Evolutionary constraints in NAL superfamily protein: Secondary structural segment trailing the beta strand 5 and alpha helix 10
The divergence in catalytic actions of N-acetyl neuraminic lyase (NAL) superfamily proteins, all of which have pyruvate as a substrate, suggests common ancestry. Lack of catalytic triad residues essential for binding pyruvate in annotated DHDPS proteins from Gram+ve B.clausii (PDBid-3E96) and O.hiyensis (PDBid-3D0C) indicated that these proteins are inactive and therefore could be possible early ancestors. Analysis revealed that the most appropriate cavity of these proteins is voluminous and has an elongated topography compared to the trimmed side-wise tilted cavity topography in all other NAL superfamily proteins. Strength and the morphology of the interface regions contouring the cavity are the significant determinants of the topography. It is possible that evolutionary forces led to modulation of the structural segments following the beta strand 5 and alpha helix 10, which are significant participants of interfacial regions. Major structural motions captured by molecular dynamics simulation differentiated the motion of the structural segment following the beta strand 5 of primitive forms as towards the periphery regions of the proteins compared to motion towards core in evolved active forms. We suggest that the motion shift towards the core consequently opened entry channel for substrates and evolution of side-wise tilted cavity.