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The Structural Dynamics of Engineered β-Lactamases Vary Broadly on Three Timescales yet Sustain Native Function. Sci Rep 2019; 9:6656. [PMID: 31040324 PMCID: PMC6491436 DOI: 10.1038/s41598-019-42866-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/10/2019] [Indexed: 12/20/2022] Open
Abstract
Understanding the principles of protein dynamics will help guide engineering of protein function: altering protein motions may be a barrier to success or may be an enabling tool for protein engineering. The impact of dynamics on protein function is typically reported over a fraction of the full scope of motional timescales. If motional patterns vary significantly at different timescales, then only by monitoring motions broadly will we understand the impact of protein dynamics on engineering functional proteins. Using an integrative approach combining experimental and in silico methodologies, we elucidate protein dynamics over the entire span of fast to slow timescales (ps to ms) for a laboratory-engineered system composed of five interrelated β-lactamases: two natural homologs and three laboratory-recombined variants. Fast (ps-ns) and intermediate (ns-µs) dynamics were mostly conserved. However, slow motions (µs-ms) were few and conserved in the natural homologs yet were numerous and widely dispersed in their recombinants. Nonetheless, modified slow dynamics were functionally tolerated. Crystallographic B-factors from high-resolution X-ray structures were partly predictive of the conserved motions but not of the new slow motions captured in our solution studies. Our inspection of protein dynamics over a continuous range of timescales vividly illustrates the complexity of dynamic impacts of protein engineering as well as the functional tolerance of an engineered enzyme system to new slow motions.
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Gobeil SMC, Gagné D, Doucet N, Pelletier JN. 15N, 13C and 1H backbone resonance assignments of an artificially engineered TEM-1/PSE-4 class A β-lactamase chimera and its deconvoluted mutant. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:93-99. [PMID: 26386961 PMCID: PMC5419827 DOI: 10.1007/s12104-015-9645-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
The widespread use of β-lactam antibiotics has given rise to a dramatic increase in clinically-relevant β-lactamases. Understanding the structure/function relation in these variants is essential to better address the ever-growing incidence of antibiotic resistance. We previously reported the backbone resonance assignments of a chimeric protein constituted of segments of the class A β-lactamases TEM-1 and PSE-4 (Morin et al. in Biomol NMR Assign 4:127-130, 2010. doi: 10.1007/s12104-010-9227-8 ). That chimera, cTEM17m, held 17 amino acid substitutions relative to TEM-1 β-lactamase, resulting in a well-folded and fully functional protein with increased dynamics. Here we report the (1)H, (13)C and (15)N backbone resonance assignments of chimera cTEM-19m, which includes 19 substitutions and exhibits increased active-site perturbation, as well as one of its deconvoluted variants, as the first step in the analysis of their dynamic behaviours.
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Affiliation(s)
- Sophie M C Gobeil
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Donald Gagné
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
- INRS-Institut Armand-Frappier, Université du Québec, Québec, QC, Canada
- GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA
| | - Nicolas Doucet
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
- INRS-Institut Armand-Frappier, Université du Québec, Québec, QC, Canada
- GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC, Canada
| | - Joelle N Pelletier
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada.
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada.
- Department of Chemistry, Université de Montréal, Montréal, Canada.
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Gobeil SMC, Clouthier CM, Park J, Gagné D, Berghuis AM, Doucet N, Pelletier JN. Maintenance of native-like protein dynamics may not be required for engineering functional proteins. ACTA ACUST UNITED AC 2014; 21:1330-1340. [PMID: 25200606 DOI: 10.1016/j.chembiol.2014.07.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 06/27/2014] [Accepted: 07/09/2014] [Indexed: 12/16/2022]
Abstract
Proteins are dynamic systems, and understanding dynamics is critical for fully understanding protein function. Therefore, the question of whether laboratory engineering has an impact on protein dynamics is of general interest. Here, we demonstrate that two homologous, naturally evolved enzymes with high degrees of structural and functional conservation also exhibit conserved dynamics. Their similar set of slow timescale dynamics is highly restricted, consistent with evolutionary conservation of a functionally important feature. However, we also show that dynamics of a laboratory-engineered chimeric enzyme obtained by recombination of the two homologs exhibits striking difference on the millisecond timescale, despite function and high-resolution crystal structure (1.05 Å) being conserved. The laboratory-engineered chimera is thus functionally tolerant to modified dynamics on the timescale of catalytic turnover. Tolerance to dynamic variation implies that maintenance of native-like protein dynamics may not be required when engineering functional proteins.
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Affiliation(s)
- Sophie M C Gobeil
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Département de Biochimie, Université de Montréal, Montréal QC H3T 1J4, Canada
| | - Christopher M Clouthier
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Département de Chimie, Université de Montréal, Montréal QC H3T 1J4, Canada
| | - Jaeok Park
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Department of Biochemistry and Department of Microbiology and Immunology, McGill University, Montreal QC H3G 1Y6, Canada; GRASP Network, McGill University, Montréal QC H3G 1Y6, Canada
| | - Donald Gagné
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; GRASP Network, McGill University, Montréal QC H3G 1Y6, Canada; INRS-Institut Armand-Frappier, Université du Québec, Laval QC H7V 1B7, Canada
| | - Albert M Berghuis
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Department of Biochemistry and Department of Microbiology and Immunology, McGill University, Montreal QC H3G 1Y6, Canada; GRASP Network, McGill University, Montréal QC H3G 1Y6, Canada
| | - Nicolas Doucet
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; GRASP Network, McGill University, Montréal QC H3G 1Y6, Canada; INRS-Institut Armand-Frappier, Université du Québec, Laval QC H7V 1B7, Canada
| | - Joelle N Pelletier
- PROTEO Network, Université Laval, Québec QC G1V 0A6, Canada; Département de Biochimie, Université de Montréal, Montréal QC H3T 1J4, Canada; Département de Chimie, Université de Montréal, Montréal QC H3T 1J4, Canada; Center for Green Chemistry and Catalysis (CCVC), Montréal QC H3A 0B8, Canada.
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Meneksedag D, Dogan A, Kanlikilicer P, Ozkirimli E. Communication between the active site and the allosteric site in class A beta-lactamases. Comput Biol Chem 2013; 43:1-10. [DOI: 10.1016/j.compbiolchem.2012.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 11/22/2012] [Accepted: 12/03/2012] [Indexed: 11/16/2022]
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Clouthier CM, Morin S, Gobeil SMC, Doucet N, Blanchet J, Nguyen E, Gagné SM, Pelletier JN. Chimeric β-lactamases: global conservation of parental function and fast time-scale dynamics with increased slow motions. PLoS One 2012; 7:e52283. [PMID: 23284969 PMCID: PMC3528772 DOI: 10.1371/journal.pone.0052283] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 11/15/2012] [Indexed: 11/18/2022] Open
Abstract
Enzyme engineering has been facilitated by recombination of close homologues, followed by functional screening. In one such effort, chimeras of two class-A β-lactamases – TEM-1 and PSE-4 – were created according to structure-guided protein recombination and selected for their capacity to promote bacterial proliferation in the presence of ampicillin (Voigt et al., Nat. Struct. Biol. 2002 9:553). To provide a more detailed assessment of the effects of protein recombination on the structure and function of the resulting chimeric enzymes, we characterized a series of functional TEM-1/PSE-4 chimeras possessing between 17 and 92 substitutions relative to TEM-1 β-lactamase. Circular dichroism and thermal scanning fluorimetry revealed that the chimeras were generally well folded. Despite harbouring important sequence variation relative to either of the two ‘parental’ β-lactamases, the chimeric β-lactamases displayed substrate recognition spectra and reactivity similar to their most closely-related parent. To gain further insight into the changes induced by chimerization, the chimera with 17 substitutions was investigated by NMR spin relaxation. While high order was conserved on the ps-ns timescale, a hallmark of class A β-lactamases, evidence of additional slow motions on the µs-ms timescale was extracted from model-free calculations. This is consistent with the greater number of resonances that could not be assigned in this chimera relative to the parental β-lactamases, and is consistent with this well-folded and functional chimeric β-lactamase displaying increased slow time-scale motions.
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Affiliation(s)
- Christopher M. Clouthier
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Laval, Québec, Canada
- Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - Sébastien Morin
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Laval, Québec, Canada
- Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Laval Québec, Canada
| | - Sophie M. C. Gobeil
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Laval, Québec, Canada
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
| | - Nicolas Doucet
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Laval, Québec, Canada
- INRS–Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - Jonathan Blanchet
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Laval, Québec, Canada
- Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - Elisabeth Nguyen
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Laval, Québec, Canada
- Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - Stéphane M. Gagné
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Laval, Québec, Canada
- Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Laval Québec, Canada
| | - Joelle N. Pelletier
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Laval, Québec, Canada
- Département de Chimie, Université de Montréal, Montréal, Québec, Canada
- Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Volkov AN, Barrios H, Mathonet P, Evrard C, Ubbink M, Declercq JP, Soumillion P, Fastrez J. Engineering an allosteric binding site for aminoglycosides into TEM1-β-Lactamase. Chembiochem 2011; 12:904-13. [PMID: 21425229 DOI: 10.1002/cbic.201000568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Indexed: 11/09/2022]
Abstract
Allosteric regulation of enzyme activity is a remarkable property of many biological catalysts. Up till now, engineering an allosteric regulation into native, unregulated enzymes has been achieved by the creation of hybrid proteins in which a natural receptor, whose conformation is controlled by ligand binding, is inserted into an enzyme structure. Here, we describe a monomeric enzyme, TEM1-β-lactamase, that features an allosteric aminoglycoside binding site created de novo by directed-evolution methods. β-Lactamases are highly efficient enzymes involved in the resistance of bacteria against β-lactam antibiotics, such as penicillin. Aminoglycosides constitute another class of antibiotics that prevent bacterial protein synthesis, and are neither substrates nor ligands of the native β-lactamases. Here we show that the engineered enzyme is regulated by the binding of kanamycin and other aminoglycosides. Kinetic and structural analyses indicate that the activation mechanism involves expulsion of an inhibitor that binds to an additional, fortuitous site on the engineered protein. These analyses also led to the defining of conditions that allowed an aminoglycoside to be detected at low concentration.
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Affiliation(s)
- Alexander N Volkov
- Laboratoire d'Ingénierie des Protéines et des Peptides, Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
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Morin S, Clouthier CM, Gobeil S, Pelletier JN, Gagné SM. Backbone resonance assignments of an artificially engineered TEM-1/PSE-4 Class A β-lactamase chimera. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:127-130. [PMID: 20383614 DOI: 10.1007/s12104-010-9227-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 03/30/2010] [Indexed: 05/29/2023]
Abstract
The rapid evolution of Class A β-lactamases, which procure resistance to an increasingly broad panel of β-lactam antibiotics, underscores the urgency to better understand the relation between their sequence variation and their structural and functional features. To date, more than 300 clinically-relevant β-lactamase variants have been reported, and this number continues to increase. With the aim of obtaining insights into the evolutionary potential of β-lactamases, an artificially engineered, catalytically active chimera of the Class A TEM-1 and PSE-4 β-lactamases is under study by kinetics and NMR. Here we report the (1)H, (13)C and (15)N backbone resonance assignments for the 30 kDa chimera cTEM-17m. Despite its high molecular weight, the data provide evidence that this artificially-evolved chimeric enzyme is well folded. The hydrolytic activity of cTEM-17m was determined using the chromogenic substrate CENTA, with K (M) = 160 ± 35 μM and k (cat) = 20 ± 4 s(-1), which is in the same range as the values for TEM-1 and PSE-4 β-lactamases.
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Affiliation(s)
- Sébastien Morin
- PROTEO, the Québec Network for Research on Protein Structure, Function and Engineering, Université Laval, Québec, Canada.
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Doucet N, Savard PY, Pelletier JN, Gagné SM. NMR investigation of Tyr105 mutants in TEM-1 beta-lactamase: dynamics are correlated with function. J Biol Chem 2007; 282:21448-59. [PMID: 17426035 DOI: 10.1074/jbc.m609777200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The existence of coupled residue motions on various time scales in enzymes is now well accepted, and their detailed characterization has become an essential element in understanding the role of dynamics in catalysis. To this day, a handful of enzyme systems has been shown to rely on essential residue motions for catalysis, but the generality of such phenomena remains to be elucidated. Using NMR spectroscopy, we investigated the electronic and dynamic effects of several mutations at position 105 in TEM-1 beta-lactamase, an enzyme responsible for antibiotic resistance. Even in absence of substrate, our results show that the number and magnitude of short and long range effects on (1)H-(15)N chemical shifts are correlated with the catalytic efficiencies of the various Y105X mutants investigated. In addition, (15)N relaxation experiments on mutant Y105D show that several active-site residues of TEM-1 display significantly altered motions on both picosecond-nanosecond and microsecond-millisecond time scales despite many being far away from the site of mutation. The altered motions among various active-site residues in mutant Y105D may account for the observed decrease in catalytic efficiency, therefore suggesting that short and long range residue motions could play an important catalytic role in TEM-1 beta-lactamase. These results support previous observations suggesting that internal motions play a role in promoting protein function.
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Affiliation(s)
- Nicolas Doucet
- Département de Biochimie, Université de Montréal, Montréal, Québec H3C 3J7
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Savard PY, Gagné SM. Backbone Dynamics of TEM-1 Determined by NMR: Evidence for a Highly Ordered Protein†. Biochemistry 2006; 45:11414-24. [PMID: 16981701 DOI: 10.1021/bi060414q] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Backbone dynamics of TEM-1 beta-lactamase (263 amino acids, 28.9 kDa) were studied by 15N nuclear magnetic resonance relaxation at 11.7, 14.1, and 18.8 T. The high quality of the spectra allowed us to measure the longitudinal relaxation rate (R1), the transverse relaxation rate (R2), and the {1H}-15N NOE for up to 227 of the 250 potentially observable backbone amide groups. The model-free formalism was used to determine internal motional parameters using an axially anisotropic model. TEM-1 exhibits a small prolate axial anisotropy (D(parallel)/D(perpendicular) = 1.23 +/- 0.01) and a global correlation time (tau(m)) of 12.41 +/- 0.01 ns. The unusually high average generalized order parameter (S2) of 0.90 +/- 0.02 indicates that TEM-1 is one of the most ordered proteins studied by liquid-state NMR to date. Although the omega-loop has a high degree of order in the picosecond-to-nanosecond time scale (mean S2 value of 0.90 +/- 0.02), we observed the presence of microsecond-to-millisecond time scale motions for this loop, as for the vicinity of the active site. These motions could be relevant for the catalytic function of TEM-1. Amide exchange experiments were also performed, and several amide groups were not exchanged after 12 days, an indication that global motions in TEM-1 are also very limited. Although detailed dynamics characterization by NMR cannot be readily applied to TEM-1 in the presence of relevant substrates, the unusual picosecond-to-nanosecond dynamics behavior of TEM-1 presented here will be essential to the validation and improvement of future molecular dynamics simulations of TEM-1 in the presence of functionally relevant substrates.
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Affiliation(s)
- Pierre-Yves Savard
- Département de Biochimie et de Microbiologie and CREFSIP, Université Laval, Québec, Canada G1K 7P4
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