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Hidden symmetries in the primary sequences of beta-barrel family

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Abstract

In this paper, we analyze the symmetries of beta-barrel proteins at both structure and sequence levels by using a modified recurrent quantification analysis. It shows that the structures and sequences have the same two-fold symmetry, although the later diverged considerably. This result may be helpful to understand the mechanism of protein evolution.

Introduction

Many protein domains are combinations of recurring substructures (Edward and Hwang, 2004). However, these domains usually have almost random primary sequences (Stephen et al., 2001, Taylor et al., 2002). How and why do the proteins exhibit obvious symmetry at the level of tertiary structures, and yet seldom symmetry in their primary sequences? Many progresses have been made in this problem (Zbilut et al., 2002, Heger and Holm, 2000). In a previous paper, we have revealed the hidden three-fold repetitions in the sequences of proteins from the beta-trefoil family taking account of physicochemical properties of amino acids (Xu and Xiao, 2005). In this paper we shall extend our method to the repetition analysis of both sequence and structure and take the beta-barrel folds as an example.

The beta-barrel domains (Fig. 1) are built of beta strands that can vary in number from 4 or 5 to over 10. These beta strands form two beta sheets that have the usual twist. Two such twisted beta sheets form a barrel-like structure when they are packed against each other. According to their topology structures, this family can be divided into up-and-down beta-barrel and jelly-roll beta-barrel. The up-and-down beta-barrel is formed by an array of beta-strands arranged in an antiparallel manner with each strand hydrogen-bonded to neighboring strands nearly always adjacent in the amino acid sequence (LaLonde et al., 1994). The jelly-roll beta-barrel is usually formed by two Greek-keys, and these proteins usually form two sheets with few if any hydrogen bonds between strands that belong to the different beta sheets. From direct observation of the tertiary structures we can easily find that all of the proteins in this family have two-fold quasi-symmetric structures. This shall be further confirmed in the following by a quantitative method. We shall also try to find the hidden repetitions of the primary sequences corresponding to their tertiary structures.

Section snippets

Methods

We shall investigate the two-fold symmetries of the primary sequences and tertiary structures by using a modified recurrence quantification analysis. The recurrence quantification analysis is a QSAR-related equivalent of a known sequence analysis tool that has originally been called “distance chart analysis” (Konopka, 1994, Konopka, 1997, Konopka, 2003, Wootton, 1997, Konopka and Smythers, 1987, Konopka and Chatterjee, 1988).

The detail of the modified recurrence plot can be found in the

Results and discussions

We shall take Atpase (PDB ID: 1E32) (Fig. 1) as an example to show the hidden symmetry of its primary sequence by using the modified recurrence plot. Fig. 1c is the modified structure recurrence plot of 1E32 and it is clear that the tertiary structure has a pseudo two-fold axis of symmetry. The three-dimensional structures of subsequences 1–45 and 46–89 are similar with each other and with the dRMSD being 2.0898 (Fig. 2). The secondary structures of the two parts are also very similar (Fig. 2

Acknowledgements

This work is supported by the NSFC under Grant Nos. 30525037 and 30470412 and the Foundation of the Ministry of Education of China.

References (14)

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