Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

Abstract

We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility index quantify differences within backbone flexibility, whereas changes in the cooperativity correlation quantify differences within pairwise mechanical couplings. Regardless of metric, the same general conclusions are drawn. That is, small structural perturbations introduced by single point mutations have a frequent and pronounced affect on lysozyme flexibility that can extend over long distances. Specifically, an appreciable change occurs in backbone flexibility for 48% of the residues, and a change in cooperativity occurs in 42% of residue pairs. The average distance from mutation to a site with a change in flexibility is 17–20 Å. Interestingly, the frequency and scale of the changes within single point mutant structures are generally larger than those observed in the hen egg white lysozyme (HEWL) ortholog, which shares 61% sequence identity with human lysozyme. For example, point mutations often lead to substantial flexibility increases within the β-subdomain, which is consistent with experimental results indicating that it is the nucleation site for amyloid formation. However, β-subdomain flexibility within the human and HEWL orthologs is more similar despite the lowered sequence identity. These results suggest compensating mutations in HEWL reestablish desired properties.

Author Summary

The functional importance of protein dynamics is universally accepted, making the study of dynamical similarities and differences among proteins of the same function an intriguing problem. While some metrics are likely to be conserved across family, differences are also very common. In previous works we have used a Distance Constraint Model to quantify flexibility differences across sets of orthologous proteins, which reproduce this diversity. In the same manner, this work investigates changes occurring upon individual point mutations. Somewhat surprisingly, the small structural perturbations caused by mutation lead to changes throughout the protein. These changes can be quite large, actually surpassing the scale for differences between ortholog pairs. Moreover, changes in flexibility frequently occur at sites far from the mutation site. These results underscore the sensitivity of protein dynamics in connection with allostery, and help explain why differences across protein families are so common.