A General Mechanism for the Propagation of Mutational Effects in Proteins

Abstract

Mutations in the hydrophobic interior of proteins are generally thought to weaken the interactions only in their immediate neighborhood. This forms the basis of protein engineering-based studies of folding mechanism and function. However, mutational work on diverse proteins has shown that distant residues are thermodynamically coupled, with the network of interactions within the protein acting as signal conduits, thus raising an intriguing paradox. Are mutational effects localized, and if not, is there a general rule for the extent of percolation and the functional form of this propagation? We explore these questions from multiple perspectives in this work. Perturbation analysis of interaction networks within proteins and microsecond long molecular dynamics simulations of several aliphatic mutants of ubiquitin reveal strong evidence of the distinct alteration of distal residue-residue communication networks. We find that mutational effects consistently propagate into the second shell of the altered site (even up to 15-20 Å) in proportion to the perturbation magnitude and dissipate exponentially with a decay distance constant of ∼4-5 Å. We also report evidence for this phenomenon from published experimental nuclear magnetic resonance data that strikingly resemble predictions from network theory and molecular dynamics simulations. Reformulating these observations onto a statistical mechanical model, we reproduce the stability changes of 375 mutations from 19 single-domain proteins. Our work thus reveals a robust energy dissipation-cum-signaling mechanism in the interaction network within proteins, quantifies the partitioning of destabilization energetics around the mutation neighborhood, and presents a simple theoretical framework for modeling the allosteric effects of point mutations.

Effect of site‐directed point mutations on protein misfolding: A simulation study

“…These low misfolding and unfolding probability values demonstrate the tolerance of proteins toward most mutations and only a few site‐directed point mutations can disrupt the structure of the protein . This structural robustness of proteins may be due to the dispersion and dissipation of structural perturbations due to cumulative point mutations . The energy landscape theory clearly explains the low unfolding probability as compared to the misfolding probability.…”

“…This differential destabilizing effect of the core and surface sites indicates that the core sites are more mutation sensitive and play a dominant role in determining the stability of proteins. This higher sensitivity/destabilization of the core sites arise due to a weak packing of the hydrophobic interior due to site directed point mutations …”

“…The substitution of hydrophobic residues in the core usually stabilize the protein. But sometimes proteins misfold due to steric hindrance imposed by the substitution of bulky residues or decrease in the packing of hydrophobic interior on substitution of small residues . The substitution of polar/charged residues at the surface stabilize the protein by forming hydrogen bonds with the solvent while in the core they may disrupt the hydrophobic contacts and misfold the protein .…”

“…[2][3][4][5]7,9,12 This structural robustness of proteins may be due to the dispersion and dissipation of structural perturbations due to cumulative point mutations. 57,58 The energy landscape theory 16 residue in the designed sequences is calculated using DSSP. 59 The relative surface accessibility (RSA) is calculated as the ratio of the surface accessibility of an amino acid residue to the maximum surface accessibility of the same amino acid residue.…”

Structural effects of point mutations in proteins

“…In particular, long range perturbation, such as the propagation of the destabilization into the second shell, at the origin of the allosteric effects that have been evidence by Ref. ( ). We will further investigate these effects by analyzing all significant RMSD whether the positions are mutated or not.…”