Identification of distant co-evolving residues in antigen 85C from Mycobacterium tuberculosis using statistical coupling analysis of the esterase family proteins

Abstract

A fundamental goal in cellular signaling is to understand allosteric communication, the process by which signals originating at one site in a protein propagate reliably to affect distant functional sites. The general principles of protein structure that underlie this process remain unknown. Statistical coupling analysis (SCA) is a statistical technique that uses evolutionary data of a protein family to measure correlation between distant functional sites and suggests allosteric communication. In proteins, very distant and small interactions between collections of amino acids provide the communication which can be important for signaling process. In this paper, we present the SCA of protein alignment of the esterase family (pfam ID: PF00756) containing the sequence of antigen 85C secreted by Mycobacterium tuberculosis to identify a subset of interacting residues. Clustering analysis of the pairwise correlation highlighted seven important residue positions in the esterase family alignments. These residues were then mapped on the crystal structure of antigen 85C (PDB ID: 1DQZ). The mapping revealed correlation between 3 distant residues (Asp38, Leu123 and Met125) and suggests allosteric communication between them. This information can be used for a new drug against this fatal disease.

Keywords: Mycobacterium tuberculosis; Protein Data Bank.; antigen 85C; clustering analysis; covariance; esterase family; multiple sequence alignments; pfam; statistical coupling analysis.

Fig. 1. Sequence conservation in the esterase family multiple sequence alignment.

The degree of sequence conservation is plotted along the protein sequence with high values indicating high conservation. The plot corresponds to the diagonal elements.

Fig. 2. Histogram of pairwise correlation values.

The figure suggests that only a few pairs correlate with a significant correlation where as most of the correlation values (99%) lie around the mean value of 0.040978.

Fig. 3. Heat map of the correlation matrix.

The red pixels represent high correlation values and as we scale down the blue pixels represent low correlation values.

Fig. 4. Dendogram representing clustering analysis of pairwise correlation values.

The cluster represented in green is the cluster with the most significantly coupled residue positions. X-axis represents the residue position in the truncated alignment and Y-axis represents the clustering distance between any two-residue positions. The arrow indicates a cluster of seven residues.

Fig. 5. Mapping of the 7 residue positions highlighted by SCA onto the crystal structure of antigen 85 C (PDB ID: 1DQZ).

The residues shown are Asp38, Val66, Phe98, Leu123, Met125, Trp186 and Ser215. The pairs in red Asp38, Leu123 and Asp38, Met125 seem to show physical interaction through allostery.

Fig. 6. Structures of the Mycobacterium tuberculosis 30 kDa major secretory protein (Antigen 85B).

A mycolyl transferase (PDB ID: 1FOP), another esterase showing similar pocket.