1
|
Lu S, Hu L, Lin H, Judge A, Rivera P, Palaniappan M, Sankaran B, Wang J, Prasad BVV, Palzkill T. An active site loop toggles between conformations to control antibiotic hydrolysis and inhibition potency for CTX-M β-lactamase drug-resistance enzymes. Nat Commun 2022; 13:6726. [PMID: 36344533 PMCID: PMC9640584 DOI: 10.1038/s41467-022-34564-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
Abstract
β-lactamases inactivate β-lactam antibiotics leading to drug resistance. Consequently, inhibitors of β-lactamases can combat this resistance, and the β-lactamase inhibitory protein (BLIP) is a naturally occurring inhibitor. The widespread CTX-M-14 and CTX-M-15 β-lactamases have an 83% sequence identity. In this study, we show that BLIP weakly inhibits CTX-M-14 but potently inhibits CTX-M-15. The structure of the BLIP/CTX-M-15 complex reveals that binding is associated with a conformational change of an active site loop of β-lactamase. Surprisingly, the loop structure in the complex is similar to that in a drug-resistant variant (N106S) of CTX-M-14. We hypothesized that the pre-established favorable loop conformation of the N106S mutant would facilitate binding. The N106S substitution results in a ~100- and 10-fold increase in BLIP inhibition potency for CTX-M-14 and CTX-M-15, respectively. Thus, this indicates that an active site loop in β-lactamase toggles between conformations that control antibiotic hydrolysis and inhibitor susceptibility. These findings highlight the role of accessible active site conformations in controlling enzyme activity and inhibitor susceptibility as well as the influence of mutations in selectively stabilizing discrete conformations.
Collapse
Affiliation(s)
- Shuo Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hanfeng Lin
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Paola Rivera
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
2
|
Huang L, So PK, Chen YW, Leung YC, Yao ZP. Interdomain flexibility and interfacial integrity of β-lactamase inhibitory protein (BLIP) modulate its binding to class A β-lactamases. J Biol Chem 2021; 297:100980. [PMID: 34302811 PMCID: PMC8363833 DOI: 10.1016/j.jbc.2021.100980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/10/2021] [Accepted: 07/16/2021] [Indexed: 11/05/2022] Open
Abstract
β-Lactamase inhibitory protein (BLIP) consists of a tandem repeat of αβ domains conjugated by an interdomain loop and can effectively bind and inactivate class A β-lactamases, which are responsible for resistance of bacteria to β-lactam antibiotics. The varied ability of BLIP to bind different β-lactamases and the structural determinants for significant enhancement of BLIP variants with a point mutation are poorly understood. Here, we investigated the conformational dynamics of BLIP upon binding to three clinically prevalent class A β-lactamases (TEM1, SHV1, and PC1) with dissociation constants between subnanomolar and micromolar. Hydrogen deuterium exchange mass spectrometry revealed that the flexibility of the interdomain region was significantly suppressed upon strong binding to TEM1, but was not significantly changed upon weak binding to SHV1 or PC1. E73M and K74G mutations in the interdomain region improved binding affinity toward SHV1 and PC1, respectively, showing significantly increased flexibility of the interdomain region compared to the wild-type and favorable conformational changes upon binding. In contrast, more rigidity of the interfacial loop 135–145 was observed in these BLIP mutants in both free and bound states. Consistently, molecular dynamics simulations of BLIP exhibited drastic changes in the flexibility of the loop 135–145 in all complexes. Our results indicated for the first time that higher flexibility of the interdomain linker, as well as more rigidity of the interfacial loop 135–145, could be desirable determinants for enhancing inhibition of BLIP to class A β-lactamases. Together, these findings provide unique insights into the design of enhanced inhibitors.
Collapse
Affiliation(s)
- Liwen Huang
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen, China
| | - Pui-Kin So
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Yu Wai Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Yun-Chung Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Zhong-Ping Yao
- State Key Laboratory of Chemical Biology and Drug Discovery, Research Institute for Future Food and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China; State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen, China.
| |
Collapse
|
3
|
Huang L, So PK, Chen YW, Leung YC, Yao ZP. Conformational Dynamics of the Helix 10 Region as an Allosteric Site in Class A β-Lactamase Inhibitory Binding. J Am Chem Soc 2020; 142:13756-13767. [PMID: 32686406 DOI: 10.1021/jacs.0c04088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
β-Lactamase inhibitory protein (BLIP) can effectively inactivate class A β-lactamases, but with very different degrees of potency. Understanding the different roles of BLIP in class A β-lactamases inhibition can provide insights for inhibitor design. However, this problem was poorly solved on the basis of the static structures obtained by X-ray crystallography. In this work, ion mobility mass spectrometry, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics simulation revealed the conformational dynamics of three class A β-lactamases with varying inhibition efficiencies by BLIP. A more extended conformation of PC1 was shown compared to those of TEM1 and SHV1. Localized dynamics differed in several important loop regions, that is, the protruding loop, H10 loop, Ω loop, and SDN loop. Upon binding with BLIP, these loops cooperatively rearranged to enhance the binding interface and to inactivate the catalytic sites. In particular, unfavorable changes in conformational dynamics were found in the protruding loop of SHV1 and PC1, showing less effective binding. Intriguingly, the single mutation on BLIP could compensate for the unfavored changes in this region, and thus exhibit enhanced inhibition toward SHV1 and PC1. Additionally, the H10 region was revealed as an important allosteric site that could modulate the inhibition of class A β-lactamases. It was suggested that the rigid protruding loop and flexible H10 region might be determinants for the effective inhibition of TEM1. Our findings provided unique and explicit insights into the conformational dynamics of β-lactamases and their bindings with BLIP. This work can be extended to other β-lactamases of interest and inspire the design of novel inhibitors.
Collapse
Affiliation(s)
- Liwen Huang
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Food Safety and Technology Research Centre, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Pui-Kin So
- The University Research Facility in Life Sciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Yu Wai Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Yun-Chung Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China
| | - Zhong-Ping Yao
- State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Food Safety and Technology Research Centre, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong Special Administrative Region, China.,State Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation) and Shenzhen Key Laboratory of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen 518057, China
| |
Collapse
|
4
|
Huang W, Soeung V, Boragine DM, Palzkill T. Mapping Protein-Protein Interaction Interface Peptides with Jun-Fos Assisted Phage Display and Deep Sequencing. ACS Synth Biol 2020; 9:1882-1896. [PMID: 32502338 DOI: 10.1021/acssynbio.0c00242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions govern many cellular processes, and identifying binding interaction sites on proteins can facilitate the discovery of inhibitors to block such interactions. Here we identify peptides from a randomly fragmented plasmid encoding the β-lactamase inhibitory protein (BLIP) and the Lac repressor (LacI) that represent regions of protein-protein interactions. We utilized a Jun-Fos-assisted phage display system that has previously been used to screen cDNA and genomic libraries to identify antibody antigens. Affinity selection with polyclonal antibodies against LacI or BLIP resulted in the rapid enrichment of in-frame peptides from various regions of the proteins. Further, affinity selection with β-lactamase enriched peptides that encompass regions of BLIP previously shown to contribute strongly to the binding energy of the BLIP/β-lactamase interaction, i.e., hotspot residues. Further, one of the regions enriched by affinity selection encompassed a disulfide-constrained region of BLIP that forms part of the BLIP interaction surface in the native complex that we show also binds to β-lactamase as a disulfide-constrained macrocycle peptide with a KD of ∼1 μM. Fragmented open reading frame (ORF) libraries may efficiently identify such naturally constrained peptides at protein-protein interaction interfaces. With sufficiently deep coverage of ORFs by peptide-coding inserts, phage display and deep sequencing can provide detailed information on the domains or peptides that contribute to an interaction. Such information should enable the design of potentially therapeutic macrocycles or peptidomimetics that block the interaction.
Collapse
|
5
|
Tackling the Antibiotic Resistance Caused by Class A β-Lactamases through the Use of β-Lactamase Inhibitory Protein. Int J Mol Sci 2018; 19:ijms19082222. [PMID: 30061509 PMCID: PMC6121496 DOI: 10.3390/ijms19082222] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/27/2022] Open
Abstract
β-Lactams are the most widely used and effective antibiotics for the treatment of infectious diseases. Unfortunately, bacteria have developed several mechanisms to combat these therapeutic agents. One of the major resistance mechanisms involves the production of β-lactamase that hydrolyzes the β-lactam ring thereby inactivating the drug. To overcome this threat, the small molecule β-lactamase inhibitors (e.g., clavulanic acid, sulbactam and tazobactam) have been used in combination with β-lactams for treatment. However, the bacterial resistance to this kind of combination therapy has evolved recently. Therefore, multiple attempts have been made to discover and develop novel broad-spectrum β-lactamase inhibitors that sufficiently work against β-lactamase producing bacteria. β-lactamase inhibitory proteins (BLIPs) (e.g., BLIP, BLIP-I and BLIP-II) are potential inhibitors that have been found from soil bacterium Streptomyces spp. BLIPs bind and inhibit a wide range of class A β-lactamases from a diverse set of Gram-positive and Gram-negative bacteria, including TEM-1, PC1, SME-1, SHV-1 and KPC-2. To the best of our knowledge, this article represents the first systematic review on β-lactamase inhibitors with a particular focus on BLIPs and their inherent properties that favorably position them as a source of biologically-inspired drugs to combat antimicrobial resistance. Furthermore, an extensive compilation of binding data from β-lactamase–BLIP interaction studies is presented herein. Such information help to provide key insights into the origin of interaction that may be useful for rationally guiding future drug design efforts.
Collapse
|
6
|
Karasev DA, Veselovsky AV, Lagunin AA, Filimonov DA, Sobolev BN. Determination of Amino Acid Residues Responsible for Specific Interaction of Protein Kinases with Small Molecule Inhibitors. Mol Biol 2018. [DOI: 10.1134/s002689331802005x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Wijnands SPW, Engelen W, Lafleur RPM, Meijer EW, Merkx M. Controlling protein activity by dynamic recruitment on a supramolecular polymer platform. Nat Commun 2018; 9:65. [PMID: 29302054 PMCID: PMC5754363 DOI: 10.1038/s41467-017-02559-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022] Open
Abstract
Nature uses dynamic molecular platforms for the recruitment of weakly associating proteins into higher-order assemblies to achieve spatiotemporal control of signal transduction. Nanostructures that emulate this dynamic behavior require features such as plasticity, specificity and reversibility. Here we introduce a synthetic protein recruitment platform that combines the dynamics of supramolecular polymers with the programmability offered by DNA-mediated protein recruitment. Assembly of benzene-1,3,5-tricarboxamide (BTA) derivatives functionalized with a 10-nucleotide receptor strand into µm-long supramolecular BTA polymers is remarkably robust, even with high contents of DNA-functionalized BTA monomers and associated proteins. Specific recruitment of DNA-conjugated proteins on the supramolecular polymer results in a 1000-fold increase in protein complex formation, while at the same time enabling their rapid exchange along the BTA polymer. Our results establish supramolecular BTA polymers as a generic protein recruitment platform and demonstrate how assembly of protein complexes along the supramolecular polymer allows efficient and dynamic control of protein activity. DNA-origami allows the precise recruitment of DNA-protein conjugates but lacks the dynamics found in natural protein assemblies. Here the authors present a synthetic polymer platform that combines the dynamics of supramolecular polymers with the programmability of DNA-mediated protein recruitment.
Collapse
Affiliation(s)
- Sjors P W Wijnands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Wouter Engelen
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.,Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - René P M Lafleur
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.
| | - Maarten Merkx
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands. .,Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven, 5600 MB, The Netherlands.
| |
Collapse
|
8
|
Yang J, Li Q, Bian L. Spectroscopic analysis and docking simulation on the recognition and binding of TEM-1 β-lactamase with β-lactam antibiotics. Exp Ther Med 2017; 14:3288-3298. [PMID: 28912880 DOI: 10.3892/etm.2017.4853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 03/17/2017] [Indexed: 11/05/2022] Open
Abstract
The interaction between TEM-1 β-lactamase and antibiotics is very important in the hydrolysis of antibiotics. In the present study, the recognition and binding of TEM-1 β-lactamase with three β-lactam antibiotics, including penicillin G, cefalexin and cefoxitin, was investigated by fluorescence and ultraviolet-visible absorption spectra in combination with molecular docking in the temperature range of 278-288 K and under simulated physiological conditions. The results demonstrated that the fluorescence emissions of TEM-1 β-lactamase were extinguished by static quenching and the energy of TEM-1 β-lactamase was transferred in a non-radioactive manner. The binding of TEM-1 β-lactamase with the three antibiotics was a spontaneously exothermic process, with binding constants of 1.41×107, 7.81×106 and 5.43×104 at 278 K. Furthermore, binding was driven by enthalpy change and the binding forces between them were mainly hydrogen bonding and Van der Waals forces. A TEM-1 β-lactamase only bound with one antibiotic at a time and the binding capacity between them was closely associated with the functional groups and flexibility in the antibiotics. In addition, a conformational change occurred in the TEM-1 β-lactamases when they bound with the three antibiotics and TEM-1 β-lactamase-antibiotic complexes were formed. The present study provided an insight into the recognition and binding of TEM-1 β-lactamase with β-lactam antibiotics, which may be helpful for designing a novel substrate for TEM-1 β-lactamase and developing novel antibiotics that are resistant to the enzyme.
Collapse
Affiliation(s)
- Jianting Yang
- Department of Traditional Chinese Medicine, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, P.R. China.,Drug and Equipment Department, Weapon Industry 521 Hospital, Xi'an, Shaanxi 710065, P.R. China
| | - Qian Li
- Department of Traditional Chinese Medicine, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| | - Liujiao Bian
- Department of Traditional Chinese Medicine, College of Life Science, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| |
Collapse
|
9
|
Liu F, Zhang JZH, Mei Y. The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations. Sci Rep 2016; 6:27190. [PMID: 27249234 PMCID: PMC4888747 DOI: 10.1038/srep27190] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/13/2016] [Indexed: 11/17/2022] Open
Abstract
Previous experimental study measuring the binding affinities of biotin to the wild type streptavidin (WT) and three mutants (S45A, D128A and S45A/D128A double mutant) has shown that the loss of binding affinity from the double mutation is larger than the direct sum of those from two single mutations. The origin of this cooperativity has been investigated in this work through molecular dynamics simulations and the end-state free energy method using the polarized protein-specific charge. The results show that this cooperativity comes from both the enthalpy and entropy contributions. The former contribution mainly comes from the alternations of solvation free energy. Decomposition analysis shows that the mutated residues nearly have no contributions to the cooperativity. Instead, N49 and S88, which are located at the entry of the binding pocket and interact with the carboxyl group of biotin, make the dominant contribution among all the residues in the first binding shell around biotin.
Collapse
Affiliation(s)
- Fengjiao Liu
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - John Z. H. Zhang
- Department of Physics, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| |
Collapse
|
10
|
Hu R, Yap HK, Fung YH, Wang Y, Cheong WL, So LY, Tsang CS, Lee LYS, Lo WKC, Yuan J, Sun N, Leung YC, Yang G, Wong KY. ‘Light up’ protein–protein interaction through bioorthogonal incorporation of a turn-on fluorescent probe into β-lactamase. MOLECULAR BIOSYSTEMS 2016; 12:3544-3549. [DOI: 10.1039/c6mb00566g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aggregation induced emissive compound EPB can detect protein–protein interaction.
Collapse
|
11
|
Karasev DA, Veselovsky AV, Oparina NY, Filimonov DA, Sobolev BN. Prediction of amino acid positions specific for functional groups in a protein family based on local sequence similarity. J Mol Recognit 2015; 29:159-69. [DOI: 10.1002/jmr.2515] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Dmitry A. Karasev
- Russian National Research Medical University; Moscow Russia
- Laboratory of Structure-Function Based Drug Design; Institute of Biomedical Chemistry (IBMC); Moscow Russia
| | - Alexander V. Veselovsky
- Laboratory of Structure Bioinformatics; Institute of Biomedical Chemistry (IBMC); Moscow Russia
| | - Nina Yu. Oparina
- Department of Medical Biochemistry and Microbiology; Uppsala University; Uppsala Sweden
- Engelhardt Institute of Molecular Biology; Moscow Russia
| | - Dmitry A. Filimonov
- Laboratory of Structure Bioinformatics; Institute of Biomedical Chemistry (IBMC); Moscow Russia
| | - Boris N. Sobolev
- Laboratory of Structure-Function Based Drug Design; Institute of Biomedical Chemistry (IBMC); Moscow Russia
| |
Collapse
|
12
|
Banala S, Aper SJ, Schalk W, Merkx M. Switchable reporter enzymes based on mutually exclusive domain interactions allow antibody detection directly in solution. ACS Chem Biol 2013; 8:2127-32. [PMID: 23941162 DOI: 10.1021/cb400406x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Detection of antibodies is essential for the diagnosis of many diseases including infections, allergies, and autoimmune diseases. Current heterogeneous immunoassays require multiple time-consuming binding and washing steps, which limits their application in point-of-care diagnostics and high-throughput screening. Here, we report switchable reporter enzymes that allow simple colorimetric detection of antibodies directly in solution. Our approach is based on the antibody-induced disruption of an intramolecular interaction between TEM1 β-lactamase and its inhibitor protein BLIP. Using the HIV1-p17 antibody as an initial target, the interaction between enzyme and inhibitor was carefully tuned to yield a reporter enzyme whose activity increased 10-fold in the presence of pM antibody concentrations. Reporter enzymes for two other antibodies (HA-tag and Dengue virus type I) were obtained by simply replacing the epitope sequences. This new sensor design represents a modular and generic approach to construct antibody reporter enzymes without the cumbersome optimization required by previous engineering strategies.
Collapse
Affiliation(s)
- Sambashiva Banala
- Laboratory of Chemical Biology, Department
of Biomedical
Engineering, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Stijn J.A. Aper
- Laboratory of Chemical Biology, Department
of Biomedical
Engineering, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Werner Schalk
- Laboratory of Chemical Biology, Department
of Biomedical
Engineering, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department
of Biomedical
Engineering, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| |
Collapse
|
13
|
Brown NG, Chow DC, Ruprecht KE, Palzkill T. Identification of the β-lactamase inhibitor protein-II (BLIP-II) interface residues essential for binding affinity and specificity for class A β-lactamases. J Biol Chem 2013; 288:17156-66. [PMID: 23625930 DOI: 10.1074/jbc.m113.463521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The interactions between β-lactamase inhibitory proteins (BLIPs) and β-lactamases have been used as model systems to understand the principles of affinity and specificity in protein-protein interactions. The most extensively studied tight binding inhibitor, BLIP, has been characterized with respect to amino acid determinants of affinity and specificity for binding β-lactamases. BLIP-II, however, shares no sequence or structural homology to BLIP and is a femtomolar to picomolar potency inhibitor, and the amino acid determinants of binding affinity and specificity are unknown. In this study, alanine scanning mutagenesis was used in combination with determinations of on and off rates for each mutant to define the contribution of residues on the BLIP-II binding surface to both affinity and specificity toward four β-lactamases of diverse sequence. The residues making the largest contribution to binding energy are heavily biased toward aromatic amino acids near the center of the binding surface. In addition, substitutions that reduce binding energy do so by increasing off rates without impacting on rates. Also, residues with large contributions to binding energy generally exhibit low temperature factors in the structures of complexes. Finally, with the exception of D206A, BLIP-II alanine substitutions exhibit a similar trend of effect for all β-lactamases, i.e., a substitution that reduces affinity for one β-lactamase usually reduces affinity for all β-lactamases tested.
Collapse
Affiliation(s)
- Nicholas G Brown
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | | | |
Collapse
|
14
|
[Enterobacteriaceae and beta-lactams : wild susceptibility patterns]. ACTA ACUST UNITED AC 2012; 60:112-26. [PMID: 22280847 DOI: 10.1016/j.patbio.2011.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 12/07/2011] [Indexed: 11/21/2022]
Abstract
Four susceptibility patterns of wild types of enterobacteria against old beta-lactams including aminopenicillins, carboxypenicillins and first-generation cephalosporins were individualized during the 1980s : susceptible, penicillinase low level, cephalosporinase and a combination of penicillinase and cephalosporinase. Such indirect detection of a mechanism of resistance allowed an interpretative reading for this class of antibiotics. At the present time, seven susceptibility patterns were proposed for this family of gram negative bacilli. Nevertheless, an analysis of results in terms of MICs and diameters of inhibition zone sizes of the main bacterial species of enterobacteria, mainly obtained from the databank of European Committee on Antimicrobial Susceptibility Testing (EUCAST), compared to that observed when overproducing strains were isolated in vivo and in vitro and to the type of beta-lactamase identified and their amino acid sequences conducted to a proposal of five susceptibility patterns. The fifth wild type individualized in several enterobacteria since 2005 is related to the synthesis of various chromosomal extended-spectrum beta-lactamases (ESBL) which hydrolyze many beta-lactams including oxyimino-cephalosporins such as ceftriaxone or cefotaxime. Their expression in a wild strain is characteristic and conducted to our interest for their role as progenitors of the transferable CTM-M types. Otherwise, a medical biologist must consider the possibility of selection of a mutant with a chromosomal overproduced beta-lactamase. But within the same beta-lactam susceptibility pattern such as for Klebsiella pneumoniae and K. oxytoca or Citrobacter amalonaticus, the spectrum of inactivation will be highly variable according to the type of enzyme overproduced. Finally, a nice synergy observed between clavulanic acid and cefotaxime or ceftriaxone or even aztreonam does not mean anytime a transferable ESBL. In some cases according to the result of enterobacterial identification, the epidemiological impact will be very low, because without multidrug resistance (MDR).
Collapse
|