Distribution of amino acids in functional sites of proteins with high melting temperature

Abstract

The stability of proteins in its native state has an important implication on its function and evolution. The functional site analysis may lead to better understanding of how these amino acid distributions influence the melting temperature of proteins. It has been reported that increasing the fraction of hydrophobic contacts in a protein tends to raise melting temperature; increasing the fraction of repulsive charge contacts decrease the melting temperature and consistent with a destabilizing effect. The role of amino acid distribution as hydrophobic, charged and polar residues in proteins and mainly in its functional sites has been studied. Due to limited data availability, redundancy check and controlled environment parameters, the study was carried out with ten single chain-wild proteins having melting temperature above 80°C at pH 7. The analysis depicts that, the entire protein, hydrophobic residues are more frequent in single chain proteins and charged residues are more frequent in multi-chains proteins. In functional sites of these proteins, hydrophobic and charged residues are equally frequent in single chain proteins and charged residues are very high in multi-chains proteins. But, the polar residue distribution remains same for both single chain and multi-chain proteins and its functional sites.

Keywords: Classified amino acids; Functional residues; Melting temperature; Single and Multi-chain; Thermo-stable proteins.

Figure 1

1.a: The plot depicts the melting temperature of various proteins obtained by DSC technique at different pH; 1.b): The plot depicts the melting temperature of various proteins obtained by CD technique at different pH; 1.c); The plot depicts melting temperature of various proteins obtained by Absorption technique at different pH; 1.d): The plot depicts melting temperature of various proteins obtained by Fluorescence technique at different pH; 1.e): The plot depicts melting temperature of various proteins obtained by NMR technique at different pH.

Figure 2

2.a: The plot depicts the single chain proteins having melting temperature above 80°C at different pH [16]. 2. b) The plot depicts the multi-chains proteins having melting temperature above 80°C at different pH [16].

Figure 3

3.1a: Illustration of amini acids distribution among single-chains proteins having Tm> 100°c at different pH; 3.1b) Illustration of amini acids distribution among multi-chains proteins having Tm> 100°C at different pH; 3.2) Illustration of Proteins with many single chains as well as few multi-chains having Tm> 40°C at pH7; 3.3) Illustration of single chain two state proteins having Tm> 80°C at pH 7; 3.4) Illustration of multi-chain two state proteins having Tm> 80°C at pH 7; 3.5a) Illustration of functional site residues of single chain proteins having Tm> 80°C at pH 7; 3.5b) Illustration of functional site residues of multichains proteins having Tm> 80°C at pH 7

Figure 4

plot depicting the amino acid distribution (%) of single and multi-chain proteins having Tm>100°C and at different pH [19]. (Note: Different proteins used for our study are highlighted in VIBGYOR coloring scheme by its PDB ID)

Figure 5

5.a: Pictorial representation of the output of MAFFT program which depicts the multiple sequence alignment of usersubmitted sequences (note:cinsensus positions of amino acids are highlighted in VIBGYOR coloring scheme); 5.b): Snapshot for the phylogentic tree of user-submitted multiple sequence alignment for wild proteins particularly with single chain having Tm > 80°was performed using the software MAFFT [20].