Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

Yang, Jordan; Naik, Nandita; Patel, Jagdish Suresh; Wylie, C. Scott; Gu, Wenze; Huang, Jessie; Ytreberg, F. Marty; Naik, Mandar T.; Weinreich, Daniel; Rubenstein, Brenda M.

doi:10.1371/journal.pone.0233509

Cited by 28 publications

(27 citation statements)

References 96 publications

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“…With regard to MD simulations, we find the strongest correlations between simulation observables and the experimental properties of thermal stability and KM. This appears to be in line with past results in which computational techniques predict thermal stability more easily than catalytic activity [72,73]. The finding that increased hydrophobic surface area on helix residues strongly correlates with increased thermal stability is curious.…”

Section: Discussionsupporting

confidence: 88%

Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity

Zhao

Rodrigues

Lozovsky

et al. 2021

Preprint

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To what degree are individual structural elements within proteins modular such that similar structures from unrelated proteins can be interchanged? We study sub-domain modularity by creating 20 chimeras of an enzyme, E. coli dihydrofolate reductase (DHFR), in which a catalytically important, 10-residue α-helical sequence is replaced by α-helical sequences from a diverse set of proteins. The chimeras stably fold but have a range of diminished thermal stabilities and catalytic activities. Evolutionary coupling analysis indicates that the residues of this α-helix are under selection pressure to maintain catalytic activity in DHFR. We performed molecular dynamics simulations using replica exchange with solute-tempering. Chimeras with low catalytic activity exhibit non-helical conformations that block the binding site and disrupt the positioning of the catalytically essential residue D27. Simulation observables and in vitro measurements of thermal stability and substrate binding affinity are strongly correlated. Several E. coli strains with chromosomally integrated chimeric DHFRs can grow, with growth rates that follow predictions from a kinetic flux model that depends on the intracellular abundance and catalytic activity of DHFR. Our findings show that although α-helices are not universally substitutable, the molecular and fitness effects of modular segments can be predicted by the biophysical compatibility of the replacement segment.

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Section: Discussionsupporting

confidence: 88%

Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity

Zhao

Rodrigues

Lozovsky

et al. 2021

Preprint

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“…While “ampicillin, 2500 μg/mL” [Stiffler et al, 2015] has been the ground truth assay of choice for previous work using unsupervised models to infer mutation effect for β ℓ [Hopf et al, 2017, Riesselman et al, 2018], and correlates strongly with “ampicillin, fitness” [Firnberg et al, 2014] and “amoxicillin, MIC” [Jacquier et al, 2013], it negatively correlates with “ampicillin, ΔΔG stat ” [Deng et al, 2012], and variably correlates with the same assay from the same paper but at lower concentrations “ampicillin [39, 156, 625] μg/mL” [Stiffler et al, 2015]. Similarly, if the consideration is instead how a mutation impacts β ℓ ’s ability to hydrolyze “cefotaxime, 0.15 μg/mL”, a different β -lactam antibiotic [Stiffler et al, 2015], or thermostability [Yang et al, 2020] - the outcomes also vary.…”

Section: Datamentioning

confidence: 99%

The structure-fitness landscape of pairwise relations in generative sequence models

Marshall

Wang

Stiffler³

et al. 2020

Preprint

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If disentangled properly, patterns distilled from evolutionarily related sequences of a given protein family can inform their traits - such as their structure and function. Recent years have seen an increase in the complexity of generative models towards capturing these patterns; from sitewise to pairwise to deep and variational. In this study we evaluate the degree of structure and fitness patterns learned by a suite of progressively complex models. We introduce pairwise saliency, a novel method for evaluating the degree of captured structural information. We also quantify the fitness information learned by these models by using them to predict the fitness of mutant sequences and then correlate these predictions against their measured fitness values. We observe that models that inform structure do not necessarily inform fitness and vice versa, contrasting recent claims in this field. Our work highlights a dearth of consistency across fitness assays as well as divergently provides a general approach for understanding the pairwise decomposable relations learned by a given generative sequence model.

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“…Both the test systems in this study were previously used by our lab to predict ∆∆G values for the same eight mutations using the non-rigorous methods FoldX and MD+FoldX, and rigorous coarsegrained umbrella sampling MD simulations. 56 The pmx with double-system/single-box approach clearly outperforms our previous FoldX 12,13 (1BRS:R 2 =0.59, 3HFM:R 2 =−0.005) and MD+FoldX [57][58][59] (1BRS:R 2 =0.62, 3HFM:R 2 =0.04) estimates in both the complexes. Interestingly, the all-atom pmx with double-system/single-box approach in both the complexes performs similarly to our previous coarse-grained (1BRS:R 2 =0.85, 3HFM:R 2 =0.35) method.…”

Section: Resultsmentioning

confidence: 69%

Implementing and assessing an alchemical method for calculating protein-protein binding free energy

Patel

Ytreberg

2020

Preprint

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Protein-protein binding is fundamental to most biological processes. It is important to be able to use computation to accurately estimate the change in protein-protein binding free energy due to mutations in order to answer biological questions that would be experimentally challenging, laborious or time consuming. Although non-rigorous free energy methods are faster, rigorous alchemical molecular dynamics-based methods are considerably more accurate and are becoming more feasible with the advancement of computer hardware and molecular simulation software. Even with sufficient computational resources, there are still major challenges to using alchemical free energy methods for protein-protein complexes, such as generating hybrid structures and topologies, maintaining a neutral net charge of the system when there is a charge-changing mutation, and setting up the simulation. In the current study, we have used the pmx package to generate hybrid structures and topologies, and a double-system/single-box approach to maintain the net charge of the system. To test the approach, we predicted relative binding affinities for two protein-protein complexes using a non-equilibrium alchemical method based on the Crooks fluctuation theorem and compared the results with experimental values. The method correctly identified stabilizing from destabilizing mutations for a small protein-protein complex, but was not as successful to the larger, more challenging antibody complex. In addition, the correlation between predicted and experimental relative binding affinities was high for smaller complex, and low for the other larger complex.

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Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

Cited by 28 publications

References 96 publications

Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity

Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity

The structure-fitness landscape of pairwise relations in generative sequence models

Implementing and assessing an alchemical method for calculating protein-protein binding free energy

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