1
|
Paresi CJ, Liu Q, Li YM. Benzimidazole covalent probes and the gastric H(+)/K(+)-ATPase as a model system for protein labeling in a copper-free setting. MOLECULAR BIOSYSTEMS 2017; 12:1772-80. [PMID: 26952080 DOI: 10.1039/c6mb00024j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Affinity probes are useful tools for determining molecular targets and elucidating mechanism of action for novel, bioactive compounds. In the case of covalent inhibitors, activity based probes are particularly valuable for ensuring acceptable selectivity margins. However, there is a variety of bioorthogonal chemistry reactions available for modifying compounds of interest with clickable tags. Here, we describe a direct comparison of tetrazine ligation and strain promoted azide-alkyne cycloaddition using benzimidazole based probes to bind their known target, the gastric proton pump, ATP4A. This study validates the use of chemical probes for target identification and illustrates the superior efficiency of tetrazine ligation for copper-free click systems. In addition, we have identified several novel binding partners of benzimidazole probes: Isoform 2 of deleted in malignant brain tumors 1 protein (DMBT1) and three uncharacterized proteins.
Collapse
Affiliation(s)
- Chelsea J Paresi
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. and Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Qi Liu
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA. and Program of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| |
Collapse
|
2
|
Dach I, Olesen C, Signor L, Nissen P, le Maire M, Møller JV, Ebel C. Active detergent-solubilized H+,K+-ATPase is a monomer. J Biol Chem 2012; 287:41963-78. [PMID: 23055529 DOI: 10.1074/jbc.m112.398768] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The H(+),K(+)-ATPase pumps protons or hydronium ions and is responsible for the acidification of the gastric fluid. It is made up of an α-catalytic and a β-glycosylated subunit. The relation between cation translocation and the organization of the protein in the membrane are not well understood. We describe here how pure and functionally active pig gastric H(+),K(+)-ATPase with an apparent Stokes radius of 6.3 nm can be obtained after solubilization with the non-ionic detergent C(12)E(8), followed by exchange of C(12)E(8) with Tween 20 on a Superose 6 column. Mass spectroscopy indicates that the β-subunit bears an excess mass of 9 kDa attributable to glycosylation. From chemical analysis, there are 0.25 g of phospholipids and around 0.024 g of cholesterol bound per g of protein. Analytical ultracentrifugation shows one main complex, sedimenting at s(20,)(w) = 7.2 ± 0.1 S, together with minor amounts of irreversibly aggregated material. From these data, a buoyant molecular mass is calculated, corresponding to an H(+),K(+)-ATPase α,β-protomer of 147.3 kDa. Complementary sedimentation velocity with deuterated water gives a picture of an α,β-protomer with 0.9-1.4 g/g of bound detergent and lipids and a reasonable frictional ratio of 1.5, corresponding to a Stokes radius of 7.1 nm. An α(2),β(2) dimer is rejected by the data. Light scattering coupled to gel filtration confirms the monomeric state of solubilized H(+),K(+)-ATPase. Thus, α,β H(+),K(+)-ATPase is active at least in detergent and may plausibly function as a monomer, as has been established for other P-type ATPases, Ca(2+)-ATPase and Na(+),K(+)-ATPase.
Collapse
Affiliation(s)
- Ingrid Dach
- Center for Membrane Pumps in Cells and Diseases, Danish Research Foundation, DK-8000 Aarhus, Denmark
| | | | | | | | | | | | | |
Collapse
|
3
|
Powell LR, Dukes KD, Lammi RK. Probing the efficacy of peptide-based inhibitors against acid- and zinc-promoted oligomerization of amyloid-β peptide via single-oligomer spectroscopy. Biophys Chem 2012; 160:12-9. [PMID: 21945664 PMCID: PMC3210411 DOI: 10.1016/j.bpc.2011.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/26/2011] [Accepted: 08/29/2011] [Indexed: 01/18/2023]
Abstract
One avenue for prevention and treatment of Alzheimer's disease involves inhibiting the aggregation of amyloid-β peptide (Aβ). Given the deleterious effects reported for Aβ dimers and trimers, it is important to investigate inhibition of the earliest association steps. We have employed quantized photobleaching of dye-labeled Aβ peptides to characterize four peptide-based inhibitors of fibrillogenesis and/or cytotoxicity, assessing their ability to inhibit association in the smallest oligomers (n=2-5). Inhibitors were tested at acidic pH and in the presence of zinc, conditions that may promote oligomerization in vivo. Distributions of peptide species were constructed by examining dozens of surface-tethered monomers and oligomers, one at a time. Results show that all four inhibitors shift the distribution of Aβ species toward monomers; however, efficacies vary for each compound and sample environment. Collectively, these studies highlight promising design strategies for future oligomerization inhibitors, affording insight into oligomer structures and inhibition mechanisms in two physiologically significant environments.
Collapse
Affiliation(s)
- Lyndsey R Powell
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29733, USA
| | | | | |
Collapse
|
4
|
Dukes KD, Rodenberg CF, Lammi RK. Monitoring the earliest amyloid-β oligomers via quantized photobleaching of dye-labeled peptides. Anal Biochem 2008; 382:29-34. [DOI: 10.1016/j.ab.2008.07.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 07/08/2008] [Accepted: 07/14/2008] [Indexed: 10/21/2022]
|
5
|
Shin JM, Vagin O, Munson K, Kidd M, Modlin IM, Sachs G. Molecular mechanisms in therapy of acid-related diseases. Cell Mol Life Sci 2008; 65:264-81. [PMID: 17928953 PMCID: PMC3081136 DOI: 10.1007/s00018-007-7249-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inhibition of gastric acid secretion is the mainstay of the treatment of gastroesophageal reflux disease and peptic ulceration; therapies to inhibit acid are among the best-selling drugs worldwide. Highly effective agents targeting the histamine H2 receptor were first identified in the 1970s. These were followed by the development of irreversible inhibitors of the parietal cell hydrogen-potassium ATPase (the proton pump inhibitors) that inhibit acid secretion much more effectively. Reviewed here are the chemistry, biological targets and pharmacology of these drugs, with reference to their current and evolving clinical utilities. Future directions in the development of acid inhibitory drugs include modifications of current agents and the emergence of a novel class of agents, the acid pump antagonists.
Collapse
Affiliation(s)
- J. M. Shin
- Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California USA
- VA Greater Los Angeles Healthcare System, West LA Medical Center, 11301 Wilshire Boulevard, Building 113, Los Angeles, California 90073 USA
| | - O. Vagin
- Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California USA
- VA Greater Los Angeles Healthcare System, West LA Medical Center, 11301 Wilshire Boulevard, Building 113, Los Angeles, California 90073 USA
| | - K. Munson
- Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California USA
- VA Greater Los Angeles Healthcare System, West LA Medical Center, 11301 Wilshire Boulevard, Building 113, Los Angeles, California 90073 USA
| | - M. Kidd
- Department of Surgery, Yale University School of Medicine, TMP202, 333 Cedar Street, New Haven Connecticut, 06520-8062 USA
| | - I. M. Modlin
- Department of Surgery, Yale University School of Medicine, TMP202, 333 Cedar Street, New Haven Connecticut, 06520-8062 USA
| | - G. Sachs
- Department of Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California USA
- VA Greater Los Angeles Healthcare System, West LA Medical Center, 11301 Wilshire Boulevard, Building 113, Los Angeles, California 90073 USA
| |
Collapse
|
6
|
Tanoue K, Kaya S, Hayashi Y, Abe K, Imagawa T, Taniguchi K, Sakaguchi K. New evidence for ATP binding induced catalytic subunit interactions in pig kidney Na/K-ATPase. J Biochem 2006; 140:599-607. [PMID: 16987945 DOI: 10.1093/jb/mvj191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pig kidney Na/K-ATPase preparations showed a positive cooperative effect for pNPP in Na-pNPPase activity. Measurements of the Na-pNPPase activity, Na-ATPase activity and the accumulation of phosphoenzyme (EP) under conditions of pNPP saturation showed several different ATP affinities. The presence of pNPP reduced both the maximum amount of EP and Na-ATPase activity to half showing a value of 4 and a 3,700-fold reduced ATP affinity for EP formation, and a 7 and 1,300-fold reduced affinity for Na-ATPase activity. The presence of low concentrations of ATP in the phosphorylation induced a 2-fold enhancement in Na-pNPPase activity despite a reduction in available pNPP sites. However, higher concentrations of ATP inhibited the Na-pNPPase activity and a much higher concentration of ATP increased both the phosphorylation and Na-ATPase activity to the maximum levels. The maximum Na-pNPPase activity was 1.7 and 3.4-fold higher without and with ATP, respectively, than the maximum Na-ATPase activity. These data and the pNPP dependent reduction in both Na-ATPase activity and the amount of enzyme bound ATP provide new evidence to show that ATP, pNPP and ATP with pNPP, respectively, induce different subunit interactions resulting a difference in the maximum Na(+)-dependent catalytic activity in tetraprotomeric Na/K-ATPase.
Collapse
Affiliation(s)
- Kan Tanoue
- Biological Chemistry, Division of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810.
| | | | | | | | | | | | | |
Collapse
|
7
|
Robinson MA, Wood JP, Capaldi SA, Baron AJ, Gell C, Smith DA, Stonehouse NJ. Affinity of molecular interactions in the bacteriophage phi29 DNA packaging motor. Nucleic Acids Res 2006; 34:2698-709. [PMID: 16714447 PMCID: PMC1464111 DOI: 10.1093/nar/gkl318] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA packaging in the bacteriophage φ29 involves a molecular motor with protein and RNA components, including interactions between the viral connector protein and molecules of pRNA, both of which form multimeric complexes. Data are presented to demonstrate the higher order assembly of pRNA together with the affinity of pRNA:pRNA and pRNA:connector interactions, which are used to propose a model for motor function. In solution, pRNA can form dimeric and trimeric multimers in a magnesium-dependent manner, with dissociation constants for multimerization in the micromolar range. pRNA:connector binding is also facilitated by the presence of magnesium ions, with a nanomolar apparent dissociation constant for the interaction. From studies with a mutant pRNA, it appears that multimerization of pRNA is not essential for connector binding and it is likely that connector protein is involved in the stabilization of higher order RNA multimers. It is proposed that magnesium ions may promote conformational change that facilitate pRNA:connector interactions, essential for motor function.
Collapse
Affiliation(s)
- Mark A. Robinson
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT, UK
| | - Jonathan P.A. Wood
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT, UK
| | - Stephanie A. Capaldi
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT, UK
| | - Andrew J. Baron
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT, UK
| | - Christopher Gell
- Institute of Molecular Biophysics, University of LeedsLeeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT, UK
| | - D. Alastair Smith
- Institute of Molecular Biophysics, University of LeedsLeeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT, UK
| | - Nicola J. Stonehouse
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of LeedsLeeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeeds, LS2 9JT, UK
- To whom correspondence should be addressed. Tel: + 44 113 343 3102; Fax: + 44 113 343 2835;
| |
Collapse
|
8
|
Affiliation(s)
- Jai Moo Shin
- Department of Physiology and Medicine, University of California at Los Angeles, and VA Greater Los Angeles Healthcare System, Los Angeles, California 90073, USA
| | | |
Collapse
|
9
|
Homareda H, Ushimaru M. Stimulation of p-nitrophenylphosphatase activity of Na+/K+-ATPase by NaCl with oligomycin or ATP. FEBS J 2005; 272:673-84. [PMID: 15670149 DOI: 10.1111/j.1742-4658.2004.04496.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is known that the addition of NaCl with oligomycin or ATP stimulates ouabain-sensitive and K+-dependent p-nitrophenylphosphatase (pNPPase) activity of Na+/K+-ATPase. We investigated the mechanism of the stimulation. The combination of oligomycin and NaCl increased the affinity of pNPPase activity for K+. When the ratio of Na+ to Rb+ was 10 in the presence of oligomycin, Rb+-binding and pNPPase activity reached a maximal level and Na+ was occluded. Phosphorylation of Na+/K+-ATPase by p-nitrophenylphosphate (pNPP) was not affected by oligomycin. Because oligomycin stabilizes the Na+-occluded E1 state of Na+/K+-ATPase, it seemed that the Na+-occluded E1 state increased the affinity of the phosphoenzyme formed from pNPP for K+. On the other hand, the combination of ATP and NaCl also increased the affinity of pNPPase for K+ and activated ATPase activity. Both activities were affected by the ligand conditions. Oligomycin noncompetitively affected the activation of pNPPase by NaCl and ATP. Nonhydrolyzable ATP analogues could not substitute for ATP. As NaE1P, which is the high-energy phosphoenzyme formed from ATP with Na+, is also the Na+-occluded E1 state, it is suggested that the Na+-occluded E1 state increases the affinity of the phosphoenzyme from pNPP for K+ through the interaction between alpha subunits. Therefore, membrane-bound Na+/K+-ATPase would function as at least an (alphabeta)2-diprotomer with interacting alpha subunits at the phosphorylation step.
Collapse
Affiliation(s)
- Haruo Homareda
- Department of Biochemistry, Kyorin University School of Medicine, Mitaka, Tokyo, Japan.
| | | |
Collapse
|
10
|
Lowe J, Vieyra A, Catty P, Guillain F, Mintz E, Cuillel M. A mutational study in the transmembrane domain of Ccc2p, the yeast Cu(I)-ATPase, shows different roles for each Cys-Pro-Cys cysteine. J Biol Chem 2004; 279:25986-94. [PMID: 15078884 DOI: 10.1074/jbc.m308736200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ccc2p is homologous to the human Menkes and Wilson copper ATPases and is herein studied as a model for human copper transport. Most studies to date have sought to understand how mutations in the human Menkes or Wilson genes impair copper homeostasis and induce disease. Here we analyze whether eight conserved amino acids of the transmembrane domain are important for copper transport. Wild-type Ccc2p and variants were expressed in a ccc2-Delta yeast strain to check whether they were able to restore copper transport by complementation. Wild-type Ccc2p and variants were also expressed in Sf9 cells using baculovirus to study their enzymatic properties on membrane preparations. The latter system allowed us to measure a copper-activated ATPase activity of about 20 nmol/mg/min for the wild-type Ccc2p at 37 degrees C. None of the variants was as efficient as the wild type in restoring copper homeostasis. The mutation of each cysteine of the (583)CPC(585) motif into a serine resulted in nonfunctional proteins that could not restore copper homeostasis in yeast and had no ATPase activity. Phosphorylation by ATP was still possible with the C583S variant, although it was not possible with the C585S variant, suggesting that the cysteines of the CPC motif have a different role in copper transport. Cys(583) would be necessary for copper dissociation and/or enzyme dephosphorylation and Cys(585) would be necessary for ATP phosphorylation, suggesting a role in copper binding.
Collapse
Affiliation(s)
- Jennifer Lowe
- Laboratorio de Fisico-Quimica Biologica Aida Hasson-Voloch, Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brasil
| | | | | | | | | | | |
Collapse
|