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Nomura S, Takahashi M, Kato AH, Wada Y, Watanabe Y, Yamashita F, Mukai H. Biosorption-based 64Cu-labeling of bacteria for pharmacokinetic positron-emission tomography. Int J Pharm 2020; 590:119950. [PMID: 33027635 DOI: 10.1016/j.ijpharm.2020.119950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023]
Abstract
Biosorption-based bacterial 64Cu-labeling and its application in pharmacokinetic positron-emission tomography (PET) were investigated. Both gram-positive and gram-negative bacteria were efficiently labeled with [64Cu]Cu2+ ion in saline at room temperature within 5 min. The labeling ratio for Escherichia coli drastically decreased with trypsin pretreatment and the co-presence of excess Cu2+ ion, indicating the existence of specific Cu2+ binding sites on the E. coli cell surface. Washing with lysogeny broth medium was effective in purifying 64Cu-labeled E. coli for kinetic study; the labeling stability was approximately 90% in serum for 15 min. According to dynamic PET imaging in colon-26 tumor-bearing mice, 64Cu-labeled E. coli immediately disappeared from the blood circulation and primarily accumulated in the liver. In addition, transient pulmonary distribution was observed, being in a dose-dependently accelerated manner. Considering the simplicity and versatility of biosorption-based bacterial 64Cu-labeling without genetic modification, the early-phase pharmacokinetic PET with 64Cu-labeled bacteria is promising for assessing toxicological aspects of bacteria-mediated cancer therapy as well as a variety of bacterial pathogenicities in infectious diseases.
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Affiliation(s)
- Shoko Nomura
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-shimoadachi cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Maiko Takahashi
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Akari Hashiba Kato
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasuhiro Wada
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasuyoshi Watanabe
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Fumiyoshi Yamashita
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-shimoadachi cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hidefumi Mukai
- Laboratory for Molecular Delivery and Imaging Technology, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Pharmaceutical Informatics, Graduate School of Biomedical Science, Nagasaki University, 1-7-1 Sakamotomachi, Nagasaki 852-8588, Japan.
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Chang H, Gnanasekaran K, Gianneschi NC, Geiger FM. Bacterial Model Membranes Deform (resp. Persist) upon Ni2+ Binding to Inner Core (resp. O-Antigen) of Lipopolysaccharides. J Phys Chem B 2019; 123:4258-4270. [DOI: 10.1021/acs.jpcb.9b02762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- HanByul Chang
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60660, United States
| | - Karthikeyan Gnanasekaran
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60660, United States
| | - Nathan C. Gianneschi
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60660, United States
| | - Franz M. Geiger
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60660, United States
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Gorkhali R, Huang K, Kirberger M, Yang JJ. Defining potential roles of Pb(2+) in neurotoxicity from a calciomics approach. Metallomics 2017; 8:563-78. [PMID: 27108875 DOI: 10.1039/c6mt00038j] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ions play crucial roles in numerous biological processes, facilitating biochemical reactions by binding to various proteins. An increasing body of evidence suggests that neurotoxicity associated with exposure to nonessential metals (e.g., Pb(2+)) involves disruption of synaptic activity, and these observed effects are associated with the ability of Pb(2+) to interfere with Zn(2+) and Ca(2+)-dependent functions. However, the molecular mechanism behind Pb(2+) toxicity remains a topic of debate. In this review, we first discuss potential neuronal Ca(2+) binding protein (CaBP) targets for Pb(2+) such as calmodulin (CaM), synaptotagmin, neuronal calcium sensor-1 (NCS-1), N-methyl-d-aspartate receptor (NMDAR) and family C of G-protein coupled receptors (cGPCRs), and their involvement in Ca(2+)-signalling pathways. We then compare metal binding properties between Ca(2+) and Pb(2+) to understand the structural implications of Pb(2+) binding to CaBPs. Statistical and biophysical studies (e.g., NMR and fluorescence spectroscopy) of Pb(2+) binding are discussed to investigate the molecular mechanism behind Pb(2+) toxicity. These studies identify an opportunistic, allosteric binding of Pb(2+) to CaM, which is distinct from ionic displacement. Together, these data suggest three potential modes of Pb(2+) activity related to molecular and/or neural toxicity: (i) Pb(2+) can occupy Ca(2+)-binding sites, inhibiting the activity of the protein by structural modulation, (ii) Pb(2+) can mimic Ca(2+) in the binding sites, falsely activating the protein and perturbing downstream activities, or (iii) Pb(2+) can bind outside of the Ca(2+)-binding sites, resulting in the allosteric modulation of the protein activity. Moreover, the data further suggest that even low concentrations of Pb(2+) can interfere at multiple points within the neuronal Ca(2+) signalling pathways to cause neurotoxicity.
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Affiliation(s)
- Rakshya Gorkhali
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Drug Design and Biotechnology, Georgia State University, Atlanta, GA 3030, USA.
| | - Kenneth Huang
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Drug Design and Biotechnology, Georgia State University, Atlanta, GA 3030, USA.
| | - Michael Kirberger
- Department of Chemistry and Physics, Clayton State University, Morrow, GA 30260, USA.
| | - Jenny J Yang
- Department of Chemistry, Center for Diagnostics and Therapeutics, and Drug Design and Biotechnology, Georgia State University, Atlanta, GA 3030, USA.
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Liu JP, Li J, Lu Y, Wang L, Chen G. Impulse control disorder, lysosomal malfunction and ATP13A2 insufficiency in Parkinsonism. Clin Exp Pharmacol Physiol 2016; 44:172-179. [PMID: 27997702 DOI: 10.1111/1440-1681.12714] [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: 11/24/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/27/2022]
Abstract
Lysosomal transport of cargos in neurons is essential for neuronal proteostasis, transmission and functional motors and behaviours. Lysosomal malfunction including storage disorders is involved in the pathogenesis of Parkinson's disease (PD). Given the unclear molecular mechanisms of diverse defects in PD phenotypes, especially behavioural deficits, this mini review explores the cellular contexts of PD impulse control disorders and the molecular aspects of lysosomal cross-membrane transports. Focuses are paid to trace metal involvements in α-synuclein assembly in Lewy bodies, the functions and molecular interactions of ATP13A2 as ATPase transporters in lysosomal membranes for cross-membrane trafficking and lysosomal homeostasis, and our current understandings of the neural circuits in ICD. Erroneously polarized distributions of cargos such as metals and lipids on each side of lysosomal membranes triggered by gene mutations and deregulated expression of ATP13A2 may thus instigate sensing protein structural changes such as aggregations, organelle degeneration, and specific neuronal ageing and death in Parkinsonism.
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Affiliation(s)
- Jun-Ping Liu
- School of Medicine, Institute of Ageing Research, Hangzhou Normal University, Hangzhou, Zhejiang Province, China.,Department of Molecular and Translational Science, Faculty of Medicine, Hudson Institute of Medical Research, Monash University, Clayton, VIC, Australia.,Department of Immunology, Faculty of Medicine, Central Clinical School, Monash University, Prahran, VIC, Australia
| | - Jianfeng Li
- School of Medicine, Institute of Ageing Research, Hangzhou Normal University, Hangzhou, Zhejiang Province, China
| | - Yanhua Lu
- School of Medicine, Institute of Ageing Research, Hangzhou Normal University, Hangzhou, Zhejiang Province, China
| | - Lihui Wang
- School of Medicine, Institute of Ageing Research, Hangzhou Normal University, Hangzhou, Zhejiang Province, China
| | - Gang Chen
- School of Medicine, Institute of Ageing Research, Hangzhou Normal University, Hangzhou, Zhejiang Province, China
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Nymeyer H. How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach. J Chem Theory Comput 2015; 4:626-36. [PMID: 26620937 DOI: 10.1021/ct7003337] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Replica exchange molecular dynamics (REMD) has become a standard technique for accelerating relaxation in biosimulations. Despite its widespread use, questions remain about its efficiency compared with conventional, constant temperature molecular dynamics (MD). An analytic approach is taken to describe the relative efficiency of REMD with respect to MD. This is applied to several simple two-state models and to several real proteins-protein L and the B domain of protein A-to predict the relative efficiency of REMD with respect to MD in actual applications. In agreement with others, we find the following: as long as there is a positive activation energy for folding, REMD is more efficient than MD; the effectiveness of REMD is strongly dependent on the activation enthalpy; and the efficiency of REMD for actual proteins is a strong function of the maximum temperature. Choosing the maximum temperature too high can result in REMD becoming significantly less efficient than conventional MD. A good rule of thumb appears to be to choose the maximum temperature of the REMD simulation slightly above the temperature at which the enthalpy for folding vanishes. Additionally, we find that the number of replicas in REMD, while important for simulations shorter than one or two relaxation times, has a minimal effect on the asymptotic efficiency of the method.
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Affiliation(s)
- Hugh Nymeyer
- Department of Chemistry & Biochemistry, The School of Computational Science and The Institute for Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4380
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van Severen MC, Piquemal JP, Parisel O. Lead substitution in synaptotagmin: a case study. J Phys Chem B 2010; 114:4005-9. [PMID: 20192256 DOI: 10.1021/jp910131r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum chemistry computations have been used to investigate the possibility of a Pb(2+)/Ca(2+) substitution in the three calcium sites of the synaptotagmin enzyme. Provided explicit cation solvation is taken into account, it is shown that the substitution is energetically feasible and induces a strong reorganization of the Ca(2+)-coordinating sites, which may preclude the enzyme for any efficient role when lead poisoning occurs.
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Affiliation(s)
- M-C van Severen
- UMR 7616, Laboratoire de Chimie Théorique, UPMC Université Paris 06, case courrier 137, 4 place Jussieu F-75005, Paris, France
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Philominathan STL, Matsushita O, Gensure R, Sakon J. Ca2+-induced linker transformation leads to a compact and rigid collagen-binding domain of Clostridium histolyticum collagenase. FEBS J 2009; 276:3589-601. [PMID: 19490118 DOI: 10.1111/j.1742-4658.2009.07078.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Clostridium histolyticum collagenase is responsible for extensive tissue destruction in gas gangrene, and its activity is enhanced by calcium ions. The collagen-binding domain is the minimal segment of the enzyme required for binding to insoluble collagen fibrils and for subsequent collagenolysis. The collagen-binding domain is joined to another binding module by a conserved 14-amino-acid linker. The linker undergoes secondary structural transformation from an alpha-helix to a beta-strand and forms a nonprolyl cis-peptide in the presence of calcium ions. In this study, various biophysical methods were utilized to better understand the structure and functional role of the novel calcium-activated linker. Two Ca(2+) ions bind cooperatively with macroscopic association constants of K(1) = 5.01 x 10(5) m(-1) and K(2) = 2.28 x 10(5) m(-1). The chelation of the second calcium ion is enthalpically unfavorable, which could be a result of isomerization of the nonprolyl cis-peptide. The holo protein is more stable than the apo protein against thermal denaturation (DeltaT(m) approximately 20 degrees C) and chemical denaturation (DeltaDeltaG(H2O) approximately 3 kcal x mol(-1) for urea or guanidine HCl denaturation and Delta20% v/v in 2,2,2-trifluoroethanol). The compact holo collagen-binding domain is more resistant to proteolytic digestion than the apo collagen-binding domain. The orientation of the linker appears to play a crucial role in the stability and dynamics of the collagen-binding domain.
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Dias AV, Zamble DB. Protease digestion analysis of Escherichia coli NikR: evidence for conformational stabilization with Ni(II). J Biol Inorg Chem 2005; 10:605-12. [PMID: 16133200 DOI: 10.1007/s00775-005-0008-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Accepted: 07/07/2005] [Indexed: 10/25/2022]
Abstract
The Escherichia coli NikR is a 15-kDa protein that negatively regulates transcription of the nikABCDE operon that encodes for an ATP-dependent Ni(II) permease. Thermal and chemical denaturation studies with NikR previously demonstrated that Ni(II)-NikR is more stable than the protein bound to other metals such as Cu(II), Co(II) and Zn(II). To determine if Ni(II) induces a unique conformational change in NikR, digestion experiments with selected proteases were performed in the presence of the above metals. Both denaturing-polyacrylamide gel electrophoresis and reversed-phase HPLC revealed fragmentation patterns in the presence of stoichiometric nickel that were distinct from the cleavage of apo-NikR. Digestion of Cu(II)-NikR produced fragmentation that was similar, although less dramatic, to that produced with Ni(II)-NikR, whereas the Zn(II)- and Co(II)-bound proteins were digested in a similar manner as apo-NikR. Digestion fragments were collected, identified by MALDI-MS, and then mapped onto the available crystal structure of NikR. Although the specificity of the proteases utilized differed, the data suggest that Ni(II) has a selective allosteric effect and that upon metal binding the NikR metal-binding pocket is oriented or protected in such a way as to present itself for digestion in a unique conformation. This data sheds light on the Ni(II)-selective conformational changes that allow NikR to bind DNA optimally and repress transcription of the nik operon.
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Affiliation(s)
- Alistair V Dias
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, M5S 3H6, Canada
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