Tripeptide analysis of protein structures

BMC Structural Biology

Ramesh Anishetty²  Gautam Pennathur¹  Sharmila Anishetty¹ 

[1] Centre for Biotechnology, Anna University, Chennai-25, India;The Institute of Mathematical Sciences, Chennai-113, India

关键词: Structural rigidity;    Hydrophobicity;    Structural homologs;    Tripeptide;   

Others  :  1181495
DOI  :  10.1186/1472-6807-2-9

 received in 2002-07-13, accepted in 2002-12-21,  发布年份 2002

【 摘 要 】

Background

An efficient building block for protein structure prediction can be tripeptides. 8000 different tripeptides from a dataset of 1220 high resolution (≤ 2.0°A) structures from the Protein Data Bank (PDB) have been looked at, to determine which are structurally rigid and non-rigid. This data has been statistically analyzed, discussed and summarized. The entire data can be utilized for the building of protein structures.

Results

Tripeptides have been classified into three categories: rigid, non-rigid and intermediate, based on the relative structural rigidity between C_α and C_β atoms in a tripeptide. We found that 18% of the tripeptides in the dataset can be classified as rigid, 4% as non-rigid and 78% as intermediate. Many rigid tripeptides are made of hydrophobic residues, however, there are tripeptides with polar side chains forming rigid structures. The bulk of the tripeptides fall in the intermediate class while very small numbers actually fall in the non-rigid class. Structurally all rigid tripeptides essentially form two structural classes while the intermediate and non-rigid tripeptides fall into one structural class. This notion of rigidity and non-rigidity is designed to capture side chain interactions but not secondary structures.

Conclusions

Rigid tripeptides have no correlation with the secondary structures in proteins and hence this work is complementary to such studies. Tripeptide data may be used to predict plausible structures for oligopeptides and for denovo protein design.

【 授权许可】

   
2002 Anishetty et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.

【 图 表 】

Figure 1.

Figure 2.

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