The importance of hydrogen bonds in predicting stability of thermophilic proteins is well documented in literature (Vogt et al., 1997). The number of hydrogen bonds in thermophilic proteins and their mesophilic counterparts were calculated and the results normalized with the length of proteins show no significant difference in the total number of hydrogen bonds of thermophilic proteins and mesophilic proteins in the pairs (Figure 4). Further analysis on separating the total number of hydrogen bonds into four categories; Main chain – Main chain, Side chain – Side chain and Main chain – Side chain was also not able to reveal the reason behind the thermal stability of thermophilic proteins. ...view middle of the document...
Such interactions might play a role in increasing the compactness and in turn influence the stability of thermophilic proteins.
Discrimination by amino acid properties:
Earlier studies show that amino acid properties have good correlation with stability of proteins (Gromiha et al., 1999). Here in the present study various physico-chemical amino acid properties were calculated and normalized with the length of the protein. Our study shows that several properties were capable of distinguishing thermophilic and mesophilic proteins at various levels of solvent accessibility; buried, partially buried, partially exposed and exposed regions (Figure 6). Thermophilic proteins were found to have amino acids with molecular weight higher than that of their mesophilic counterparts. Similarly shape and volume of amino acids were higher in majority of thermophiles across all regions of the protein. It is well known that shape increases with increase in carbon atoms of residues and this leads to a subsequent increase in volume and molecular weight also. This is consistent with our present observation of side chain carbon HFE and hydrogen bond analysis suggesting preferential incorporation of large amino acid residues Arg, Trp, Tyr and Glu by thermophilic proteins resulting in increased thermal stability.
Thermodynamic transfer hydrophobicity, isoelectric point, bulkiness, unfolding entropy change for the amino acids of thermophilic proteins were found to be higher across all regions of the proteins and these properties are known to influence the compressibility of proteins (Gromiha and Ponnuswamy, 1993). The amino acids which form thermophilic proteins were found to have higher helical tendency whereas the amino acids in mesophiles have higher turn and loop tendency (Figure 6). The choice of amino acids by nature that make up a protein not only determines its function but is also crucial in defining the thermal stability of that protein. Further understanding of this interesting behaviour can aid in design of stable mutants that increase the thermal stability of proteins without compromising the functional abilities of specific folds.
Influence of residue-residue contacts on protein stability:
Various studies show that...