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Wu Y, Luo XD, Xiang T, Li SJ, Ma MG, Chen ML. Activation of metabotropic glutamate receptor 1 regulates hippocampal CA1 region excitability in rats with status epilepticus by suppressing the HCN1 channel. Neural Regen Res 2023; 18:594-602. [DOI: 10.4103/1673-5374.350206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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2
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Santos-Vera B, Vaquer-Alicea ADC, Maria-Rios CE, Montiel-Ramos A, Ramos-Cardona A, Vázquez-Torres R, Sanabria P, Jiménez-Rivera CA. Protein and surface expression of HCN2 and HCN4 subunits in mesocorticolimbic areas after cocaine sensitization. Neurochem Int 2019; 125:91-98. [PMID: 30794847 DOI: 10.1016/j.neuint.2019.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 01/20/2023]
Abstract
The Ih is a mixed depolarizing current present in neurons which, upon activation by hyperpolarization, modulates neuronal excitability in the mesocorticolimbic (MCL) system, an area which regulates emotions such as pleasure, reward, and motivation. Its biophysical properties are determined by HCN protein expression profiles, specifically HCN subunits 1-4. Previously, we reported that cocaine-induced behavioral sensitization increases HCN2 protein expression in all MCL areas with the Ventral Tegmental Area (VTA) showing the most significant increase. Recent evidence suggests that HCN4 also has an important expression in the MCL system. Although there is a significant expression of HCN channels in the MCL system their role in addictive processes is largely unknown. Thus, in this study we aim to compare HCN2 and HCN4 expression profiles and their cellular compartmental distribution in the MCL system, before and after cocaine sensitization. Surface/intracellular (S/I) ratio analysis indicates that VTA HCN2 subunits are mostly expressed in the cell surface in contrast to other areas tested. Our findings demonstrate that after cocaine sensitization, the HCN2 S/I ratio in the VTA was decreased whereas in the Prefrontal Cortex it was increased. In addition, HCN4 total expression in the VTA was decreased after cocaine sensitization, although the S/I ratio was not altered. Together, these results demonstrate differential cocaine effects on HCN2 and HCN4 protein expression profiles and therefore suggest a diverse Ih modulation of cellular activity during cocaine addictive processes.
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Affiliation(s)
- Bermary Santos-Vera
- Physiology Department, University of Puerto Rico, School of Medicine, Medical Sciences Campus, San Juan, 00936-5067, Puerto Rico
| | - Ana Del C Vaquer-Alicea
- Physiology Department, University of Puerto Rico, School of Medicine, Medical Sciences Campus, San Juan, 00936-5067, Puerto Rico
| | - Cristina E Maria-Rios
- Biology Department, University of Puerto Rico, Rio Piedras Campus, San Juan, 00936-5067, Puerto Rico
| | - Alan Montiel-Ramos
- Biology Department, University of Puerto Rico, Rio Piedras Campus, San Juan, 00936-5067, Puerto Rico
| | - Aynette Ramos-Cardona
- Psychology Department, University of Puerto Rico, Rio Piedras Campus, San Juan, 00936-5067, Puerto Rico
| | - Rafael Vázquez-Torres
- Physiology Department, University of Puerto Rico, School of Medicine, Medical Sciences Campus, San Juan, 00936-5067, Puerto Rico
| | - Priscila Sanabria
- Physiology Department, Universidad Central del Caribe, Bayamon, 00960, Puerto Rico
| | - Carlos A Jiménez-Rivera
- Physiology Department, University of Puerto Rico, School of Medicine, Medical Sciences Campus, San Juan, 00936-5067, Puerto Rico.
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3
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Pietak A, Levin M. Bioelectrical control of positional information in development and regeneration: A review of conceptual and computational advances. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 137:52-68. [PMID: 29626560 PMCID: PMC10464501 DOI: 10.1016/j.pbiomolbio.2018.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 12/16/2022]
Abstract
Positional information describes pre-patterns of morphogenetic substances that alter spatio-temporal gene expression to instruct development of growth and form. A wealth of recent data indicate bioelectrical properties, such as the transmembrane potential (Vmem), are involved as instructive signals in the spatiotemporal regulation of morphogenesis. However, the mechanistic relationships between Vmem and molecular positional information are only beginning to be understood. Recent advances in computational modeling are assisting in the development of comprehensive frameworks for mechanistically understanding how endogenous bioelectricity can guide anatomy in a broad range of systems. Vmem represents an extraordinarily strong electric field (∼1.0 × 106 V/m) active over the thin expanse of the plasma membrane, with the capacity to influence a variety of downstream molecular signaling cascades. Moreover, in multicellular networks, intercellular coupling facilitated by gap junction channels may induce directed, electrodiffusive transport of charged molecules between cells of the network to generate new positional information patterning possibilities and characteristics. Given the demonstrated role of Vmem in morphogenesis, here we review current understanding of how Vmem can integrate with molecular regulatory networks to control single cell state, and the unique properties bioelectricity adds to transport phenomena in gap junction-coupled cell networks to facilitate self-assembly of morphogen gradients and other patterns. Understanding how Vmem integrates with biochemical regulatory networks at the level of a single cell, and mechanisms through which Vmem shapes molecular positional information in multicellular networks, are essential for a deep understanding of body plan control in development, regeneration and disease.
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Affiliation(s)
| | - Michael Levin
- Allen Discovery Center at Tufts, USA; Center for Regenerative and Developmental Biology, Tufts University, Medford, MA, USA
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4
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VanSchouwen B, Melacini G. Role of Dimers in the cAMP-Dependent Activation of Hyperpolarization-Activated Cyclic-Nucleotide-Modulated (HCN) Ion Channels. J Phys Chem B 2018; 122:2177-2190. [PMID: 29461059 DOI: 10.1021/acs.jpcb.7b10125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hyperpolarization-activated cyclic-nucleotide-modulated (HCN) ion channels control rhythmicity in neurons and cardiomyocytes. Cyclic AMP (cAMP) modulates HCN activity through the cAMP-induced formation of a tetrameric gating ring spanning the intracellular region (IR) of HCN. Although evidence from confocal patch-clamp fluorometry indicates that the cAMP-dependent gating of HCN occurs through a dimer of dimers, the structural and dynamical basis of cAMP allostery in HCN dimers has so far remained elusive. Thus, here we examine how dimers influence IR structural dynamics, and the role that such structural dynamics play in HCN allostery. To this end, we performed molecular dynamics (MD) simulations of HCN4 IR dimers in their fully apo, fully holo, and partially cAMP-bound states, resulting in a total simulated time of 1.2 μs. Comparative analyses of these MD trajectories, as well as previous monomer and tetramer simulations utilized as benchmarks for comparison, reveal that dimers markedly sensitize the HCN IR to cAMP-modulated allostery. Our results indicate that dimerization fine-tunes the IR dynamics to enhance, relative to both monomers and tetramers, the allosteric intra- and interprotomer coupling between the cAMP-binding domain and tetramerization domain components of the IR. The resulting allosteric model provides a viable rationalization of electrophysiological data on the role of IR dimers in HCN activation.
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Affiliation(s)
- Bryan VanSchouwen
- Department of Chemistry and Chemical Biology and ‡Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology and ‡Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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5
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VanSchouwen B, Melacini G. Structural Basis of Tonic Inhibition by Dimers of Dimers in Hyperpolarization-Activated Cyclic-Nucleotide-Modulated (HCN) Ion Channels. J Phys Chem B 2016; 120:10936-10950. [DOI: 10.1021/acs.jpcb.6b07735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bryan VanSchouwen
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Giuseppe Melacini
- Department
of Chemistry and Chemical Biology, McMaster University, 1280 Main
Street West, Hamilton, Ontario L8S 4M1, Canada
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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6
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Machado M, Pantano S. Structure-based, in silico approaches for the development of novel cAMP FRET reporters. Methods Mol Biol 2015; 1294:41-58. [PMID: 25783876 DOI: 10.1007/978-1-4939-2537-7_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A significant contribution to the research in cAMP signaling has been made by the development of genetically encoded FRET sensors that allow detection of local concentrations of second messengers in living cells. Nowadays, the availability of a number of 3D structures of cyclic nucleotide-binding domains (CNBD) undergoing conformational transitions upon cAMP binding, along with computational tools, can be exploited for the design of novel or improved sensors. In this chapter we will overview some coarse-grained geometrical considerations on fluorescent proteins, CNBD, and linker peptides to draw simple qualitative rules that may aid the design of novel sensors. Finally, we will illustrate how the application of these simple rules can be used to describe the mechanistic basis of cAMP sensors reported in the literature.
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Affiliation(s)
- Matías Machado
- Group of Biomolecular Simulations, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
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7
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VanSchouwen B, Akimoto M, Sayadi M, Fogolari F, Melacini G. Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels. J Biol Chem 2015; 290:17642-17654. [PMID: 25944904 DOI: 10.1074/jbc.m115.651877] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 01/01/2023] Open
Abstract
The hyperpolarization-activated cyclic nucleotide-modulated (HCN) ion channels control rhythmicity in neurons and cardiomyocytes. Cyclic AMP allosterically modulates HCN through the cAMP-dependent formation of a tetrameric gating ring spanning the intracellular region (IR) of HCN, to which cAMP binds. Although the apo versus holo conformational changes of the cAMP-binding domain (CBD) have been previously mapped, only limited information is currently available on the HCN IR dynamics, which have been hypothesized to play a critical role in the cAMP-dependent gating of HCN. Here, using molecular dynamics simulations validated and complemented by experimental NMR and CD data, we comparatively analyze HCN IR dynamics in the four states of the thermodynamic cycle arising from the coupling between cAMP binding and tetramerization equilibria. This extensive set of molecular dynamics trajectories captures the active-to-inactive transition that had remained elusive for other CBDs, and it provides unprecedented insight on the role of IR dynamics in HCN autoinhibition and its release by cAMP. Specifically, the IR tetramerization domain becomes more flexible in the monomeric states, removing steric clashes that the apo-CDB structure would otherwise impose. Furthermore, the simulations reveal that the active/inactive structural transition for the apo-monomeric CBD occurs through a manifold of pathways that are more divergent than previously anticipated. Upon cAMP binding, these pathways become disallowed, pre-confining the CBD conformational ensemble to a tetramer-compatible state. This conformational confinement primes the IR for tetramerization and thus provides a model of how cAMP controls HCN channel gating.
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Affiliation(s)
- Bryan VanSchouwen
- Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Madoka Akimoto
- Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Maryam Sayadi
- Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Federico Fogolari
- Department of Biomedical Science and Technology, University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Giuseppe Melacini
- Departments of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada; Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada.
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8
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Darré L, Machado MR, Brandner AF, González HC, Ferreira S, Pantano S. SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics. J Chem Theory Comput 2015; 11:723-39. [DOI: 10.1021/ct5007746] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Leonardo Darré
- Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department
of Chemistry, King’s College, London, United Kingdom
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9
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Zhou M, Luo P, Lu Y, Li CJ, Wang DS, Lu Q, Xu XL, He Z, Guo LJ. Imbalance of HCN1 and HCN2 expression in hippocampal CA1 area impairs spatial learning and memory in rats with chronic morphine exposure. Prog Neuropsychopharmacol Biol Psychiatry 2015; 56:207-14. [PMID: 25301101 DOI: 10.1016/j.pnpbp.2014.09.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/13/2014] [Accepted: 09/29/2014] [Indexed: 12/12/2022]
Abstract
The hyperpolarization-activated cyclic-nucleotide-gated non-selective cation (HCN) channels play a vital role in the neurological basis underlying nervous system diseases. However, the role of HCN channels in drug addiction is not fully understood. In the present study, we investigated the expression of HCN1 and HCN2 subunits in hippocampal CA1 and the potential molecular mechanisms underlying the modulation of HCN channels in rats with chronic morphine exposure with approaches of electrophysiology, water maze, and Western blotting. We found that chronic morphine exposure (5 mg/kg, sc, for 7 days) caused an inhibition of long-term potentiation (LTP) and impairment of spatial learning and memory, which is associated with a decrease in HCN1, and an increase in HCN2 on cell membrane of hippocampal CA1 area. Additional experiments showed that the imbalance of cell membrane HCN1 and HCN2 expression under chronic morphine exposure was related to an increase in expression of TPR containing Rab8b interacting protein (TRIP8b) (1a-4) and TRIP8b (1b-2), and phosphorylation of protein kinase A (PKA) and adaptor protein 2 μ2 (AP2 μ2). Our results demonstrate the novel information that drug addiction-induced impairment of learning and memory is involved in the imbalance of HCN1 and HCN2 subunits, which is mediated by activation of TRIP8b (1a-4), TRIP8b (1b-2), PKA and AP2 μ2.
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Affiliation(s)
- Mei Zhou
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Pan Luo
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yun Lu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chang-jun Li
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dian-shi Wang
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qing Lu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Institute of Brain Research, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xu-lin Xu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Institute of Brain Research, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhi He
- Department of Neuropsychopharmacology, Medical School of China Three Gorges University, Yichang, 443002, China.
| | - Lian-jun Guo
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Institute of Brain Research, Huazhong University of Science and Technology, Wuhan 430030, China.
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10
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Cocaine sensitization increases I h current channel subunit 2 (HCN₂) protein expression in structures of the mesocorticolimbic system. J Mol Neurosci 2012. [PMID: 23203153 DOI: 10.1007/s12031-012-9920-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Alteration of the biological activity among neuronal components of the mesocorticolimbic (MCL) system has been implicated in the pathophysiology of drug abuse. Changes in the electrophysiological properties of neurons involved in the reward circuit seem to be of utmost importance in addiction. The hyperpolarization-activated cyclic nucleotide current, I h, is a prominent mixed cation current present in neurons. The biophysical properties of the I h and its potential modulatory role in cell excitability depend on the expression profile of the hyperpolarization-activated cyclic nucleotide gated channel (HCN) subunits. We investigated whether cocaine-induced behavioral sensitization, an animal model of drug addiction, elicits region-specific changes in the expression of the HCN₂ channel's subunit in the MCL system. Tissue samples from the ventral tegmental area, prefrontal cortex, nucleus accumbens, and hippocampus were analyzed using Western blot. Our findings demonstrate that cocaine treatment induced a significant increase in the expression profile of the HCN₂ subunit in both its glycosylated and non-glycosylated protein isoforms in all areas tested. The increase in the glycosylated isoform was only observed in the ventral tegmental area. Together, these data suggest that the observed changes in MCL excitability during cocaine addiction might be associated with alterations in the subunit composition of their HCN channels.
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11
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Choi KR, Berrera M, Reischl M, Strack S, Albrizio M, Röder IV, Wagner A, Petersen Y, Hafner M, Zaccolo M, Rudolf R. Rapsyn mediates subsynaptic anchoring of PKA type I and stabilisation of acetylcholine receptor in vivo. J Cell Sci 2012; 125:714-23. [PMID: 22331361 DOI: 10.1242/jcs.092361] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The stabilisation of acetylcholine receptors (AChRs) at the neuromuscular junction depends on muscle activity and the cooperative action of myosin Va and protein kinase A (PKA) type I. To execute its function, PKA has to be present in a subsynaptic microdomain where it is enriched by anchoring proteins. Here, we show that the AChR-associated protein, rapsyn, interacts with PKA type I in C2C12 and T-REx293 cells as well as in live mouse muscle beneath the neuromuscular junction. Molecular modelling, immunoprecipitation and bimolecular fluorescence complementation approaches identify an α-helical stretch of rapsyn to be crucial for binding to the dimerisation and docking domain of PKA type I. When expressed in live mouse muscle, a peptide encompassing the rapsyn α-helical sequence efficiently delocalises PKA type I from the neuromuscular junction. The same peptide, as well as a rapsyn construct lacking the α-helical domain, induces severe alteration of acetylcholine receptor turnover as well as fragmentation of synapses. This shows that rapsyn anchors PKA type I in close proximity to the postsynaptic membrane and suggests that this function is essential for synapse maintenance.
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Affiliation(s)
- Kyeong-Rok Choi
- Institut für Toxikologie und Genetik, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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12
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Chow SS, Van Petegem F, Accili EA. Energetics of cyclic AMP binding to HCN channel C terminus reveal negative cooperativity. J Biol Chem 2011; 287:600-606. [PMID: 22084239 DOI: 10.1074/jbc.m111.269563] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclic AMP binds to the HCN channel C terminus and variably stabilizes its open state. Using isothermal titration calorimetry, we show that cAMP binds to one subunit of tetrameric HCN2 and HCN4 C termini with high affinity (∼0.12 μM) and subsequently with low affinity (∼1 μM) to the remaining three subunits. Changes induced by high affinity binding already exist in both a constrained HCN2 tetramer and the unconstrained HCN1 tetramer. Natural "preactivation" of HCN1 may explain both the smaller effect of cAMP on stabilizing its open state and the opening of unliganded HCN1, which occurs as though already disinhibited.
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Affiliation(s)
- Sarah S Chow
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Eric A Accili
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
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13
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Diskar M, Zenn HM, Kaupisch A, Kaufholz M, Brockmeyer S, Sohmen D, Berrera M, Zaccolo M, Boshart M, Herberg FW, Prinz A. Regulation of cAMP-dependent protein kinases: the human protein kinase X (PrKX) reveals the role of the catalytic subunit alphaH-alphaI loop. J Biol Chem 2010; 285:35910-8. [PMID: 20819953 PMCID: PMC2975214 DOI: 10.1074/jbc.m110.155150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 08/10/2010] [Indexed: 11/06/2022] Open
Abstract
cAMP-dependent protein kinases are reversibly complexed with any of the four isoforms of regulatory (R) subunits, which contain either a substrate or a pseudosubstrate autoinhibitory domain. The human protein kinase X (PrKX) is an exemption as it is inhibited only by pseudosubstrate inhibitors, i.e. RIα or RIβ but not by substrate inhibitors RIIα or RIIβ. Detailed examination of the capacity of five PrKX-like kinases ranging from human to protozoa (Trypanosoma brucei) to form holoenzymes with human R subunits in living cells shows that this preference for pseudosubstrate inhibitors is evolutionarily conserved. To elucidate the molecular basis of this inhibitory pattern, we applied bioluminescence resonance energy transfer and surface plasmon resonance in combination with site-directed mutagenesis. We observed that the conserved αH-αI loop residue Arg-283 in PrKX is crucial for its RI over RII preference, as a R283L mutant was able to form a holoenzyme complex with wild type RII subunits. Changing the corresponding αH-αI loop residue in PKA Cα (L277R), significantly destabilized holoenzyme complexes in vitro, as cAMP-mediated holoenzyme activation was facilitated by a factor of 2-4, and lead to a decreased affinity of the mutant C subunit for R subunits, significantly affecting RII containing holoenzymes.
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Affiliation(s)
- Mandy Diskar
- From the Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Hans-Michael Zenn
- From the Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Alexandra Kaupisch
- From the Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Melanie Kaufholz
- From the Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Stefanie Brockmeyer
- From the Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Daniel Sohmen
- the Biocenter, Section Genetics, University of Munich (LMU), Großhaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany, and
| | - Marco Berrera
- the University of Glasgow, University Avenue, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Manuela Zaccolo
- the University of Glasgow, University Avenue, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Michael Boshart
- the Biocenter, Section Genetics, University of Munich (LMU), Großhaderner Strasse 2-4, 82152 Planegg-Martinsried, Germany, and
| | - Friedrich W. Herberg
- From the Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Anke Prinz
- From the Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
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14
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Rossetti G, Magistrato A, Pastore A, Persichetti F, Carloni P. Structural Properties of Polyglutamine Aggregates Investigated via Molecular Dynamics Simulations. J Phys Chem B 2008; 112:16843-50. [DOI: 10.1021/jp806548p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Giulia Rossetti
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
| | - Alessandra Magistrato
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
| | - Annalisa Pastore
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
| | - Francesca Persichetti
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
| | - Paolo Carloni
- International School for Advanced Studies, via Beirut 2-4, Trieste, Italy, CNR-INFM-Democritos National Simulation Center, Beirut 2-4, Trieste, Italy, Italian Institute of Technology - SISSA Unit, via Beirut 2-4, Trieste, Italy, and National Institute for Medical Research, The Ridgeway London, NW71AA, U.K
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15
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Pantano S. In silico description of fluorescent probes in vivo. J Mol Graph Model 2008; 27:563-7. [PMID: 18835798 DOI: 10.1016/j.jmgm.2008.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 08/11/2008] [Accepted: 08/16/2008] [Indexed: 11/17/2022]
Abstract
Fluorescent imaging in vivo has became one of the most powerful tools to follow the temporal and spatial localization of a variety of intracellular molecular events. Genetically encoded fluorescent indicators using the FRET effect are routinely used although the molecular basis regulating their functioning is not completely known. Here, the structural and dynamics properties of a commonly used FRET sensor for the second messenger cAMP based on the cAMP-binding domains of the regulatory subunit of Protein Kinase A are presented. Molecular dynamics simulations allowed pinpointing the main features of cAMP driven conformational transition and dissecting the contributions of geometric factors governing the functioning of the biosensor. Simulations suggest that, although orientational factors are not fully isotropic, they are highly dynamic making the inter-chromophore distance the dominant feature, determining the functioning of the probes. It is expected that this computer-aided methodology may state general basis for rational design strategies of fluorescent markers for in vivo imaging.
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Affiliation(s)
- Sergio Pantano
- Institut Pasteur of Montevideo, Calle Mataojo 2020, CP 11400, Montevideo, Uruguay.
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Zhou L, Siegelbaum SA. Gating of HCN channels by cyclic nucleotides: residue contacts that underlie ligand binding, selectivity, and efficacy. Structure 2007; 15:655-70. [PMID: 17562313 PMCID: PMC1995447 DOI: 10.1016/j.str.2007.04.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 03/19/2007] [Accepted: 04/06/2007] [Indexed: 11/19/2022]
Abstract
Cyclic nucleotides (cNMPs) regulate the activity of various proteins by interacting with a conserved cyclic nucleotide-binding domain (CNBD). Although X-ray crystallographic studies have revealed the structures of several CNBDs, the residues responsible for generating the high efficacy with which ligand binding leads to protein activation remain unknown. Here, we combine molecular dynamics simulations with mutagenesis to identify ligand contacts important for the regulation of the hyperpolarization-activated HCN2 channel by cNMPs. Surprisingly, out of 7 residues that make strong contacts with ligand, only R632 in the C helix of the CNBD is essential for high ligand efficacy, due to its selective stabilization of cNMP binding to the open state of the channel. Principal component analysis suggests that a local movement of the C helix upon ligand binding propagates through the CNBD of one subunit to the C linker of a neighboring subunit to apply force to the gate of the channel.
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Affiliation(s)
- Lei Zhou
- Center for Neurobiology and Behavior, Howard Hughes Medical Institute, Columbia University, 722 W. 168 St. New York, NY 10032
| | - Steven A. Siegelbaum
- Center for Neurobiology and Behavior, Howard Hughes Medical Institute, Columbia University, 722 W. 168 St. New York, NY 10032
- Department of Pharmacology, Howard Hughes Medical Institute, Columbia University, 722 W. 168 St. New York, NY 10032
- * To whom correspondence should be addressed. E-mail: , Fax: 212-795-7997
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17
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Berrera M, Pantano S, Carloni P. Catabolite Activator Protein in Aqueous Solution: A Molecular Simulation Study. J Phys Chem B 2007; 111:1496-501. [PMID: 17243667 DOI: 10.1021/jp0667893] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The homodimeric catabolite activator protein (CAP) is a bacterial DNA binding transcription regulator whose activity is controlled by the binding of the intracellular mediator cyclic adenosine monophosphate (cAMP). Each CAP subunit consists of a cyclic nucleotide and a DNA binding domain. Here, we investigate the structural features of the ligand-bound CAP in aqueous solution by molecular dynamics simulations based on the available X-ray structures (Passner et al. J. Mol. Biol. 2000, 304, 847-859 and Chen et al. J. Mol. Biol. 2001, 314, 63-74). Our calculations suggest that the homodimer in solution assumes a symmetric arrangement in which both DNA binding domains are separated from the respective cyclic nucleotide binding domains by a cleft. This contrasts with the X-ray structure, which exhibits instead an asymmetric conformation. On the basis of electrostatics calculations, we propose that the symmetric structure in solution may be an important feature for DNA molecular recognition.
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Affiliation(s)
- Marco Berrera
- Scuola Internazionale Superiore di Studi Avanzati (SISSA) and INFM, Democritos Modeling Center for Research In Atomistic Simulation, via Beirut 4, 34014 Trieste, Italy
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