Abstract
Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.
Highlights
Among a handful of mechanisms, which the bacteria have evolved to survive and grow in the presence of β-lactams, the most problematic phenotypes are observed in Gram-negative bacteria, including Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa (Tooke et al, 2019)
Phylogenetic analysis indicates KPC-2 and SME-1 are more similar than TEM-1 and SHV-1 (Supplementary Figure S2D)
The low root mean-squared deviation (RMSD) of the systems are consistent with the previous observation that class A β-lactamases are stable structures when studied on long timescales (Galdadas et al, 2018, 2021; Gobeil et al, 2019)
Summary
Among a handful of mechanisms, which the bacteria have evolved to survive and grow in the presence of β-lactams, the most problematic phenotypes are observed in Gram-negative bacteria, including Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa (Tooke et al, 2019) These organisms rapidly exchange plasmids that often carry genes encoding broad-spectrum β-lactamase enzymes, found on transposable elements (Davies and Davies, 2010). It was soon found that KPC-2 is identical to KPC-1, and since many more variants have been discovered, differing by only one or two amino acid substitutions (Arnold et al, 2011) These highly evolved enzymes can be found worldwide and can hydrolyse all clinically available β-lactams, including clavulanates, extended-spectrum cephalosporins, monobactams, and carbapenems (Leavitt et al, 2007; Drawz and Bonomo, 2010; Stoesser et al, 2017; Bush, 2018; Tooke et al, 2020). To work towards addressing such a risk, which history is teaching us to anticipate, this study provides supporting evidence in line with the alternative allosteric approach for inhibition of class A enzymes; a strategy which has already been receiving steady interest in TEM-1 and KPC-2 (Horn and Shoichet, 2004; Meneksedag et al, 2013; Bowman et al, 2015; Avcı et al, 2016; Hart et al, 2016; Grigorenko et al, 2017; Galdadas et al, 2018, 2021)
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
