Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity

Abstract

The bacterial enzyme β-lactamase hydrolyzes the β-lactam ring of penicillin and chemically related antibiotics, rendering them ineffective. Due to rampant antibiotic overuse, the enzyme is evolving new resistance activities at an alarming rate. Related, the enzyme's global physiochemical properties exhibit various amounts of conservation and variability across the family. To that end, we characterize the extent of property conservation within twelve different class-A β-lactamases, and conclusively establish that the systematic variations therein parallel their evolutionary history. Large and systematic differences within electrostatic potential maps and pairwise residue-to-residue couplings are observed across the protein, which robustly reflect phylogenetic outgroups. Other properties are more conserved (such as residue pKa values, electrostatic networks, and backbone flexibility), yet they also have systematic variations that parallel the phylogeny in a statistically significant way. Similarly, the above properties also parallel the environmental condition of the bacteria they are from in a statistically significant way. However, it is interesting and surprising that the only one of the global properties (protein charge) parallels the functional specificity patterns; meaning antibiotic resistance activities are not significantly constraining the global physiochemical properties. Rather, extended spectrum activities can emerge from the background of nearly any set of electrostatic and dynamic properties.

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

“…Taken together, the above results demonstrate that T m is robust at N rep ≥6, whereas the mechanical properties are robust at much smaller values of N rep , which is consistent with our earlier results [25]. Upon careful inspection, low similarity pairs are more frequent in CC, relative to FI, which is also consistent with our prior results [25], [33], [34], [35], [57], [58], [59]. Good convergence to consistent results is obtained when representative structures are selected from each cluster at random (data not shown).…”

A Case Study Comparing Quantitative Stability–Flexibility Relationships Across Five Metallo-β-Lactamases Highlighting Differences Within NDM-1

“…There are four different BL classes, and the class-A enzymes are the most clinically relevant. Interestingly, the TEM-1 class-A enzyme has been shown to have an extremely rigid backbone (16), which is consistent with our results (17). Moreover, our backbone flexibility predictions are well conserved across the family, whereas allosteric couplings are overall quite variable.…”

Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations

“…As discussed above, the MPM correctly identifies the phosphorylation site as allosteric in three chemotaxis protein Y orthologs (26), which is the only conserved site identified across the set. As with the MPM results, our collective results reveal CC to be very sensitive to sequence and structural variations across protein families (28,30,31,(44)(45)(46)(47)(48)(49)(50), which is in complete agreement with various experimental comparisons of allosteric effects across protein families. Going as far back as 1970 (51), quantifiable differences in allosteric response have been used as a taxonomic marker in the 3-deoxy-D-arabino-heptulosonate-7-phosphate synthetase family.…”