A new computational model to study mass inhomogeneity and hydrophobicity inhomogeneity in proteins.
We propose a simple yet reliable computational framework that characterizes the differential mass and hydrophobicity distribution within structural classes of proteins. Radial partitioning of protein interior that could successfully distinguish the mass and hydrophobicity distribution patterns in extremophilic proteins from that in their structurally aligned mesophilic counterparts. Distance-dependent mass and hydrophobicity magnitudes could retrieve vital structural insights; needed to probe the hidden connections between packing, folding and stability within different structural classes of proteins, with causality. New computational markers; one, to represent the total mass content; other, related to hydrophobic centrality of proteins, are proposed as well. Results reveal that mass and hydrophobicity packing within extremophilic proteins is indeed more compact than that in their mesophilic counterparts. Analysis of structural constraints within them vindicate it. Total mass (and hydrophobicity) content is found to be maximum in alpha/beta thermophilic proteins and minimum for the all-alpha mesophilic proteins.
Banerji
Anirban
A
Bioinformatics Centre, University of Pune, Pune, Maharashtra, India.
Ghosh
Indira
I
D003198:Computer Simulation; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*
D011506:Proteins