Method discrepancies could significantly alter relative contact preferences.
- A case study on disulfide bridges highlighted the importance of local protein topology for contact determination.
Conclusions:
- Laguerre tessellation offers superior accuracy due to its adaptation to local protein topology.
- This enhanced accuracy has broad implications for contact-based protein folding prediction methods.
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