2Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

Doreen Pahlke,Dietmar Leitner,Christian Freund,Dirk Labudde

doi:10.1186/1472-6807-5-8

Doreen Pahlke, Dietmar Leitner + Show 2 more

Open Access

https://doi.org/10.1186/1472-6807-5-8

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Abstract

BackgroundA reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation.ResultsOne of the main results of the statistical investigations is the ranking of the secondary structure and sequence information with respect to the prediction of the Xaa-Pro peptide bond conformation. We observed a significant impact of secondary structure information on the occurrence of the Xaa-Pro peptide bond conformation, while the sequence information of amino acids neighboring proline is of little predictive value for the conformation of this bond.ConclusionIn this work, we present an extensive analysis of the occurrence of the cis and trans proline conformation in proteins. Based on the data set, we derived patterns and rules for a possible prediction of the proline conformation. Upon adoption of the Chou-Fasman parameters, we are able to derive statistically relevant correlations between the secondary structure of amino acid fragments and the Xaa-Pro peptide bond conformation.

Highlights

A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods
The cis conformation occurs rarely in polypeptides because of the higher intrinsic energy compared to the trans conformation [1]
Chou-Fasman parameters Figure (1) shows the comparison of the relative natural occurrence of the secondary structure types for cis and trans conformations of the Xaa-Pro peptide bond based on the PDB analyses

Summary

Introduction

A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. We analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation. The angles Ψ, Φ and Ω readily describe the arrangement of the six atoms in three-dimensional space: Ψ defines the angle of the N – Cα bond and Φ is given by the Cα-C' bond of the same residue whereas the Ω angle is defined between the. In contrast to other amino acids proline has a higher propensity for the cis conformation

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