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Konuma T, Takai T, Tsuchiya C, Nishida M, Hashiba M, Yamada Y, Shirai H, Motoda Y, Nagadoi A, Chikaishi E, Akagi K, Akashi S, Yamazaki T, Akutsu H, Ikegami T. Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria. Protein Sci 2024; 33:e5002. [PMID: 38723146 PMCID: PMC11081423 DOI: 10.1002/pro.5002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/26/2024] [Accepted: 04/11/2024] [Indexed: 05/13/2024]
Abstract
Bacteria that have acquired resistance to most antibiotics, particularly those causing nosocomial infections, create serious problems. Among these, the emergence of vancomycin-resistant enterococci was a tremendous shock, considering that vancomycin is the last resort for controlling methicillin-resistant Staphylococcus aureus. Therefore, there is an urgent need to develop an inhibitor of VanX, a protein involved in vancomycin resistance. Although the crystal structure of VanX has been resolved, its asymmetric unit contains six molecules aligned in a row. We have developed a structural model of VanX as a stable dimer in solution, primarily utilizing nuclear magnetic resonance (NMR) residual dipolar coupling. Despite the 46 kDa molecular mass of the dimer, the analyses, which are typically not as straightforward as those of small proteins around 10 kDa, were successfully conducted. We assigned the main chain using an amino acid-selective unlabeling method. Because we found that the zinc ion-coordinating active sites in the dimer structure were situated in the opposite direction to the dimer interface, we generated an active monomer by replacing an amino acid at the dimer interface. The monomer consists of only 202 amino acids and is expected to be used in future studies to screen and improve inhibitors using NMR.
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Affiliation(s)
- Tsuyoshi Konuma
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Tomoyo Takai
- Institute for Protein ResearchOsaka UniversityOsakaJapan
| | - Chieko Tsuchiya
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Masayuki Nishida
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Miyu Hashiba
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Yudai Yamada
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Haruka Shirai
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Yoko Motoda
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | - Aritaka Nagadoi
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | | | - Ken‐ichi Akagi
- Institute for Protein ResearchOsaka UniversityOsakaJapan
| | - Satoko Akashi
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
| | | | - Hideo Akutsu
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
- Institute for Protein ResearchOsaka UniversityOsakaJapan
| | - Takahisa Ikegami
- Graduate School of Medical Life ScienceYokohama City UniversityYokohamaKanagawaJapan
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Wang Q, Zhu L, Yu Y, Guan H, Xu Z. Microbial Screening of Marine Natural Product Inhibitors for the 6′-Aminoglycoside Acetyltransferase 2″-Aminoglycoside Phosphotransferase [AAC(6′)-APH(2″)] Bifunctional Enzyme by Ultra-High Performance Liquid Chromatography–Mass Spectrometry (UHPLC-MS). ANAL LETT 2021. [DOI: 10.1080/00032719.2021.1903025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Qian Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yi Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huashi Guan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhe Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts, Innovation Center for Marine Drugs Screening and Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
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Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
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Wang Y, Wang G, Moitessier N, Mittermaier AK. Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics. Front Mol Biosci 2020; 7:583826. [PMID: 33195429 PMCID: PMC7604385 DOI: 10.3389/fmolb.2020.583826] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Isothermal titration calorimetry (ITC) involves accurately measuring the heat that is released or absorbed in real time when one solution is titrated into another. This technique is usually used to measure the thermodynamics of binding reactions. However, there is mounting interest in using it to measure reaction kinetics, particularly enzymatic catalysis. This application of ITC has been steadily growing for the past two decades, and the method is proving to be sensitive, generally applicable, and capable of providing information on enzyme activity that is difficult to obtain using traditional biochemical assays. This review aims to give a broad overview of the use of ITC to measure enzyme kinetics. It describes several different classes of ITC experiment, their strengths and weaknesses, and recent methodological advancements. A summary of applications in the literature is given and several examples where ITC has been used to investigate challenging aspects of enzyme behavior are presented in more detail. These include examples of allostery, where small-molecule binding outside the active site modulates activity. We describe the use of ITC to measure the strength, mode (i.e., competitive, uncompetitive, or mixed), and association and dissociation kinetics of enzyme inhibitors. Further, we provide examples of ITC applied to complex, heterogeneous mixtures, such as insoluble substrates and live cells. These studies exemplify the wide range of problems where ITC can provide answers, and illustrate the versatility of the technique and potential for future development and applications.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | - Guanyu Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
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