title: Modelling proteins' hidden conformations to predict antibiotic resistance.
abstract: TEM β-lactamase confers bacteria with resistance to many antibiotics and rapidly evolves activity against new drugs. However, functional changes are not easily explained by differences in crystal structures. We employ Markov state models to identify hidden conformations and explore their role in determining TEM's specificity. We integrate these models with existing drug-design tools to create a new technique, called Boltzmann docking, which better predicts TEM specificity by accounting for conformational heterogeneity. Using our MSMs, we identify hidden states whose populations correlate with activity against cefotaxime. To experimentally detect our predicted hidden states, we use rapid mass spectrometric footprinting and confirm our models' prediction that increased cefotaxime activity correlates with reduced Ω-loop flexibility. Finally, we design novel variants to stabilize the hidden cefotaximase states, and find their populations predict activity against cefotaxime in vitro and in vivo. Therefore, we expect this framework to have numerous applications in drug and protein design.
authors.affiliation: Department of Biochemistry &Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA.
authors.forename: Kathryn M
authors.initials: KM
authors.lastname: Hart
authors.affiliation: Department of Biochemistry &Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA.
authors.forename: Chris M W
authors.initials: CM
authors.lastname: Ho
authors.affiliation: Department of Chemistry, Washington University in St Louis, One Brookings Drive, St Louis, Missouri 63130, USA.
authors.forename: Supratik
authors.initials: S
authors.lastname: Dutta
authors.affiliation: Department of Chemistry, Washington University in St Louis, One Brookings Drive, St Louis, Missouri 63130, USA.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Gross
authors.affiliation: Department of Biochemistry &Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA.|Department of Biomedical Engineering, and Center for Biological Systems Engineering, Washington University in St Louis, One Brookings Drive, St Louis, Missouri 63130, USA.
authors.forename: Gregory R
authors.initials: GR
authors.lastname: Bowman
mesh_terms: D000465:Algorithms; D000900:Anti-Bacterial Agents / Q000737:chemistry*; D002439:Cefotaxime / Q000737:chemistry; D018360:Crystallography, X-Ray; D015195:Drug Design; D024881:Drug Resistance, Bacterial; D004926:Escherichia coli / Q000201:enzymology*; D007700:Kinetics; D008390:Markov Chains; D013058:Mass Spectrometry; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D012680:Sensitivity and Specificity; D012997:Solvents; D001618:beta-Lactamases / Q000737:chemistry*
chemical_list: D000900:Anti-Bacterial Agents; D012997:Solvents; D001618:beta-Lactamases; C034413:beta-lactamase TEM-1; D002439:Cefotaxime