Analysis of salt-bridges in prolyl oligopeptidase from Pyrococcus furiosus and Homo sapiens

Abstract

Hyper thermophilic archaea not only tolerate high temperature but also operate its biochemical machineries, normally under these conditions. However, the structural signatures in proteins that answer for the hyper thermo-stability relative to its mesophilic homologue remains poorly understood. We present comparative analyses of sequences, structures and salt-bridges of prolyl-oligopeptidase from Pyrococcus furiosus (pfPOP - PDB ID: 5T88) and human (huPOP - PDB ID: 3DDU). A similar level of hydrophobic and hydrophilic residues in pfPOP and huPOP is observed. A low level of interactions between shell-waters and atom-types in pfPOP indicated hyper thermophilic features are negligible. Salt-bridge-forming-residues (sbfrs) are high in pfPOP's core and surface (pfPOP). Increased sbfrs largely indicate specific-electrostatic is important for thermo stability in pfPOP. Four classes of sbfrs are found namely positionally non-conservative (PNCS), conservative (PCS), unchanged (PU) and interchanged (PIC) type of substitutions. PNCS-sbfrs constitutes 28% and it is associated with the topology of pfPOP at high temperature. PCS helps to increase the salt-bridge population. It is also found that PU maintains similar salt-bridges at the active site and other binding sites while PIC abolishes mesophilic patterns.

Intrinsic basis of thermostability of prolyl oligopeptidase from Pyrococcus furiosus

“…Relative to 3ddu, such changes in intrinsic properties, such as an increase in the hydrophilicity of the sequence of 5t88, are due to an increase in the number of salt-bridges. It has been shown earlier that the number of salt-bridges in 5t88 is higher 19 , 24 , 33 . Our current work shows that the above observation is not the only reason for 5t88's thermostability.…”

“…Since the above-mentioned favorable characteristics and weak forces are originated from the amino acid sequence and since there are many variations in the homologous position in different sequences, a general strategy of protein thermostability is unlikely. Compared to HuP, the number of loops in PfP has decreased by 94 residues and the number of ion-pairs, in turn, has increased 19 , 24 , 33 . Incidentally, the energy and binary properties of these ion-pairs and their microenvironments are unknown today.…”

“…Since most of 5t88's salt-bridges are at the surface (67%), the desolvation cost will be lower than that of 3ddu (58%). The difference between the homologous positions of PfP and HuP is about 75% 24 . In the case of the former, most of these substituted residues are hydrophilic, facilitating the salt-bridge to move towards the surface.…”

“…In comparison to HuP, reduction of the loops and increase in the frequency of the salt-bridge have been the cause of thermostability of the PfP 19 , 24 , 33 . The energy contribution of salt-bridge and microenvironment in this context is still unknown.…”

Salt-Bridges in the Microenvironment of Stable Protein Structures

“…Salt-bridge is a specific electrostatic interaction whose importance especially in protein structure specific binary design (core vs surface, local vs long-ranged, etc. ), folding, and stability has been worked out [ 8 , 9 , 10 , 11 ]. There are two types of salt-bridges, namely isolated-pair (ip) and network-pair (nu) [ 12 ].…”