Structural design principles for specific ultra-high affinity interactions between colicins/pyocins and immunity proteins

Abstract

The interactions of the antibiotic proteins colicins/pyocins with immunity proteins is a seminal model system for studying protein–protein interactions and specificity. Yet, a precise and quantitative determination of which structural elements and residues determine their binding affinity and specificity is still lacking. Here, we used comparative structure-based energy calculations to map residues that substantially contribute to interactions across native and engineered complexes of colicins/pyocins and immunity proteins. We show that the immunity protein α1–α2 motif is a unique structurally-dissimilar element that restricts interaction specificity towards all colicins/pyocins, in both engineered and native complexes. This motif combines with a diverse and extensive array of electrostatic/polar interactions that enable the exquisite specificity that characterizes these interactions while achieving ultra-high affinity. Surprisingly, the divergence of these contributing colicin residues is reciprocal to residue conservation in immunity proteins. The structurally-dissimilar immunity protein α1–α2 motif is recognized by divergent colicins similarly, while the conserved immunity protein α3 helix interacts with diverse colicin residues. Electrostatics thus plays a key role in setting interaction specificity across all colicins and immunity proteins. Our analysis and resulting residue-level maps illuminate the molecular basis for these protein–protein interactions, with implications for drug development and rational engineering of these interfaces.

Evolution of homo‐oligomerization of methionine S‐adenosyltransferases is replete with structure–function constrains

“…Energy calculations to analyze per‐residue contributions were performed following the methodology described previously. 45 , 85 , 86 The Finite Difference Poisson–Boltzmann method, as implemented in DelPhi, 87 was used to calculate the net electrostatic/polar contributions (ΔΔ G elec ) of each residue within 15 Å of the small interface in each tetramer complex. For each residue, electrostatic contributions from each side chain or the entire residue were calculated separately, and comparison of these separate calculations was used to determine if electrostatic contributions originate from the side‐chain of a residue, the main chain, or both.…”

“…Hydrogen atoms were added using CHARMM and the structures were subjected to conjugate gradient minimization with a harmonic restraint force of 50 kcal/mol/Å 2 applied to the heavy atoms. Energy calculations to analyze per‐residue contributions were performed following the methodology described previously 45,85,86 . The Finite Difference Poisson–Boltzmann method, as implemented in DelPhi, 87 was used to calculate the net electrostatic/polar contributions (ΔΔ G elec ) of each residue within 15 Å of the small interface in each tetramer complex.…”

Soluble Antimicrobial Peptide Pyocin of Pseudomonas aeruginosa and its Therapeutics: A Review Article

“…These are FpvAI, FpvAII and FptA, all of which are involved in the uptake of ironsiderophore complexes 35 . 36 Before being translocated through the membrane and killing their target. the order of the receptor recognition domain and translocation domain is generally reversed: the N-terminal domain is involved in recognition of the cell surface receptor 10 , domain II (not present in pyocin S1) has an unknown function and is dispensable for killing activity, the third domain is responsible for pyocin translocation and penetration,and the C-terminal domain carries the lethal activity 36 .…”