1
|
Mendez Q, Driscoll HA, Mirando GR, Acca F, Chapados CD, Jones KS, Weiner M, Li X, Ferguson MR. MILKSHAKE Western blot and Sundae ELISA: We all scream for better antibody validation. J Immunol Methods 2023; 521:113540. [PMID: 37597727 PMCID: PMC10568614 DOI: 10.1016/j.jim.2023.113540] [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: 06/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Knowing that an antibody's sensitivity and specificity is accurate is crucial for reliable data collection. This certainty is especially difficult to achieve for antibodies (Abs) which bind post-translationally modified proteins. Here we describe two validation methods using surrogate proteins in western blot and ELISA. The first method, which we termed "MILKSHAKE" is a modified maltose binding protein, hence the name, that is enzymatically conjugated to a peptide from the chosen target which is either modified or non-modified at the residue of interest. The surety of the residue's modification status can be used to confirm Ab specificity to the target's post-translational modification (PTM). The second method uses a set of surrogate proteins, which we termed "Sundae". Sundae consists of a set of modified maltose binding proteins with a genetically encoded target sequence, each of which contains a single amino acid substitution at one position of interest. With Sundae, Abs can be evaluated for binding specificities to all twenty amino acids at a single position. Combining MILKSHAKE and Sundae methods, Ab specificity can be determined at a single-residue resolution. These data improve evaluation of commercially available Abs and identify off-target effects for Research-Use-Only and therapeutic Abs.
Collapse
Affiliation(s)
- Qiana Mendez
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Holland A Driscoll
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Gregory R Mirando
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Felicity Acca
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Cassandra D Chapados
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Kezzia S Jones
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Michael Weiner
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Xiaofeng Li
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Mary R Ferguson
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| |
Collapse
|
2
|
Yip D, Accili E. Kinetic modelling of voltage-dependent gating in funny channels. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 166:182-188. [PMID: 34310984 DOI: 10.1016/j.pbiomolbio.2021.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Delbert Yip
- Department of Cellular and Physiological Sciences, University of British Columbia, Health Sciences Mall, V6T 1Z3, 2350, Canada
| | - Eric Accili
- Department of Cellular and Physiological Sciences, University of British Columbia, Health Sciences Mall, V6T 1Z3, 2350, Canada.
| |
Collapse
|
3
|
Sunkara MR, Schwabe T, Ehrlich G, Kusch J, Benndorf K. All four subunits of HCN2 channels contribute to the activation gating in an additive but intricate manner. J Gen Physiol 2018; 150:1261-1271. [PMID: 29959170 PMCID: PMC6122924 DOI: 10.1085/jgp.201711935] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 04/25/2018] [Accepted: 06/14/2018] [Indexed: 01/25/2023] Open
Abstract
HCN pacemaker channels are dually gated by hyperpolarizing voltages and cyclic nucleotide binding. Sunkara et al. show that each of the four binding sites promotes channel opening, most likely by exerting a turning momentum on the tetrameric intracellular gating ring. Hyperpolarization-activated cyclic nucleotide–modulated (HCN) channels are tetramers that elicit electrical rhythmicity in specialized brain neurons and cardiomyocytes. The channels are dually activated by voltage and binding of cyclic adenosine monophosphate (cAMP) to their four cyclic nucleotide-binding domains (CNBDs). Here we analyze the effects of cAMP binding to different concatemers of HCN2 channel subunits, each having a defined number of functional CNBDs. We show that each liganded CNBD promotes channel activation in an additive manner and that, in the special case of two functional CNBDs, functionality does not depend on the arrangement of the subunits. Correspondingly, the reverse process of deactivation is slowed by progressive liganding, but only if four and three ligands as well as two ligands in trans position (opposite to each other) are bound. In contrast, two ligands bound in cis positions (adjacent to each other) and a single bound ligand do not affect channel deactivation. These results support an activation mechanism in which each single liganded CNBD causes a turning momentum on the tetrameric ring-like structure formed by all four CNBDs and that at least two liganded subunits in trans positions are required to maintain activation.
Collapse
Affiliation(s)
- Mallikarjuna Rao Sunkara
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Tina Schwabe
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Gunter Ehrlich
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Jana Kusch
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Klaus Benndorf
- Institut für Physiologie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| |
Collapse
|
4
|
Putrenko I, Yip R, Schwarz SKW, Accili EA. Cation and voltage dependence of lidocaine inhibition of the hyperpolarization-activated cyclic nucleotide-gated HCN1 channel. Sci Rep 2017; 7:1281. [PMID: 28455536 PMCID: PMC5430837 DOI: 10.1038/s41598-017-01253-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 03/28/2017] [Indexed: 12/17/2022] Open
Abstract
Lidocaine is known to inhibit the hyperpolarization-activated mixed cation current (Ih) in cardiac myocytes and neurons, as well in cells transfected with cloned Hyperpolarization-activated Cyclic Nucleotide-gated (HCN) channels. However, the molecular mechanism of Ih inhibition by this drug has been limitedly explored. Here, we show that inhibition of Ih by lidocaine, recorded from Chinese hamster ovary (CHO) cells expressing the HCN1 channel, reached a steady state within one minute and was reversible. Lidocaine inhibition of Ih was greater at less negative voltages and smaller current amplitudes whereas the voltage-dependence of Ih activation was unchanged. Lidocaine inhibition of Ih measured at −130 mV (a voltage at which Ih is fully activated) was reduced, and Ih amplitude was increased, when the concentration of extracellular potassium was raised to 60 mM from 5.4 mM. By contrast, neither Ih inhibition by the drug nor Ih amplitude at +30 mV (following a test voltage-pulse to −130 mV) were affected by this rise in extracellular potassium. Together, these data indicate that lidocaine inhibition of Ih involves a mechanism which is antagonized by hyperpolarizing voltages and current flow.
Collapse
Affiliation(s)
- Igor Putrenko
- Department of Cellular and Physiological Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Anesthesiology, Pharmacology & Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Raymond Yip
- Department of Cellular and Physiological Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephan K W Schwarz
- Department of Anesthesiology, Pharmacology & Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.,Department of Anesthesia, St. Paul's Hospital/Providence Health Care, Vancouver, British Columbia, Canada
| | - Eric A Accili
- Department of Cellular and Physiological Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
5
|
Lyashchenko AK, Redd KJ, Goldstein PA, Tibbs GR. cAMP control of HCN2 channel Mg2+ block reveals loose coupling between the cyclic nucleotide-gating ring and the pore. PLoS One 2014; 9:e101236. [PMID: 24983358 PMCID: PMC4077740 DOI: 10.1371/journal.pone.0101236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/04/2014] [Indexed: 12/24/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-regulated HCN channels underlie the Na+-K+ permeable IH pacemaker current. As with other voltage-gated members of the 6-transmembrane KV channel superfamily, opening of HCN channels involves dilation of a helical bundle formed by the intracellular ends of S6 albeit this is promoted by inward, not outward, displacement of S4. Direct agonist binding to a ring of cyclic nucleotide-binding sites, one of which lies immediately distal to each S6 helix, imparts cAMP sensitivity to HCN channel opening. At depolarized potentials, HCN channels are further modulated by intracellular Mg2+ which blocks the open channel pore and blunts the inhibitory effect of outward K+ flux. Here, we show that cAMP binding to the gating ring enhances not only channel opening but also the kinetics of Mg2+ block. A combination of experimental and simulation studies demonstrates that agonist acceleration of block is mediated via acceleration of the blocking reaction itself rather than as a secondary consequence of the cAMP enhancement of channel opening. These results suggest that the activation status of the gating ring and the open state of the pore are not coupled in an obligate manner (as required by the often invoked Monod-Wyman-Changeux allosteric model) but couple more loosely (as envisioned in a modular model of protein activation). Importantly, the emergence of second messenger sensitivity of open channel rectification suggests that loose coupling may have an unexpected consequence: it may endow these erstwhile “slow” channels with an ability to exert voltage and ligand-modulated control over cellular excitability on the fastest of physiologically relevant time scales.
Collapse
Affiliation(s)
- Alex K. Lyashchenko
- Department of Anesthesiology, Columbia University, New York, New York, United States of America
| | - Kacy J. Redd
- Department of Neuroscience, Columbia University, New York, New York, United States of America
| | - Peter A. Goldstein
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York, United States of America
| | - Gareth R. Tibbs
- Department of Anesthesiology, Columbia University, New York, New York, United States of America
- Department of Anesthesiology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
6
|
Akimoto M, Zhang Z, Boulton S, Selvaratnam R, VanSchouwen B, Gloyd M, Accili EA, Lange OF, Melacini G. A mechanism for the auto-inhibition of hyperpolarization-activated cyclic nucleotide-gated (HCN) channel opening and its relief by cAMP. J Biol Chem 2014; 289:22205-20. [PMID: 24878962 DOI: 10.1074/jbc.m114.572164] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channels control neuronal and cardiac electrical rhythmicity. There are four homologous isoforms (HCN1-4) sharing a common multidomain architecture that includes an N-terminal transmembrane tetrameric ion channel followed by a cytoplasmic "C-linker," which connects a more distal cAMP-binding domain (CBD) to the inner pore. Channel opening is primarily stimulated by transmembrane elements that sense membrane hyperpolarization, although cAMP reduces the voltage required for HCN activation by promoting tetramerization of the intracellular C-linker, which in turn relieves auto-inhibition of the inner pore gate. Although binding of cAMP has been proposed to relieve auto-inhibition by affecting the structure of the C-linker and CBD, the nature and extent of these cAMP-dependent changes remain limitedly explored. Here, we used NMR to probe the changes caused by the binding of cAMP and of cCMP, a partial agonist, to the apo-CBD of HCN4. Our data indicate that the CBD exists in a dynamic two-state equilibrium, whose position as gauged by NMR chemical shifts correlates with the V½ voltage measured through electrophysiology. In the absence of cAMP, the most populated CBD state leads to steric clashes with the activated or "tetrameric" C-linker, which becomes energetically unfavored. The steric clashes of the apo tetramer are eliminated either by cAMP binding, which selects for a CBD state devoid of steric clashes with the tetrameric C-linker and facilitates channel opening, or by a transition of apo-HCN to monomers or dimer of dimers, in which the C-linker becomes less structured, and channel opening is not facilitated.
Collapse
Affiliation(s)
- Madoka Akimoto
- From the Departments of Chemistry and Chemical Biology and
| | - Zaiyong Zhang
- the Biomolecular NMR and Munich Center for Integrated Protein Science, Department of Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Stephen Boulton
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | | | | | - Melanie Gloyd
- From the Departments of Chemistry and Chemical Biology and Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Eric A Accili
- the Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada, and
| | - Oliver F Lange
- the Biomolecular NMR and Munich Center for Integrated Protein Science, Department of Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany, the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Giuseppe Melacini
- From the Departments of Chemistry and Chemical Biology and Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada,
| |
Collapse
|