1
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Miton CM, Tokuriki N. Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw. Biochemistry 2023; 62:148-157. [PMID: 35830609 DOI: 10.1021/acs.biochem.2c00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the years, protein engineers have studied nature and borrowed its tricks to accelerate protein evolution in the test tube. While there have been considerable advances, our ability to generate new proteins in the laboratory is seemingly limited. One explanation for these shortcomings may be that insertions and deletions (indels), which frequently arise in nature, are largely overlooked during protein engineering campaigns. The profound effect of indels on protein structures, by way of drastic backbone alterations, could be perceived as "saltation" events that bring about significant phenotypic changes in a single mutational step. Should we leverage these effects to accelerate protein engineering and gain access to unexplored regions of adaptive landscapes? In this Perspective, we describe the role played by indels in the functional diversification of proteins in nature and discuss their untapped potential for protein engineering, despite their often-destabilizing nature. We hope to spark a renewed interest in indels, emphasizing that their wider study and use may prove insightful and shape the future of protein engineering by unlocking unique functional changes that substitutions alone could never achieve.
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Affiliation(s)
- Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 BC, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 BC, Canada
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2
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Galani I, Karaiskos I, Giamarellou H. Multidrug-resistant Klebsiella pneumoniae: mechanisms of resistance including updated data for novel β-lactam-β-lactamase inhibitor combinations. Expert Rev Anti Infect Ther 2021; 19:1457-1468. [PMID: 33945387 DOI: 10.1080/14787210.2021.1924674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Multi-drug-resistant Klebsiella pneumoniae is currently one of the most pressing emerging issues in bacterial resistance. Treatment of K.pneumoniae infections is often problematic due to the lack of available therapeutic options, with a relevant impact in terms of morbidity, mortality and healthcare-associated costs. Soon after the launch of Ceftazidime-Avibactam, one of the approved new β-lactam/β-lactamase inhibitor combinations, reports of ceftazidime-avibactam-resistant strains developing resistance during treatment were published. Being a hospital-associated pathogen, K.pneumoniae is continuously exposed to multiple antibiotics resulting in constant selective pressure, which in turn leads to additional mutations that are positively selected.Areas covered: Herein the authors present the K.pneumoniae mechanisms of resistance to different antimicrobials, including updated data for ceftazidime-avibactam.Expert opinion: K.pneumoniae is a nosocomial pathogen commonly implicated in hospital outbreaks with a propensity for antimicrobial resistance toward mainstay β-lactam antibiotics and multiple other antibiotic classes. Following the development of drug resistance and understanding the mechanisms involved, we can improve the efficacy of current antimicrobials, by applying careful stewardship and rational use to preserve their potential utility. The knowledge on antibiotic resistance mechanisms should be used to inform the design of novel therapeutic agents that might not be subject to, or can circumvent, mechanisms of resistance.
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Affiliation(s)
- Irene Galani
- Medicine, Infectious Diseases Laboratory, 4thDepartment of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ilias Karaiskos
- 1st Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Helen Giamarellou
- 1 Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
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3
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KPC Beta-Lactamases Are Permissive to Insertions and Deletions Conferring Substrate Spectrum Modifications and Resistance to Ceftazidime-Avibactam. Antimicrob Agents Chemother 2020; 64:AAC.01175-20. [PMID: 33020157 DOI: 10.1128/aac.01175-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/30/2020] [Indexed: 12/17/2022] Open
Abstract
To explore the mutational possibilities of insertions and deletions (indels) in the Klebsiella pneumoniae carbapenemase (KPC) beta-lactamase, we selected for ceftazidime-avibactam-resistant mutants. Of 96 screened mutants, we obtained 19 indels (2 to 15 amino acids), all located in the loops surrounding the active site. Three antibiotic susceptibility phenotypes emerged: an extended-spectrum-beta-lactamase-like phenotype, an activity restricted to ceftazidime, and a carbapenem-susceptible KPC-like phenotype. Tolerance for indels reflects the evolvability of KPC beta-lactamase, which could challenge the therapeutic management of patients.
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4
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Gonzalez CE, Roberts P, Ostermeier M. Fitness Effects of Single Amino Acid Insertions and Deletions in TEM-1 β-Lactamase. J Mol Biol 2019; 431:2320-2330. [PMID: 31034887 DOI: 10.1016/j.jmb.2019.04.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 11/16/2022]
Abstract
Short insertions and deletions (InDels) are a common type of mutation found in nature and a useful source of variation in protein engineering. InDel events have important consequences in protein evolution, often opening new pathways for adaptation. However, much less is known about the effects of InDels compared to point mutations and amino acid substitutions. In particular, deep mutagenesis studies on the distribution of fitness effects of mutations have focused almost exclusively on amino acid substitutions. Here, we present a near-comprehensive analysis of the fitness effects of single amino acid InDels in TEM-1 β-lactamase. While we found InDels to be largely deleterious, partially overlapping deletion-tolerant and insertion-tolerant regions were observed throughout the protein, especially in unstructured regions and at the end of helices. The signal sequence of TEM-1 tolerated InDels more than the mature protein. Most regions of the protein tolerated insertions more than deletions, but a few regions tolerated deletions more than insertions. We examined the relationship between InDel tolerance and a variety of measures to help understand its origin. These measures included evolutionary variation in β-lactamases, secondary structure identity, tolerance to amino acid substitutions, solvent accessibility, and side-chain weighted contact number. We found secondary structure, weighted contact number, and evolutionary variation in class A beta-lactamases to be the somewhat predictive of InDel fitness effects.
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Affiliation(s)
- Courtney E Gonzalez
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Paul Roberts
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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5
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Peng Y, Zeng W, Ye H, Han K, Dharmarajan V, Novick S, Wilson I, Griffin P, Friedman J, Lerner R. A General Method for Insertion of Functional Proteins within Proteins via Combinatorial Selection of Permissive Junctions. ACTA ACUST UNITED AC 2015; 22:1134-43. [DOI: 10.1016/j.chembiol.2015.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/12/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
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6
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Van de Water K, Soror SH, Wohlkonig A, van Nuland NAJ, Volkov AN. Crystallization and preliminary X-ray diffraction analysis of kanamycin-binding β-lactamase in complex with its ligand. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:703-6. [PMID: 21636917 PMCID: PMC3107148 DOI: 10.1107/s1744309111013832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 04/12/2011] [Indexed: 11/10/2022]
Abstract
TEM-1 β-lactamase is a highly efficient enzyme that is involved in bacterial resistance against β-lactam antibiotics such as penicillin. It is also a robust scaffold protein which can be engineered by molecular-evolution techniques to bind a variety of targets. One such β-lactamase variant (BlaKr) has been constructed to bind kanamycin (kan) and other aminoglycoside antibiotics, which are neither substrates nor ligands of native β-lactamases. In addition to recognizing kan, BlaKr activity is up-regulated by its binding via an activation mechanism which is not yet understood at the molecular level. In order to fill this gap, determination of the structure of the BlaKr-kan complex was embarked upon. A crystallization condition for BlaKr-kan was identified using high-throughput screening, and crystal growth was further optimized using streak-seeding and hanging-drop methods. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 47.01, b = 72.33, c = 74.62 Å, and diffracted to 1.67 Å resolution using synchrotron radiation. The X-ray structure of BlaKr with its ligand kanamycin should provide the molecular-level details necessary for understanding the activation mechanism of the engineered enzyme.
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Affiliation(s)
- Karen Van de Water
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Sameh H. Soror
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Alexandre Wohlkonig
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Nico A. J. van Nuland
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Alexander N. Volkov
- Department of Molecular and Cellular Interactions, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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7
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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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8
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Mathieu V, Fastrez J, Soumillion P. Engineering allosteric regulation into the hinge region of a circularly permuted TEM-1 beta-lactamase. Protein Eng Des Sel 2010; 23:699-709. [PMID: 20591901 DOI: 10.1093/protein/gzq041] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In nature, the activity of many enzymes involved in important biochemical pathways is controlled by binding a ligand in a site remote from the active site. The allosteric sites are frequently located in hinge regulatory subunits, in which a conformational change can occur and propagate to the active site. The enzymatic activity is then enhanced or decreased depending on the type of effectors. Many artificial binding sites have been created to engineer an allosteric regulation. Generally, these sites were engineered near the active site in loops or at the surface of contiguous helices or strands but rarely in hinge regions. This work aims at exploring the possibility of regulating a monomeric enzyme whose active site is located at the interface between two domains. We anticipated that binding of a ligand in the hinge region linking the domains would modify their positioning and, consequently, modulate the activity. Here, we describe the design of two mutants in a circularly permuted TEM-1 (cpTEM-1) beta-lactamase. The first one, cpTEM-1-His(3) was created by a rational design. It shows little regulation upon metal ion binding except for a weak activation with Zn(2+). The second one, cpTEM-1-3M-His(2), was selected by a directed evolution strategy. It is allosterically down-regulated by Zn(2+), Ni(2+) and Co(2+) with binding affinities around 300 microM.
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Affiliation(s)
- Valéry Mathieu
- Biochimie et Génétique Moléculaire Bactérienne, Institut des Sciences de la Vie, Université catholique de Louvain, Place Croix du Sud, 4-5 boîte 3, 1348 Louvain-la-Neuve, Belgium
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9
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Abstract
The insertion of peptide loops into the polypeptide chain of proteins at surface-exposed regions is an attractive avenue to modify the protein's properties or to evolve new functionalities. The strategy of peptide loop insertion has, for example, been used to create new binding sites in protein scaffolds and has led to the isolation of proteins with excellent binding affinities for various biological structures. Peptide loops have also been inserted into enzymes to modulate their catalytic properties. We recently used loop insertion mutagenesis to evolve a mutant of O(6)-alkylguanine-DNA-alkyltransferase (AGT) that reacts with the nonnatural substrate O(6)-propargylguanine for applications in molecular imaging. In this chapter, we describe in detail the protocols that we have applied (1) to identify sites in AGT that are permissive to loop insertion, (2) to manipulate DNA to create large loop insertion libraries, and (3) to identify mutants with desired properties. The experimental procedures are general and can easily be adapted for the insertion of peptide loops into other classes of enzymes or into any protein of interest.
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Affiliation(s)
- Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de, Lausanne (EPFL), Lausanne, Switzerland
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10
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11
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Rogers TA, Daniel RM, Bommarius AS. Deactivation of TEM-1 β-Lactamase Investigated by Isothermal Batch and Non-Isothermal Continuous Enzyme Membrane Reactor Methods. ChemCatChem 2009; 1:131-137. [PMID: 22039393 PMCID: PMC3203640 DOI: 10.1002/cctc.200900120] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Indexed: 11/08/2022]
Abstract
The thermal deactivation of TEM-1 β-lactamase was examined using two experimental techniques: a series of isothermal batch assays and a single, continuous, non-isothermal assay in an enzyme membrane reactor (EMR). The isothermal batch-mode technique was coupled with the three-state "Equilibrium Model" of enzyme deactivation, while the results of the EMR experiment were fitted to a four-state "molten globule model". The two methods both led to the conclusions that the thermal deactivation of TEM-1 β-lactamase does not follow the Lumry-Eyring model and that the T(eq) of the enzyme (the point at which active and inactive states are present in equal amounts due to thermodynamic equilibrium) is at least 10 °C from the T(m) (melting temperature), contrary to the idea that the true temperature optimum of a biocatalyst is necessarily close to the melting temperature.
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Affiliation(s)
- Thomas A. Rogers
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA (USA) 30332-0323 (USA), Fax: (+ 1) 404-894-2291
| | - Roy M. Daniel
- Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, 3240 (New Zealand), Fax: (+ 64) 7-8384324
| | - Andreas S. Bommarius
- School of Chemical and Biomolecular Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA (USA) 30332-0323 (USA), Fax: (+ 1) 404-894-2291
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12
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An antibody loop replacement design feasibility study and a loop-swapped dimer structure. Protein Eng Des Sel 2008; 22:93-101. [DOI: 10.1093/protein/gzn072] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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13
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14
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Vandevenne M, Filee P, Scarafone N, Cloes B, Gaspard G, Yilmaz N, Dumoulin M, François JM, Frère JM, Galleni M. The Bacillus licheniformis BlaP beta-lactamase as a model protein scaffold to study the insertion of protein fragments. Protein Sci 2007; 16:2260-71. [PMID: 17893363 PMCID: PMC2204133 DOI: 10.1110/ps.072912407] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Using genetic engineering technologies, the chitin-binding domain (ChBD) of the human macrophage chitotriosidase has been inserted into the host protein BlaP, a class A beta-lactamase produced by Bacillus licheniformis. The product of this construction behaved as a soluble chimeric protein that conserves both the capacity to bind chitin and to hydrolyze beta-lactam moiety. Here we describe the biochemical and biophysical properties of this protein (BlaPChBD). This work contributes to a better understanding of the reciprocal structural and functional effects of the insertion on the host protein scaffold and the heterologous structured protein fragments. The use of BlaP as a protein carrier represents an efficient approach to the functional study of heterologous protein fragments.
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Affiliation(s)
- Marylène Vandevenne
- Macromolécules Biologiques, Centre d'Ingénierie des Protéines, Université de Liège, Liège, Belgium
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15
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Herman A, Tawfik DS. Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Eng Des Sel 2007; 20:219-26. [PMID: 17483523 DOI: 10.1093/protein/gzm014] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The directed evolution of proteins has benefited greatly from site-specific methods of diversification such as saturation mutagenesis. These techniques target diversity to a number of chosen positions that are usually non-contiguous in the protein's primary structure. However, the number of targeted positions can be large, thus leading to impractically large library size, wherein almost all library variants are inactive and the likelihood of selecting desirable properties is extremely small. We describe a versatile combinatorial method for the partial diversification of large sets of residues. Our library oligonucleotides comprise randomized codons that are flanked by wild-type sequences. Adding these oligonucleotides to an assembly PCR of wild-type gene fragments incorporates the randomized cassettes, at their target sites, into the reassembled gene. Varying the oligonucleotides concentration resulted in library variants that carry a different average number of mutated positions that comprise a random subset of the entire set of diversified codons. This method, dubbed Incorporating Synthetic Oligos via Gene Reassembly (ISOR), was used to create libraries of a cytosine-C5 methyltransferase wherein 45 individual positions were randomized. One library, containing an average of 5.6 mutated residues per gene, was selected, and mutants with wild-type-like activities isolated. We also created libraries of serum paraoxonase PON1 harboring insertions and deletions (indels) in various areas surrounding the active site. Screening these libraries yielded a range of mutants with altered substrate specificities and indicated that certain regions of this enzyme have a surprisingly high tolerance to indels.
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Affiliation(s)
- Asael Herman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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16
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Wright CM, Heins RA, Ostermeier M. As easy as flipping a switch? Curr Opin Chem Biol 2007; 11:342-6. [PMID: 17466569 DOI: 10.1016/j.cbpa.2007.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 04/17/2007] [Indexed: 11/15/2022]
Abstract
Proteins that behave as switches help to establish the complex molecular logic that is central to biological systems. Aspiring to be nature's equal, researchers have successfully created protein switches of their own design; in particular, numerous and varied zinc-triggered switches have been made. Recent studies in which such switches have been readily identified from combinatorial protein libraries support the notion that proteins are primed to show allosteric behavior and that newly created ligand-binding sites will often be functionally coupled to the original activity of the protein. If true, this notion suggests that switch engineering might be more tractable than previously thought, boding well for the basic science, sensing and biomedical applications for which protein switches hold much promise.
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Affiliation(s)
- Chapman M Wright
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218-2681, USA
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17
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Liang J, Kim JR, Boock JT, Mansell TJ, Ostermeier M. Ligand binding and allostery can emerge simultaneously. Protein Sci 2007; 16:929-37. [PMID: 17400921 PMCID: PMC2206642 DOI: 10.1110/ps.062706007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A heterotropic allosteric effect involves an effector molecule that is distinct from the substrate or ligand of the protein. How heterotropic allostery originates is an unanswered question. We have previously created several heterotropic allosteric enzymes by recombining the genes for TEM1 beta-lactamase (BLA) and maltose binding protein (MBP) to create BLAs that are positively or negatively regulated by maltose. We show here that one of these engineered enzymes has approximately 10(6) M(-1) affinity for Zn(2+), a property that neither of the parental proteins possesses. Furthermore, Zn(2+) is a negative effector that noncompetitively switches off beta-lactam hydrolysis activity. Mutagenesis experiments indicate that the Zn(2+)-binding site does not involve a histidine or a cysteine, which is atypical of natural Zn(2+)-binding sites. These studies also implicate helices 1 and 12 of the BLA domain in allosteric signal propagation. These results support a model for the evolution of heterotropic allostery in which effector affinity and allosteric signaling emerge simultaneously.
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Affiliation(s)
- Jing Liang
- Program in Molecular and Computational Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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18
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Mathonet P, Barrios H, Soumillion P, Fastrez J. Selection of allosteric beta-lactamase mutants featuring an activity regulation by transition metal ions. Protein Sci 2006; 15:2335-43. [PMID: 16963642 PMCID: PMC2242392 DOI: 10.1110/ps.062304406] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Libraries of phage-displayed beta-lactamase mutants in which up to three loops have been engineered by genetic introduction of random peptide sequences or by randomization of the wild-type sequence have been submitted to selection protocols designed to find mutants in which binding of transition metal ions to the engineered secondary binding site leads to significant effects on the enzymatic activity. A double-selection protocol was applied: The phage-displayed libraries were first selected for transition metal ions affinity by panning on IMAC support, then a second selection step was applied to isolate mutants that have retained significant catalytic activity. The analysis of the kinetic properties of mutants in the presence of nickel, copper, or zinc ions allowed isolation of a few mutants whose activity was either enhanced or inhibited by factors up to three and >10, respectively, in a metal-specific manner. A remarkable mutant exhibiting differential allosteric regulation depending on the metal was found. Its activity was activated by nickel ion binding, inhibited by cupric ion binding, and nearly unaffected by zinc ions. These observations point to an interesting potential for up- or down-regulation of activity within a monomeric enzyme by binding to an "allosteric site" relatively remote from the active site.
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Affiliation(s)
- Pascale Mathonet
- Laboratoire de Biochimie Physique et des Biopolymères, Institut des Sciences de la Vie, Université catholique de Louvain, B1348 Louvain la Neuve, Belgium
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