Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations

Abstract

A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.

Modularity of the hydrophobic core and evolution of functional diversity in fold A glycosyltransferases

“…Protein kinases contain an extended hydrophobic network connecting the ATP and substrate-binding lobes, termed the “spines,” which are dynamically assembled during kinase activation ( 22 ) and the suboptimal packing of the spine residues enable dynamic regulation of catalytic activity ( 19 , 23 , 24 ). Indeed, malleable cores have been implicated in allosteric regulation or inhibition in other enzyme families as well ( 25 , 26 , 27 ), but the role of conserved core in GT-A evolution and function has not been systematically investigated.…”