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Putkey JA, Hoffman L, Berka V, Wang X. Neurogranin modulates the rate of association between calmodulin and target peptides. Biophys J 2024; 123:1676-1689. [PMID: 38751114 PMCID: PMC11213993 DOI: 10.1016/j.bpj.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Accepted: 05/10/2024] [Indexed: 05/28/2024] Open
Abstract
The best-known mode of action of calmodulin (CaM) is binding of Ca2+ to its N- and C-domains, followed by binding to target proteins. An underappreciated facet of this process is that CaM is typically bound to proteins at basal levels of free Ca2+, including the small, intrinsically disordered, neuronal IQ-motif proteins called PEP-19 and neurogranin (Ng). PEP-19 and Ng would not be effective competitive inhibitors of high-affinity Ca2+-dependent CaM targets at equilibrium because they bind to CaM with relatively low affinity, but they could influence the time course of CaM signaling by affecting the rate of association of CaM with high-affinity Ca2+-dependent targets. This mode of regulation may be domain specific because PEP-19 binds to the C-domain of CaM, whereas Ng binds to both N- and C-domains. In this report, we used a model CaM binding peptide (CKIIp) to characterize the preferred pathway of complex formation with Ca2+-CaM at low levels of free Ca2+ (0.25-1.5 μM), and how PEP-19 and Ng affect this process. We show that the dominant encounter complex involves association of CKIIp with the N-domain of CaM, even though the C-domain has a greater affinity for Ca2+. We also show that Ng greatly decreases the rate of association of Ca2+-CaM with CKIIp due to the relatively slow dissociation of Ng from CaM, and to interactions between the Gly-rich C-terminal region of Ng with the N-domain of CaM, which inhibits formation of the preferred encounter complex with CKIIp. These results provide the general mechanistic paradigms that binding CaM to targets can be driven by its N-domain, and that low-affinity regulators of CaM signaling have the potential to influence the rate of activation of high-affinity CaM targets and potentially affect the distribution of limited CaM among multiple targets during Ca2+ oscillations.
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Affiliation(s)
- John A Putkey
- Department of Biochemistry and Molecular Biology, University of Texas McGovern Medical School, Houston, Texas.
| | - Laurel Hoffman
- Department of Biochemistry and Molecular Biology, University of Texas McGovern Medical School, Houston, Texas
| | - Vladimir Berka
- Department of Biochemistry and Molecular Biology, University of Texas McGovern Medical School, Houston, Texas
| | - Xu Wang
- Department of Biochemistry and Molecular Biology, University of Texas McGovern Medical School, Houston, Texas
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2
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Putkey JA, Hoffman L, Berka V, Wang X. Neurogranin modulates the Rate of Association between Calmodulin and Target Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586151. [PMID: 38562851 PMCID: PMC10983935 DOI: 10.1101/2024.03.21.586151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The best-known mode of action of calmodulin (CaM) is binding of Ca 2+ to its N- and C-domains, followed by binding to target proteins. An underappreciated facet of this process is that CaM is typically bound to proteins at basal levels of free Ca 2+ , including the small, intrinsically disordered, neuronal IQ-motif proteins called PEP-19 and neurogranin (Ng). PEP-19 and Ng would not be effective competitive inhibitors of high-affinity Ca 2+ -dependent CaM targets at equilibrium since they bind to CaM with relatively low affinity, but they could influence the time course of CaM signaling by affecting the rate of association of CaM with high-affinity Ca 2+ -dependent targets. This mode of regulation may domain specific since PEP-19 binds to the C-domain of CaM, while Ng binds to both N- and C-domains. In this report, we used a model CaM binding peptide (CKIIp) to characterize the preferred pathway of complex formation with Ca 2+ -CaM at low levels of free Ca 2+ (0.25 to 1.5 µM), and how PEP-19 and Ng affect this process. We show that the dominant encounter complex involves association of CKIIp with the N-domain of CaM, even though the C-domain has a greater affinity for Ca 2+ . We also show that Ng greatly decreases the rate of association of Ca 2+ -CaM with CKIIp due to the relatively slow dissociation of Ng from CaM, and to interactions between the Gly-rich C-terminal region of Ng with the N-domain of CaM, which inhibits formation of the preferred encounter complex with CKIIp. These results provide the general mechanistic paradigms that binding CaM to targets can be driven by its N-domain, and that low-affinity regulators of CaM signaling have the potential to influence the rate of activation of high-affinity CaM targets and potentially affect the distribution of limited CaM among multiple targets during Ca 2+ oscillations. STATEMENT OF SIGNIFICANCE Calmodulin is a small, essential regulator of multiple cellular processes including growth and differentiation. Its best-known mode of action is to first bind calcium and then bind and regulate the activity of target proteins. Each domain of CaM has distinct calcium binding properties and can interact with targets in distinct ways. We show here that the N-domain of calmodulin can drive its association with targets, and that a small, intrinsically disordered regulator of calmodulin signaling called neurogranin can greatly decrease the rate of association of CaM with high-affinity Ca 2+ -dependent targets. These results demonstrate the potential of neurogranin, and potentially other proteins, to modulate the time course of activation of targets by a limited intracellular supply of calmodulin.
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Piserchio A, Dalby KN, Ghose R. Revealing eEF-2 kinase: recent structural insights into function. Trends Biochem Sci 2024; 49:169-182. [PMID: 38103971 PMCID: PMC10950556 DOI: 10.1016/j.tibs.2023.11.004] [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: 08/15/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
The α-kinase eukaryotic elongation factor 2 kinase (eEF-2K) regulates translational elongation by phosphorylating its ribosome-associated substrate, the GTPase eEF-2. eEF-2K is activated by calmodulin (CaM) through a distinctive mechanism unlike that in other CaM-dependent kinases (CAMK). We describe recent structural insights into this unique activation process and examine the effects of specific regulatory signals on this mechanism. We also highlight key unanswered questions to guide future structure-function studies. These include structural mechanisms which enable eEF-2K to interact with upstream/downstream partners and facilitate its integration of diverse inputs, including Ca2+ transients, phosphorylation mediated by energy/nutrient-sensing pathways, pH changes, and metabolites. Answering these questions is key to establishing how eEF-2K harmonizes translation with cellular requirements within the boundaries of its molecular landscape.
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Affiliation(s)
- Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas, Austin, TX 78712, USA.
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; The Graduate Center of The City University of New York (CUNY), New York, NY 10016, USA.
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4
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Satarić MV, Nemeš T. On the role of calcium diffusion and its rapid buffering in intraflagellar signaling. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:705-720. [PMID: 37851099 DOI: 10.1007/s00249-023-01685-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 09/13/2023] [Accepted: 09/23/2023] [Indexed: 10/19/2023]
Abstract
We have considered the realistic mechanism of rapid Ca2+ (calcium ion) buffering within the wave of calcium ions progressing along the flagellar axoneme. This buffering is an essential part of the Ca2+ signaling pathway aimed at controlling the bending dynamics of flagella. It is primarily achieved by the mobile region of calmodulin molecules and by stationary calaxin, as well as by the part of calmodulin bound to calcium/calmodulin-dependent kinase II and kinase C. We derived and elaborated a model of Ca2+ diffusion within a signaling wave in the presence of these molecules which rapidly buffer Ca2+. This approach has led to a single nonlinear transport equation for the Ca2+ wave that contains the effects brought about by both as necessary buffers for signaling. The presence of mobile buffer calmodulin gives rise to a transport equation that is not strictly diffusive but also exhibits a sink-like effect. We solved straightforwardly the final transport equation in an analytical framework and obtained the implied function of calcium concentration. The effective diffusion coefficient depends on local Ca2+ concentration. It is plausible that these buffers' presence can impact Ca2+ wave speed and shape, which are essential for decoding Ca2+ signaling in flagella. We present the solution of the transport equation for a few specified cases with physiologically reasonable sets of parameters involved.
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Affiliation(s)
- M V Satarić
- Serbian Academy of Science and Arts, Belgrade, Serbia
| | - T Nemeš
- Faculty of Technical Sciences, University of Novi Sad, Novi Sad, Serbia.
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5
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Curtis AJ, Zhu J, Penny CJ, Gold MG. Molecular basis of interactions between CaMKII and α-actinin-2 that underlie dendritic spine enlargement. eLife 2023; 12:e85008. [PMID: 37489746 PMCID: PMC10484527 DOI: 10.7554/elife.85008] [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: 11/18/2022] [Accepted: 07/24/2023] [Indexed: 07/26/2023] Open
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) is essential for long-term potentiation (LTP) of excitatory synapses that is linked to learning and memory. In this study, we focused on understanding how interactions between CaMKIIα and the actin-crosslinking protein α-actinin-2 underlie long-lasting changes in dendritic spine architecture. We found that association of the two proteins was unexpectedly elevated within 2 minutes of NMDA receptor stimulation that triggers structural LTP in primary hippocampal neurons. Furthermore, disruption of interactions between the two proteins prevented the accumulation of enlarged mushroom-type dendritic spines following NMDA receptor activation. α-Actinin-2 binds to the regulatory segment of CaMKII. Calorimetry experiments, and a crystal structure of α-actinin-2 EF hands 3 and 4 in complex with the CaMKII regulatory segment, indicate that the regulatory segment of autoinhibited CaMKII is not fully accessible to α-actinin-2. Pull-down experiments show that occupation of the CaMKII substrate-binding groove by GluN2B markedly increases α-actinin-2 access to the CaMKII regulatory segment. Furthermore, in situ labelling experiments are consistent with the notion that recruitment of CaMKII to NMDA receptors contributes to elevated interactions between the kinase and α-actinin-2 during structural LTP. Overall, our study provides new mechanistic insight into the molecular basis of structural LTP and reveals an added layer of sophistication to the function of CaMKII.
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Affiliation(s)
- Ashton J Curtis
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Jian Zhu
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Christopher J Penny
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Matthew G Gold
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
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Nde J, Zhang P, Waxham MN, Cheung MS. Experiment and Simulation Reveal Residue Details for How Target Binding Tunes Calmodulin's Calcium-Binding Properties. J Phys Chem B 2023; 127:2900-2908. [PMID: 36977372 DOI: 10.1021/acs.jpcb.2c08734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
We aim to elucidate the molecular mechanism of the reciprocal relation of calmodulin's (CaM) target binding and its affinity for calcium ions (Ca2+), which is central to decoding CaM-dependent Ca2+ signaling in a cell. We employed stopped-flow experiments and coarse-grained molecular simulations that learn the coordination chemistry of Ca2+ in CaM from first-principle calculations. The associative memories as part of the coarse-grained force fields built on known protein structures further influence CaM's selection of its polymorphic target peptides in the simulations. We modeled the peptides from the Ca2+/CaM-binding domain of Ca2+/CaM-dependent kinase II (CaMKII), CaMKIIp (293-310) and selected distinctive mutations at the N-terminus. Our stopped-flow experiments have shown that the CaM's affinity for Ca2+ in the bound complex of Ca2+/CaM/CaMKIIp decreased significantly when Ca2+/CaM bound to the mutant peptide (296-AAA-298) compared to that bound to the wild-type peptide (296-RRK-298). The coarse-grained molecular simulations revealed that the 296-AAA-298 mutant peptide destabilized the structures of Ca2+-binding loops at the C-domain of CaM (c-CaM) due to both loss of electrostatic interactions and differences in polymorphic structures. We have leveraged a powerful coarse-grained approach to advance a residue-level understanding of the reciprocal relation in CaM, that could not be possibly achieved by other computational approaches.
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Affiliation(s)
- Jules Nde
- Department of Physics, University of Washington, Seattle, Washington 98105, United States
| | - Pengzhi Zhang
- Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, Texas 77030, United States
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Margaret S Cheung
- Department of Physics, University of Washington, Seattle, Washington 98105, United States
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Yuan H, Xu Y, Luo Y, Zhang J, Zhu X, Xiao J. Ganoderic acid D prevents oxidative stress-induced senescence by targeting 14-3-3ε to activate CaM/CaMKII/NRF2 signaling pathway in mesenchymal stem cells. Aging Cell 2022; 21:e13686. [PMID: 35929187 PMCID: PMC9470892 DOI: 10.1111/acel.13686] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 01/25/2023] Open
Abstract
Stem cell senescence is an important cause of aging. Delaying senescence may present a novel way to combat aging and age-associated diseases. This study provided a mechanistic insight into the protective effect of ganoderic acid D (GA-D) against human amniotic mesenchymal stem cell (hAMSCs) senescence. GA-D, a Ganoderma lucidum-derived triterpenoid, markedly prevented hAMSCs senescence via activating the Ca2+ calmodulin (CaM)/CaM-dependent protein kinase II (CaMKII)/nuclear erythroid 2-related factor 2 (Nrf2) axis, and 14-3-3ε was identified as a target of GA-D. 14-3-3ε-encoding gene (YWHAE) knockdown in hAMSCs reversed the activation of the CaM/CaMKII/Nrf2 signals to attenuate the GA-D anti-aging effect and increase senescence-associated β-galactosidase (SA-β-gal), p16 and p21 expression levels, including reactive oxygen species (ROS) production, thereby promoting cell cycle arrest and decreasing differentiation potential. YWHAE overexpression maintained or slightly enhanced the GA-D anti-aging effect. GA-D prevented d-galactose-caused aging in mice by significantly increasing the total antioxidant capacity, as well as superoxide dismutase and glutathione peroxidase activity, and reducing the formation of malondialdehyde, advanced glycation end products, and receptor of advanced glycation end products. Consistent with the protective mechanism of GA-D against hAMSCs senescence, GA-D delayed the senescence of bone-marrow mesenchymal stem cells in this aging model in vivo, reduced SA-β-gal and ROS production, alleviated cell cycle arrest, and enhanced cell viability and differentiation via regulating 14-3-3ε and CaM/CaMKII/Nrf2 axis. Therefore, GA-D retards hAMSCs senescence by targeting 14-3-3ε to activate the CaM/CaMKII/Nrf2 signaling pathway. Furthermore, the in vivo GA-D anti-aging effect may involve the regulation of stem cell senescence via the same signal axis.
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Affiliation(s)
- Huan Yuan
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina,Zunyi Municiptal Key Laboratory of Medicinal Biotechnology and Guizhou Provincial Research Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Yan Xu
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina,Zunyi Municiptal Key Laboratory of Medicinal Biotechnology and Guizhou Provincial Research Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Yi Luo
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina,Zunyi Municiptal Key Laboratory of Medicinal Biotechnology and Guizhou Provincial Research Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Jia‐Rong Zhang
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Xin‐Xin Zhu
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Jian‐Hui Xiao
- Institute of Medicinal BiotechnologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina,Zunyi Municiptal Key Laboratory of Medicinal Biotechnology and Guizhou Provincial Research Center for Translational MedicineAffiliated Hospital of Zunyi Medical UniversityZunyiChina
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Qin T, Sun C, Kazim A, Cui S, Wang Y, Richard D, Yao P, Bi Z, Liu Y, Bai J. Comparative Transcriptome Analysis of Deep-Rooting and Shallow-Rooting Potato ( Solanum tuberosum L.) Genotypes under Drought Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:2024. [PMID: 35956505 PMCID: PMC9370241 DOI: 10.3390/plants11152024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
The selection and breeding of deep rooting and drought-tolerant varieties has become a promising approach for improving the yield and adaptability of potato (Solanum tuberosum L.) in arid and semiarid areas. Therefore, the discovery of root-development-related genes and drought tolerance signaling pathways in potato is important. In this study, we used deep-rooting (C119) and shallow-rooting (C16) potato genotypes, with different levels of drought tolerance, to achieve this objective. Both genotypes were treated with 150 mM mannitol for 0 h (T0), 2 h (T2), 6 h (T6), 12 h (T12), and 24 h (T24), and their root tissues were subjected to comparative transcriptome analysis. A total of 531, 1571, 1247, and 3540 differentially expressed genes (DEGs) in C16 and 1531, 1108, 674, and 4850 DEGs in C119 were identified in T2 vs. T0, T6 vs. T2, T12 vs. T6, and T24 vs. T12 comparisons, respectively. Gene expression analysis indicated that a delay in the onset of drought-induced transcriptional changes in C16 compared with C119. Functional enrichment analysis revealed genotype-specific biological processes involved in drought stress tolerance. The metabolic pathways of plant hormone transduction and MAPK signaling were heavily involved in the resistance of C16 and C119 to drought, while abscisic acid (ABA), ethylene, and salicylic acid signal transduction pathways likely played more important roles in C119 stress responses. Furthermore, genes involved in root cell elongation and division showed differential expression between the two genotypes under drought stress. Overall, this study provides important information for the marker-assisted selection and breeding of drought-tolerant potato genotypes.
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Affiliation(s)
- Tianyuan Qin
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Chao Sun
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Ali Kazim
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan;
| | - Song Cui
- School of Agriculture, Middle Tennessee State University, Murfreesboro, TN 37132, USA;
| | - Yihao Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Dormatey Richard
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Panfeng Yao
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Zhenzhen Bi
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Jiangping Bai
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
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9
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Yaduvanshi S, Ero R, Kumar V. The mechanism of complex formation between calmodulin and voltage gated calcium channels revealed by molecular dynamics. PLoS One 2021; 16:e0258112. [PMID: 34610038 PMCID: PMC8491939 DOI: 10.1371/journal.pone.0258112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/18/2021] [Indexed: 11/18/2022] Open
Abstract
Calmodulin, a ubiquitous eukaryotic calcium sensor responsible for the regulation of many fundamental cellular processes, is a highly flexible protein and exhibits an unusually wide range of conformations. Furthermore, CaM is known to interact with more than 300 cellular targets. Molecular dynamics (MD) simulation trajectories suggest that EF-hand loops show different magnitudes of flexibility. Therefore, the four EF-hand motifs have different affinities for Ca2+ ions, which enables CaM to function on wide range of Ca2+ ion concentrations. EF-hand loops are 2-3 times more flexible in apo CaM whereas least flexible in Ca2+/CaM-IQ motif complexes. We report a unique intermediate conformation of Ca2+/CaM while transitioning from extended to compact form. We also report the complex formation process between Ca2+/CaM and IQ CaM-binding motifs. Our results showed how IQ motif recognise its binding site on the CaM and how CaM transforms from extended to compact form upon binding to IQ motif.
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Affiliation(s)
- Shivani Yaduvanshi
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Noida, Noida, Uttar Pradesh, India
| | - Rya Ero
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Veerendra Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Noida, Noida, Uttar Pradesh, India
- * E-mail:
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10
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Berchtold MW, Munk M, Kulej K, Porth I, Lorentzen L, Panina S, Zacharias T, Larsen MR, la Cour JM. The heart arrhythmia-linked D130G calmodulin mutation causes premature inhibitory autophosphorylation of CaMKII. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119119. [PMID: 34391760 DOI: 10.1016/j.bbamcr.2021.119119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
The Ca2+/calmodulin (CaM)-dependent kinase II (CaMKII) is well known for transmitting Ca2+-signals, which leads to a multitude of physiological responses. Its functionality is believed to involve CaMKII holoenzyme dynamics where trans-autophosphorylation of the crucial phosphorylation site, T286 occurs. Phosphorylation of this site does not occur when stimulated exclusively with the arrhythmia associated D130G mutant form of CaM in vitro. Here, we present evidence that the loss-of-CaMKII function correlates with premature phosphorylation of its inhibitory phosphosite T306 in CaMKIIα and T307 in CaMKIIδ as this site was up to 20-fold more phosphorylated in the presence of D130G CaM compared to wildtype CaM. Indeed, changing this phosphosite to a non-phosphorylatable alanine reversed the inhibitory effect of D130G both in vitro and in live cell experiments. In addition, several phosphosites with so far undescribed functions directing the Ca2+-sensitivity of the CaMKII sensor were also affected by the presence of the D130G mutation implicating a role of several additional autophosphosites (besides T286 and T306/T307) so far not known to regulate CaMKII Ca2+ sensitivity. Furthermore, we show that introducing a D130G mutation in the CALM2 gene of the P19CL6 pluripotent mouse embryonic carcinoma cell line using CRISPR/Cas9 decreased the spontaneous beat frequency compared to wildtype cells when differentiated into cardiomyocytes supporting an alteration of cardiomyocyte physiology caused by this point mutation. In conclusion, our observations shed for the first time light on how the D130G CaM mutation interferes with the function of CaMKII and how it affects the beating frequency of cardiomyocyte-like cells.
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Affiliation(s)
| | - Mads Munk
- Department of Biology, University of Copenhagen, Denmark
| | - Katarzyna Kulej
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Isabel Porth
- Department of Biology, University of Copenhagen, Denmark
| | - Lasse Lorentzen
- Department of Biology, University of Copenhagen, Denmark; Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Svetlana Panina
- Department of Biology, University of Copenhagen, Denmark; MonTa Biosciences ApS, Diplomvej 381, 2800 kgs Lyngby, Denmark
| | | | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
| | - Jonas M la Cour
- Department of Biology, University of Copenhagen, Denmark; ChemoMetec A/S, Gydevang 43, 3450 Lillerød, Denmark
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11
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Pharris MC, Patel NM, VanDyk TG, Bartol TM, Sejnowski TJ, Kennedy MB, Stefan MI, Kinzer-Ursem TL. A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation. PLoS Comput Biol 2019; 15:e1006941. [PMID: 31869343 PMCID: PMC6957207 DOI: 10.1371/journal.pcbi.1006941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 01/13/2020] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII) accounts for up to 2 percent of all brain protein and is essential to memory function. CaMKII activity is known to regulate dynamic shifts in the size and signaling strength of neuronal connections, a process known as synaptic plasticity. Increasingly, computational models are used to explore synaptic plasticity and the mechanisms regulating CaMKII activity. Conventional modeling approaches may exclude biophysical detail due to the impractical number of state combinations that arise when explicitly monitoring the conformational changes, ligand binding, and phosphorylation events that occur on each of the CaMKII holoenzyme's subunits. To manage the combinatorial explosion without necessitating bias or loss in biological accuracy, we use a specialized syntax in the software MCell to create a rule-based model of a twelve-subunit CaMKII holoenzyme. Here we validate the rule-based model against previous experimental measures of CaMKII activity and investigate molecular mechanisms of CaMKII regulation. Specifically, we explore how Ca2+/CaM-binding may both stabilize CaMKII subunit activation and regulate maintenance of CaMKII autophosphorylation. Noting that Ca2+/CaM and protein phosphatases bind CaMKII at nearby or overlapping sites, we compare model scenarios in which Ca2+/CaM and protein phosphatase do or do not structurally exclude each other's binding to CaMKII. Our results suggest a functional mechanism for the so-called "CaM trapping" phenomenon, wherein Ca2+/CaM may structurally exclude phosphatase binding and thereby prolong CaMKII autophosphorylation. We conclude that structural protection of autophosphorylated CaMKII by Ca2+/CaM may be an important mechanism for regulation of synaptic plasticity.
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Affiliation(s)
- Matthew C. Pharris
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Neal M. Patel
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Tyler G. VanDyk
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Thomas M. Bartol
- Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Terrence J. Sejnowski
- Salk Institute for Biological Studies, La Jolla, California, United States of America
- Institute for Neural Computation, University of California San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Mary B. Kennedy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Melanie I. Stefan
- Salk Institute for Biological Studies, La Jolla, California, United States of America
- EMBL-European Bioinformatics Institute, Hinxton, United Kingdom
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- ZJU-UoE Institute, Zhejiang University, Haining, China
- * E-mail: (MIS); (TLKU)
| | - Tamara L. Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (MIS); (TLKU)
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The KN-93 Molecule Inhibits Calcium/Calmodulin-Dependent Protein Kinase II (CaMKII) Activity by Binding to Ca 2+/CaM. J Mol Biol 2019; 431:1440-1459. [PMID: 30753871 DOI: 10.1016/j.jmb.2019.02.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/14/2018] [Accepted: 02/04/2019] [Indexed: 12/22/2022]
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) is a multifunctional serine/threonine protein kinase that transmits calcium signals in various cellular processes. CaMKII is activated by calcium-bound calmodulin (Ca2+/CaM) through a direct binding mechanism involving a regulatory C-terminal α-helix in CaMKII. The Ca2+/CaM binding triggers transphosphorylation of critical threonine residues proximal to the CaM-binding site leading to the autoactivated state of CaMKII. The demonstration of its critical roles in pathophysiological processes has elevated CaMKII to a key target in the management of numerous diseases. The molecule KN-93 is the most widely used inhibitor for studying the cellular and in vivo functions of CaMKII. It is widely believed that KN-93 binds directly to CaMKII, thus preventing kinase activation by competing with Ca2+/CaM. Herein, we employed surface plasmon resonance, NMR, and isothermal titration calorimetry to characterize this presumed interaction. Our results revealed that KN-93 binds directly to Ca2+/CaM and not to CaMKII. This binding would disrupt the ability of Ca2+/CaM to interact with CaMKII, effectively inhibiting CaMKII activation. Our findings also indicated that KN-93 can specifically compete with a CaMKIIδ-derived peptide for binding to Ca2+/CaM. As indicated by the surface plasmon resonance and isothermal titration calorimetry data, apparently at least two KN-93 molecules can bind to Ca2+/CaM. Our findings provide new insight into how in vitro and in vivo data obtained with KN-93 should be interpreted. They further suggest that other Ca2+/CaM-dependent, non-CaMKII activities should be considered in KN-93-based mechanism-of-action studies and drug discovery efforts.
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13
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Pharris MC, Patel NM, Kinzer-Ursem TL. Competitive Tuning Among Ca 2+/Calmodulin-Dependent Proteins: Analysis of in silico Model Robustness and Parameter Variability. Cell Mol Bioeng 2018; 11:353-365. [PMID: 31105797 DOI: 10.1007/s12195-018-0549-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Introduction Calcium/Calmodulin-dependent (Ca2+/CaM-dependent) regulation of protein signaling has long been recognized for its importance in a number of physiological contexts. Found in almost all eukaryotic cells, Ca2+/CaM-dependent signaling participates in muscle development, immune responses, cardiac myocyte function and regulation of neuronal connectivity. In excitatory neurons, dynamic changes in the strength of synaptic connections, known as synaptic plasticity, occur when calcium ions (Ca2+) flux through NMDA receptors and bind the Ca2+-sensor calmodulin (CaM). Ca2+/CaM, in turn, regulates downstream protein signaling in actin polymerization, receptor trafficking, and transcription factor activation.The activation of downstream Ca2+/CaM-dependent binding proteins (CBPs) is a function of the frequency of Ca2+ flux, such that each CBP is preferentially "tuned" to different Ca2+ input signals. We have recently reported that competition among CBPs for CaM binding is alone sufficient to recreate in silico the observed in vivo frequency-dependence of several CBPs. However, CBP activation may strongly depend on the identity and concentration of proteins that constitute the competitive pool; with important implications in the regulation of CBPs in both normal and disease states. Methods Here, we extend our previous deterministic model of competition among CBPs to include phosphodiesterases, AMPAR receptors that are important in synaptic plasticity, and enzymatic function of CBPs: cAMP regulation, kinase activity, and phosphatase activity. After rigorous parameterization and validation by global sensitivity analysis using Latin Hypercube Sampling (LHS) and Partial Rank Correlation Coefficients (PRCC), we explore how perturbing the competitive pool of CBPs influences downstream signaling events. In particular, we hypothesize that although perturbations may decrease activation of one CBP, increased activation of a separate, but enzymatically-related CBP could compensate for this loss, providing a homeostatic effect. Results and Conclusions First we compare dynamic model output of two models: a two-state model of Ca2+/CaM binding and a four-state model of Ca2+/CaM binding. We find that a four-state model of Ca2+/CaM binding best captures the dynamic nature of the rapid response of CaM and CBPs to Ca2+ flux in the system. Using global sensitivity analysis, we find that model output is robust to parameter variability. Indeed, although variations in the expression of the CaM buffer neurogranin (Ng) may cause a decrease in Ca2+/CaM-dependent kinase II (CaMKII) activation, overall AMPA receptor phosphorylation is preserved; ostensibly by a concomitant increase in adenylyl cyclase 8 (AC8)-mediated activation of protein kinase A (PKA). Indeed phosphorylation of AMPAR receptors by CaMKII and PKA is robust across a wide range of Ng concentrations, though increases in AMPAR phosphorylation is seen at low Ng levels approaching zero. Our results may explain recent counter-intuitive results in neurogranin knockout mice and provide further evidence that competitive tuning is an important mechanism in synaptic plasticity. These results may be readily translated to other Ca2+/CaM-dependent signaling systems in other cell types and can be used to suggest targeted experimental investigation to explain counter-intuitive or unexpected downstream signaling outcomes.Tamara Kinzer-Ursem is an Assistant Professor in the Weldon School of Biomedical Engineering. She received her B.S. in Bioengineering from the University of Toledo and her M.S. and Ph.D. degrees in Chemical Engineering from the University of Michigan, and her post-doctoral training in Molecular Neuroscience at the California Institute of Technology. Prior to joining Purdue she was the Head of R&D in Biochemistry at Maven Biotechnologies and Visiting Associate in Chemical Engineering at the California Institute of Technology.Research in the Kinzer-Ursem lab focuses on developing tools to advance quantitative descriptions of cellular processes and disease within three areas of expertise: 1) Using particle diffusivity measurements to quantify biomolecular processes. Particle diffusometry is being used as a sensitive biosensor to detect the presence of pathogens in environmental and patient samples. 2) Development of novel protein tagging technologies that are used to label proteins in vivo to enable quantitative description of protein function and elucidate disease mechanisms. 3) Computational modeling of signal transduction mechanisms to understand cellular processes. Using computational techniques, we have recently described "competitive tuning" as a mechanism that might be used to regulate information transfer through protein networks, with implications in cell behavior and drug target analysis.
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Affiliation(s)
- Matthew C Pharris
- Weldon School of Biomedical Engineering, Purdue University, 260 South Martin Jischke Drive, West Lafayette, IN 47907 USA
| | - Neal M Patel
- Weldon School of Biomedical Engineering, Purdue University, 260 South Martin Jischke Drive, West Lafayette, IN 47907 USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, 260 South Martin Jischke Drive, West Lafayette, IN 47907 USA
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14
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Abstract
Calmodulin (CaM) regulation of voltage-gated calcium (CaV) channels is a powerful Ca2+ feedback mechanism that adjusts Ca2+ influx, affording rich mechanistic insights into Ca2+ decoding. CaM possesses a dual-lobed architecture, a salient feature of the myriad Ca2+-sensing proteins, where two homologous lobes that recognize similar targets hint at redundant signaling mechanisms. Here, by tethering CaM lobes, we demonstrate that bilobal architecture is obligatory for signaling to CaV channels. With one lobe bound, CaV carboxy tail rearranges itself, resulting in a preinhibited configuration precluded from Ca2+ feedback. Reconstitution of two lobes, even as separate molecules, relieves preinhibition and restores Ca2+ feedback. CaV channels thus detect the coincident binding of two Ca2+-free lobes to promote channel opening, a molecular implementation of a logical NOR operation that processes spatiotemporal Ca2+ signals bifurcated by CaM lobes. Overall, a unified scheme of CaV channel regulation by CaM now emerges, and our findings highlight the versatility of CaM to perform exquisite Ca2+ computations.
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15
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Li X, Holmes WR. Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach. PLoS Comput Biol 2018; 14:e1005946. [PMID: 29401454 PMCID: PMC5814094 DOI: 10.1371/journal.pcbi.1005946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 02/15/2018] [Accepted: 12/19/2017] [Indexed: 12/02/2022] Open
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) holoenzymes play a critical role in decoding Ca2+ signals in neurons. Understanding how this occurs has been the focus of numerous studies including many that use models. However, CaMKII is notoriously difficult to simulate in detail because of its multi-subunit nature, which causes a combinatorial explosion in the number of species that must be modeled. To study the Ca2+-calmodulin-CaMKII reaction network with detailed kinetics while including the effect of diffusion, we have customized an existing stochastic particle-based simulator, Smoldyn, to manage the problem of combinatorial explosion. With this new method, spatial and temporal aspects of the signaling network can be studied without compromising biochemical details. We used this new method to examine how calmodulin molecules, both partially loaded and fully loaded with Ca2+, choose pathways to interact with and activate CaMKII under various Ca2+ input conditions. We found that the dependence of CaMKII phosphorylation on Ca2+ signal frequency is intrinsic to the network kinetics and the activation pattern can be modulated by the relative amount of Ca2+ to calmodulin and by the rate of Ca2+ diffusion. Depending on whether Ca2+ influx is saturating or not, calmodulin molecules could choose different routes within the network to activate CaMKII subunits, resulting in different frequency dependence patterns. In addition, the size of the holoenzyme produces a subtle effect on CaMKII activation. The more extended the subunits are organized, the easier for calmodulin molecules to access and activate the subunits. The findings suggest that particular intracellular environmental factors such as crowding and calmodulin availability can play an important role in decoding Ca2+ signals and can give rise to distinct CaMKII activation patterns in dendritic spines, Ca2+ channel nanodomains and cytoplasm.
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Affiliation(s)
- Ximing Li
- Department of Biological Sciences, Neuroscience Program, Ohio University, Athens, Ohio, United States of America
| | - William R. Holmes
- Department of Biological Sciences, Neuroscience Program, Ohio University, Athens, Ohio, United States of America
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16
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Tavares CDJ, Giles DH, Stancu G, Chitjian CA, Ferguson SB, Wellmann RM, Kaoud TS, Ghose R, Dalby KN. Signal Integration at Elongation Factor 2 Kinase: THE ROLES OF CALCIUM, CALMODULIN, AND SER-500 PHOSPHORYLATION. J Biol Chem 2016; 292:2032-2045. [PMID: 27956550 DOI: 10.1074/jbc.m116.753277] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/28/2016] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K), the only calmodulin (CaM)-dependent member of the unique α-kinase family, impedes protein synthesis by phosphorylating eEF-2. We recently identified Thr-348 and Ser-500 as two key autophosphorylation sites within eEF-2K that regulate its activity. eEF-2K is regulated by Ca2+ ions and multiple upstream signaling pathways, but how it integrates these signals into a coherent output, i.e. phosphorylation of eEF-2, is unclear. This study focuses on understanding how the post-translational phosphorylation of Ser-500 integrates with Ca2+ and CaM to regulate eEF-2K. CaM is shown to be absolutely necessary for efficient activity of eEF-2K, and Ca2+ is shown to enhance the affinity of CaM toward eEF-2K. Ser-500 is found to undergo autophosphorylation in cells treated with ionomycin and is likely also targeted by PKA. In vitro, autophosphorylation of Ser-500 is found to require Ca2+ and CaM and is inhibited by mutations that compromise binding of phosphorylated Thr-348 to an allosteric binding pocket on the kinase domain. A phosphomimetic Ser-500 to aspartic acid mutation (eEF-2K S500D) enhances the rate of activation (Thr-348 autophosphorylation) by 6-fold and lowers the EC50 for Ca2+/CaM binding to activated eEF-2K (Thr-348 phosphorylated) by 20-fold. This is predicted to result in an elevation of the cellular fraction of active eEF-2K. In support of this mechanism, eEF-2K knock-out MCF10A cells reconstituted with eEF-2K S500D display relatively high levels of phospho-eEF-2 under basal conditions. This study reports how phosphorylation of a regulatory site (Ser-500) integrates with Ca2+ and CaM to influence eEF-2K activity.
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Affiliation(s)
- Clint D J Tavares
- From the Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas 78712; Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712.
| | - David H Giles
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712
| | - Gabriel Stancu
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712
| | - Catrina A Chitjian
- From the Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas 78712; Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712
| | - Scarlett B Ferguson
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712
| | - Rebecca M Wellmann
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712
| | - Ranajeet Ghose
- the Department of Chemistry, City College of New York, New York, New York 10031; the Graduate Center, City University of New York, New York, New York 10016
| | - Kevin N Dalby
- From the Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas 78712; Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712.
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17
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Stochastic Induction of Long-Term Potentiation and Long-Term Depression. Sci Rep 2016; 6:30899. [PMID: 27485552 PMCID: PMC4971485 DOI: 10.1038/srep30899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/10/2016] [Indexed: 01/23/2023] Open
Abstract
Long-term depression (LTD) and long-term potentiation (LTP) of granule-Purkinje cell synapses are persistent synaptic alterations induced by high and low rises of the intracellular calcium ion concentration ([Ca2+]), respectively. The occurrence of LTD involves the activation of a positive feedback loop formed by protein kinase C, phospholipase A2, and the extracellular signal-regulated protein kinase pathway, and its expression comprises the reduction of the population of synaptic AMPA receptors. Recently, a stochastic computational model of these signalling processes demonstrated that, in single synapses, LTD is probabilistic and bistable. Here, we expanded this model to simulate LTP, which requires protein phosphatases and the increase in the population of synaptic AMPA receptors. Our results indicated that, in single synapses, while LTD is bistable, LTP is gradual. Ca2+ induced both processes stochastically. The magnitudes of the Ca2+ signals and the states of the signalling network regulated the likelihood of LTP and LTD and defined dynamic macroscopic Ca2+ thresholds for the synaptic modifications in populations of synapses according to an inverse Bienenstock, Cooper and Munro (BCM) rule or a sigmoidal function. In conclusion, our model presents a unifying mechanism that explains the macroscopic properties of LTP and LTD from their dynamics in single synapses.
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18
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Tavares CDJ, Devkota AK, Dalby KN, Cho EJ. Application of Eukaryotic Elongation Factor-2 Kinase (eEF-2K) for Cancer Therapy: Expression, Purification, and High-Throughput Inhibitor Screening. Methods Mol Biol 2016; 1360:19-33. [PMID: 26501899 DOI: 10.1007/978-1-4939-3073-9_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein kinases have emerged as an important class of therapeutic targets, as they are known to be involved in pathological pathways linked to numerous human disorders. Major efforts to discover kinase inhibitors in both academia and pharmaceutical companies have centered on the development of robust assays and cost-effective approaches to isolate them. Drug discovery procedures often start with hit identification for lead development, by screening a library of chemicals using an appropriate assay in a high-throughput manner. Considering limitations unique to each assay technique and screening capability, intelligent integration of various assay schemes and level of throughput, in addition to the choice of chemical libraries, is the key to success of this initial step. Here, we describe the purification of the protein kinase, eEF-2K, and the utilization of three biochemical assays in the course of identifying small molecules that block its enzymatic reaction.
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Affiliation(s)
- Clint D J Tavares
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ashwini K Devkota
- Texas Screening Alliance for Cancer Therapeutics, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Kevin N Dalby
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA.
- Texas Screening Alliance for Cancer Therapeutics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Eun Jeong Cho
- Texas Screening Alliance for Cancer Therapeutics, The University of Texas at Austin, Austin, TX, 78712, USA.
- College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA.
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19
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Abstract
Calcium plays a role in long-term plasticity by triggering postsynaptic signaling pathways for both the strengthening (LTP) and weakening (LTD) of synapses. Since these are opposing processes, several hypotheses have been developed to explain how calcium can trigger LTP in some situations and LTD in others. These hypotheses fall broadly into three categories, based on the amplitude of calcium concentration, the duration of the calcium elevation, and the location of the calcium influx. Here we review the experimental evidence for and against each of these hypotheses and the recent computational models utilizing each. We argue that with new experimental techniques for the precise visualization of calcium and new computational techniques for the modeling of calcium diffusion, it is time to take a new look at the location hypothesis.
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Affiliation(s)
- R C Evans
- George Mason University, The Krasnow Institute for Advanced Studies, MS 2A1, Fairfax, Virginia 22030-444
| | - K T Blackwell
- George Mason University, The Krasnow Institute for Advanced Studies, MS 2A1, Fairfax, Virginia 22030-444
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20
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Tripathi S, Wang Q, Zhang P, Hoffman L, Waxham MN, Cheung MS. Conformational frustration in calmodulin-target recognition. J Mol Recognit 2015; 28:74-86. [PMID: 25622562 DOI: 10.1002/jmr.2413] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022]
Abstract
Calmodulin (CaM) is a primary calcium (Ca(2+) )-signaling protein that specifically recognizes and activates highly diverse target proteins. We explored the molecular basis of target recognition of CaM with peptides representing the CaM-binding domains from two Ca(2+) -CaM-dependent kinases, CaMKI and CaMKII, by employing experimentally constrained molecular simulations. Detailed binding route analysis revealed that the two CaM target peptides, although similar in length and net charge, follow distinct routes that lead to a higher binding frustration in the CaM-CaMKII complex than in the CaM-CaMKI complex. We discovered that the molecular origin of the binding frustration is caused by intermolecular contacts formed with the C-domain of CaM that need to be broken before the formation of intermolecular contacts with the N-domain of CaM. We argue that the binding frustration is important for determining the kinetics of the recognition process of proteins involving large structural fluctuations.
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Affiliation(s)
- Swarnendu Tripathi
- Department of Physics, University of Houston, Houston, TX, 77204, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
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21
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Tavares CDJ, Ferguson SB, Giles DH, Wang Q, Wellmann RM, O'Brien JP, Warthaka M, Brodbelt JS, Ren P, Dalby KN. The molecular mechanism of eukaryotic elongation factor 2 kinase activation. J Biol Chem 2014; 289:23901-16. [PMID: 25012662 DOI: 10.1074/jbc.m114.577148] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Calmodulin (CaM)-dependent eukaryotic elongation factor 2 kinase (eEF-2K) impedes protein synthesis through phosphorylation of eukaryotic elongation factor 2 (eEF-2). It is subject to complex regulation by multiple upstream signaling pathways, through poorly described mechanisms. Precise integration of these signals is critical for eEF-2K to appropriately regulate protein translation rates. Here, an allosteric mechanism comprising two sequential conformations is described for eEF-2K activation. First, Ca(2+)/CaM binds eEF-2K with high affinity (Kd(CaM)(app) = 24 ± 5 nm) to enhance its ability to autophosphorylate Thr-348 in the regulatory loop (R-loop) by > 10(4)-fold (k(auto) = 2.6 ± 0.3 s(-1)). Subsequent binding of phospho-Thr-348 to a conserved basic pocket in the kinase domain potentially drives a conformational transition of the R-loop, which is essential for efficient substrate phosphorylation. Ca(2+)/CaM binding activates autophosphorylated eEF-2K by allosterically enhancing k(cat)(app) for peptide substrate phosphorylation by 10(3)-fold. Thr-348 autophosphorylation results in a 25-fold increase in the specificity constant (k(cat)(app)/K(m)(Pep-S) (app)), with equal contributions from k(cat)(app) and K(m)(Pep-S)(app), suggesting that peptide substrate binding is partly impeded in the unphosphorylated enzyme. In cells, Thr-348 autophosphorylation appears to control the catalytic output of active eEF-2K, contributing more than 5-fold to its ability to promote eEF-2 phosphorylation. Fundamentally, eEF-2K activation appears to be analogous to an amplifier, where output volume may be controlled by either toggling the power switch (switching on the kinase) or altering the volume control (modulating stability of the active R-loop conformation). Because upstream signaling events have the potential to modulate either allosteric step, this mechanism allows for exquisite control of eEF-2K output.
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Affiliation(s)
- Clint D J Tavares
- From the Graduate Program in Cell and Molecular Biology, the Division of Medicinal Chemistry, College of Pharmacy,
| | | | - David H Giles
- the Division of Medicinal Chemistry, College of Pharmacy
| | - Qiantao Wang
- the Division of Medicinal Chemistry, College of Pharmacy, the Department of Biomedical Engineering, Cockrell School of Engineering, and
| | | | - John P O'Brien
- the Department of Chemistry and Biochemistry, College of Natural Sciences, University of Texas, Austin, Texas 78712
| | | | - Jennifer S Brodbelt
- the Department of Chemistry and Biochemistry, College of Natural Sciences, University of Texas, Austin, Texas 78712
| | - Pengyu Ren
- the Department of Biomedical Engineering, Cockrell School of Engineering, and
| | - Kevin N Dalby
- From the Graduate Program in Cell and Molecular Biology, the Division of Medicinal Chemistry, College of Pharmacy,
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22
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Jin SX, Bartolome C, Arai JA, Hoffman L, Uzturk BG, Kumar-Singh R, Waxham MN, Feig LA. Domain contributions to signaling specificity differences between Ras-guanine nucleotide releasing factor (Ras-GRF) 1 and Ras-GRF2. J Biol Chem 2014; 289:16551-64. [PMID: 24755227 DOI: 10.1074/jbc.m114.557959] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ras-GRF1 (GRF1) and Ras-GRF2 (GRF2) constitute a family of similar calcium sensors that regulate synaptic plasticity. They are both guanine exchange factors that contain a very similar set of functional domains, including N-terminal pleckstrin homology, coiled-coil, and calmodulin-binding IQ domains and C-terminal Dbl homology Rac-activating domains, Ras-exchange motifs, and CDC25 Ras-activating domains. Nevertheless, they regulate different forms of synaptic plasticity. Although both GRF proteins transduce calcium signals emanating from NMDA-type glutamate receptors in the CA1 region of the hippocampus, GRF1 promotes LTD, whereas GRF2 promotes θ-burst stimulation-induced LTP (TBS-LTP). GRF1 can also mediate high frequency stimulation-induced LTP (HFS-LTP) in mice over 2-months of age, which involves calcium-permeable AMPA-type glutamate receptors. To add to our understanding of how proteins with similar domains can have different functions, WT and various chimeras between GRF1 and GRF2 proteins were tested for their abilities to reconstitute defective LTP and/or LTD in the CA1 hippocampus of Grf1/Grf2 double knock-out mice. These studies revealed a critical role for the GRF2 CDC25 domain in the induction of TBS-LTP by GRF proteins. In contrast, the N-terminal pleckstrin homology and/or coiled-coil domains of GRF1 are key to the induction of HFS-LTP by GRF proteins. Finally, the IQ motif of GRF1 determines whether a GRF protein can induce LTD. Overall, these findings show that for the three forms of synaptic plasticity that are regulated by GRF proteins in the CA1 hippocampus, specificity is encoded in only one or two domains, and a different set of domains for each form of synaptic plasticity.
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Affiliation(s)
- Shan-Xue Jin
- From the Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111 and
| | - Christopher Bartolome
- From the Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111 and
| | - Junko A Arai
- From the Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111 and
| | - Laurel Hoffman
- the Department of Neurobiology and Anatomy, University of Texas, Houston, Texas
| | - B Gizem Uzturk
- From the Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111 and
| | - Rajendra Kumar-Singh
- From the Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111 and
| | - M Neal Waxham
- the Department of Neurobiology and Anatomy, University of Texas, Houston, Texas
| | - Larry A Feig
- From the Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111 and
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23
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Michalski PJ. The delicate bistability of CaMKII. Biophys J 2014; 105:794-806. [PMID: 23931327 DOI: 10.1016/j.bpj.2013.06.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/13/2013] [Accepted: 06/25/2013] [Indexed: 01/08/2023] Open
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) is a synaptic, autophosphorylating kinase that is essential for learning and memory. Previous models have suggested that CaMKII functions as a bistable switch that could be the molecular correlate of long-term memory, but experiments have failed to validate these predictions. These models involved significant approximations to overcome the combinatorial complexity inherent in a multisubunit, multistate system. Here, we develop a stochastic particle-based model of CaMKII activation and dynamics that overcomes combinatorial complexity without significant approximations. We report four major findings. First, the CaMKII model system is never bistable at resting calcium concentrations, which suggests that CaMKII activity does not function as the biochemical switch underlying long-term memory. Second, the steady-state activation curves are either laserlike or steplike. Both are characterized by a well-defined threshold for activation, which suggests that thresholding is a robust feature of this system. Third, transiently activated CaMKII can maintain its activity over the time course of many experiments, and such slow deactivation may account for the few reports of bistability in the literature. And fourth, under in vivo conditions, increases in phosphatase activity can increase CaMKII activity. This is a surprising and counterintuitive effect, as dephosphorylation is generally associated with CaMKII deactivation.
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Affiliation(s)
- P J Michalski
- Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut, USA.
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24
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Evans RC, Maniar YM, Blackwell KT. Dynamic modulation of spike timing-dependent calcium influx during corticostriatal upstates. J Neurophysiol 2013; 110:1631-45. [PMID: 23843436 DOI: 10.1152/jn.00232.2013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The striatum of the basal ganglia demonstrates distinctive upstate and downstate membrane potential oscillations during slow-wave sleep and under anesthetic. The upstates generate calcium transients in the dendrites, and the amplitude of these calcium transients depends strongly on the timing of the action potential (AP) within the upstate. Calcium is essential for synaptic plasticity in the striatum, and these large calcium transients during the upstates may control which synapses undergo plastic changes. To investigate the mechanisms that underlie the relationship between calcium and AP timing, we have developed a realistic biophysical model of a medium spiny neuron (MSN). We have implemented sophisticated calcium dynamics including calcium diffusion, buffering, and pump extrusion, which accurately replicate published data. Using this model, we found that either the slow inactivation of dendritic sodium channels (NaSI) or the calcium inactivation of voltage-gated calcium channels (CDI) can cause high calcium corresponding to early APs and lower calcium corresponding to later APs. We found that only CDI can account for the experimental observation that sensitivity to AP timing is dependent on NMDA receptors. Additional simulations demonstrated a mechanism by which MSNs can dynamically modulate their sensitivity to AP timing and show that sensitivity to specifically timed pre- and postsynaptic pairings (as in spike timing-dependent plasticity protocols) is altered by the timing of the pairing within the upstate. These findings have implications for synaptic plasticity in vivo during sleep when the upstate-downstate pattern is prominent in the striatum.
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Affiliation(s)
- R C Evans
- The Krasnow Institute for Advanced Studies, George Mason University, Fairfax, Virginia; and
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25
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Masada N, Schaks S, Jackson SE, Sinz A, Cooper DMF. Distinct mechanisms of calmodulin binding and regulation of adenylyl cyclases 1 and 8. Biochemistry 2012; 51:7917-29. [PMID: 22971080 PMCID: PMC3466776 DOI: 10.1021/bi300646y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Calmodulin (CaM), by mediating the stimulation of the activity of two adenylyl cyclases (ACs), plays a key role in integrating the cAMP and Ca(2+) signaling systems. These ACs, AC1 and AC8, by decoding discrete Ca(2+) signals can contribute to fine-tuning intracellular cAMP dynamics, particularly in neurons where they predominate. CaM comprises an α-helical linker separating two globular regions at the N-terminus and the C-terminus that each bind two Ca(2+) ions. These two lobes have differing affinities for Ca(2+), and they can interact with target proteins independently. This study explores previous indications that the two lobes of CaM can regulate AC1 and AC8 differently and thereby yield different responses to cellular transitions in [Ca(2+)](i). We first compared by glutathione S-transferase pull-down assays and offline nanoelectrospray ionization mass spectrometry the interaction of CaM and Ca(2+)-binding deficient mutants of CaM with the internal CaM binding domain (CaMBD) of AC1 and the two terminal CaMBDs of AC8. We then examined the influence of these three CaMBDs on Ca(2+) binding by native and mutated CaM in stopped-flow experiments to quantify their interactions. The three CaMBDs show quite distinct interactions with the two lobes of CaM. These findings establish the critical kinetic differences between the mechanisms of Ca(2+)-CaM activation of AC1 and AC8, which may underpin their different physiological roles.
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Affiliation(s)
- Nanako Masada
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
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26
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Michalski PJ, Loew LM. CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation. Phys Biol 2012; 9:036010. [PMID: 22683827 DOI: 10.1088/1478-3975/9/3/036010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The combinatorial explosion produced by the multi-state, multi-subunit character of CaMKII has made analysis and modeling of this key signaling protein a significant challenge. Using rule-based and particle-based approaches, we construct exact models of CaMKII holoenzyme dynamics and study these models as a function of the number of subunits per holoenzyme, N. Without phosphatases the dynamics of activation are independent of the holoenzyme structure unless phosphorylation significantly alters the kinase activity of a subunit. With phosphatases the model is independent of holoenzyme size for N > 6. We introduce an infinite subunit holoenzyme approximation (ISHA), which simplifies the modeling by eliminating the combinatorial complexities encountered in any finite holoenzyme model. The ISHA is an excellent approximation to the full system over a broad range of physiologically relevant parameters. Finally, we demonstrate that the ISHA reproduces the behavior of exact models during synaptic plasticity protocols, which justifies its use as a module in large models of synaptic plasticity.
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Affiliation(s)
- P J Michalski
- Richard D Berlin Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030, USA.
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27
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Jalan-Sakrikar N, Bartlett RK, Baucum AJ, Colbran RJ. Substrate-selective and calcium-independent activation of CaMKII by α-actinin. J Biol Chem 2012; 287:15275-83. [PMID: 22427672 PMCID: PMC3346149 DOI: 10.1074/jbc.m112.351817] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/14/2012] [Indexed: 11/06/2022] Open
Abstract
Protein-protein interactions are thought to modulate the efficiency and specificity of Ca(2+)/calmodulin (CaM)-dependent protein kinase II (CaMKII) signaling in specific subcellular compartments. Here we show that the F-actin-binding protein α-actinin targets CaMKIIα to F-actin in cells by binding to the CaMKII regulatory domain, mimicking CaM. The interaction with α-actinin is blocked by CaMKII autophosphorylation at Thr-306, but not by autophosphorylation at Thr-305, whereas autophosphorylation at either site blocks Ca(2+)/CaM binding. The binding of α-actinin to CaMKII is Ca(2+)-independent and activates the phosphorylation of a subset of substrates in vitro. In intact cells, α-actinin selectively stabilizes CaMKII association with GluN2B-containing glutamate receptors and enhances phosphorylation of Ser-1303 in GluN2B, but inhibits CaMKII phosphorylation of Ser-831 in glutamate receptor GluA1 subunits by competing for activation by Ca(2+)/CaM. These data show that Ca(2+)-independent binding of α-actinin to CaMKII differentially modulates the phosphorylation of physiological targets that play key roles in long-term synaptic plasticity.
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Affiliation(s)
| | | | | | - Roger J. Colbran
- From the Department of Molecular Physiology and Biophysics
- Vanderbilt Brain Institute, and
- Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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28
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The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics. PLoS Comput Biol 2011; 7:e1002114. [PMID: 21829336 PMCID: PMC3145654 DOI: 10.1371/journal.pcbi.1002114] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/23/2011] [Indexed: 11/20/2022] Open
Abstract
The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells. Proteins are workhorses for driving biological functions inside cells. Calmodulin (CaM) is a protein that can carry cellular signals by triggered conformational changes due to calcium binding that alters target binding. Interestingly, CaM is able to bind over 300 targets. One of the challenges in characterizing CaM's ability to bind multiple targets lies in that CaM is a flexible protein and its structure is easily modulated by the physicochemical changes in its surroundings, particularly inside a complex cellular milieu. In order to determine structure-function relationships of CaM, we employed a combined approach of experiments, computer simulations and statistical physics in the investigation of the effect of calcium-binding, salt concentration, and macromolecular crowding on CaM. The results revealed unique folding energy landscapes of CaM in the absence and presence of calcium ions and the structural implications of CaM are interpreted under cell-like conditions. Further, a large conformational change in CaM in response to environmental impacts, dictates the packing of local helices that may be critical to its function of target binding and recognition among vast target selections.
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29
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Evans TIA, Hell JW, Shea MA. Thermodynamic linkage between calmodulin domains binding calcium and contiguous sites in the C-terminal tail of Ca(V)1.2. Biophys Chem 2011; 159:172-87. [PMID: 21757287 DOI: 10.1016/j.bpc.2011.06.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 06/15/2011] [Accepted: 06/15/2011] [Indexed: 11/30/2022]
Abstract
Calmodulin (CaM) binding to the intracellular C-terminal tail (CTT) of the cardiac L-type Ca(2+) channel (Ca(V)1.2) regulates Ca(2+) entry by recognizing sites that contribute to negative feedback mechanisms for channel closing. CaM associates with Ca(V)1.2 under low resting [Ca(2+)], but is poised to change conformation and position when intracellular [Ca(2+)] rises. CaM binding Ca(2+), and the domains of CaM binding the CTT are linked thermodynamic functions. To better understand regulation, we determined the energetics of CaM domains binding to peptides representing pre-IQ sites A(1588), and C(1614) and the IQ motif studied as overlapping peptides IQ(1644) and IQ'(1650) as well as their effect on calcium binding. (Ca(2+))(4)-CaM bound to all four peptides very favorably (K(d)≤2 nM). Linkage analysis showed that IQ(1644-1670) bound with a K(d)~1 pM. In the pre-IQ region, (Ca(2+))(2)-N-domain bound preferentially to A(1588), while (Ca(2+))(2)-C-domain preferred C(1614). When bound to C(1614), calcium binding in the N-domain affected the tertiary conformation of the C-domain. Based on the thermodynamics, we propose a structural mechanism for calcium-dependent conformational change in which the linker between CTT sites A and C buckles to form an A-C hairpin that is bridged by calcium-saturated CaM.
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Affiliation(s)
- T Idil Apak Evans
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, United States.
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30
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Abramczyk O, Tavares CDJ, Devkota AK, Ryazanov AG, Turk BE, Riggs AF, Ozpolat B, Dalby KN. Purification and characterization of tagless recombinant human elongation factor 2 kinase (eEF-2K) expressed in Escherichia coli. Protein Expr Purif 2011; 79:237-44. [PMID: 21605678 DOI: 10.1016/j.pep.2011.05.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 01/28/2023]
Abstract
The eukaryotic elongation factor 2 kinase (eEF-2K) modulates the rate of protein synthesis by impeding the elongation phase of translation by inactivating the eukaryotic elongation factor 2 (eEF-2) via phosphorylation. eEF-2K is known to be activated by calcium and calmodulin, whereas the mTOR and MAPK pathways are suggested to negatively regulate kinase activity. Despite its pivotal role in translation regulation and potential role in tumor survival, the structure, function, and regulation of eEF-2K have not been described in detail. This deficiency may result from the difficulty of obtaining the recombinant kinase in a form suitable for biochemical analysis. Here we report the purification and characterization of recombinant human eEF-2K expressed in the Escherichia coli strain Rosetta-gami 2(DE3). Successive chromatography steps utilizing Ni-NTA affinity, anion-exchange, and gel filtration columns accomplished purification. Cleavage of the thioredoxin-His(6)-tag from the N-terminus of the expressed kinase with TEV protease yielded 9 mg of recombinant (G-D-I)-eEF-2K per liter of culture. Light scattering shows that eEF-2K is a monomer of ∼85 kDa. In vitro kinetic analysis confirmed that recombinant human eEF-2K is able to phosphorylate wheat germ eEF-2 with kinetic parameters comparable to the mammalian enzyme.
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Affiliation(s)
- Olga Abramczyk
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
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31
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Cheriyan J, Kumar P, Mayadevi M, Surolia A, Omkumar RV. Calcium/calmodulin dependent protein kinase II bound to NMDA receptor 2B subunit exhibits increased ATP affinity and attenuated dephosphorylation. PLoS One 2011; 6:e16495. [PMID: 21423658 PMCID: PMC3057968 DOI: 10.1371/journal.pone.0016495] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 12/18/2010] [Indexed: 11/18/2022] Open
Abstract
Calcium/calmodulin dependent protein kinase II (CaMKII) is implicated to play a key role in learning and memory. NR2B subunit of N-methyl-D-aspartate receptor (NMDAR) is a high affinity binding partner of CaMKII at the postsynaptic membrane. NR2B binds to the T-site of CaMKII and modulates its catalysis. By direct measurement using isothermal titration calorimetry (ITC), we show that NR2B binding causes about 11 fold increase in the affinity of CaMKII for ATPγS, an analogue of ATP. ITC data is also consistent with an ordered binding mechanism for CaMKII with ATP binding the catalytic site first followed by peptide substrate. We also show that dephosphorylation of phospho-Thr(286)-α-CaMKII is attenuated when NR2B is bound to CaMKII. This favors the persistence of Thr(286) autophosphorylated state of CaMKII in a CaMKII/phosphatase conjugate system in vitro. Overall our data indicate that the NR2B- bound state of CaMKII attains unique biochemical properties which could help in the efficient functioning of the proposed molecular switch supporting synaptic memory.
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Affiliation(s)
- John Cheriyan
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Parimal Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Madhavan Mayadevi
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
- National Institute of Immunology, New Delhi, India
| | - Ramakrishnapillai V. Omkumar
- Molecular Neurobiology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
- * E-mail:
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32
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Jama AM, Gabriel J, Al-Nagar AJ, Martin S, Baig SZ, Soleymani H, Chowdhury Z, Beesley P, Török K. Lobe-specific functions of Ca2+·calmodulin in alphaCa2+·calmodulin-dependent protein kinase II activation. J Biol Chem 2011; 286:12308-16. [PMID: 21300804 PMCID: PMC3069434 DOI: 10.1074/jbc.m110.157057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
N-Methyl-d-aspartic acid receptor-dependent long term potentiation (LTP), a model of memory formation, requires Ca2+·calmodulin-dependent protein kinase II (αCaMKII) activity and Thr286 autophosphorylation via both global and local Ca2+ signaling, but the mechanisms of signal transduction are not understood. We tested the hypothesis that the Ca2+-binding activator protein calmodulin (CaM) is the primary decoder of Ca2+ signals, thereby determining the output, e.g. LTP. Thus, we investigated the function of CaM mutants, deficient in Ca2+ binding at sites 1 and 2 of the N-terminal lobe or sites 3 and 4 of the C-terminal CaM lobe, in the activation of αCaMKII. Occupancy of CaM Ca2+ binding sites 1, 3, and 4 is necessary and sufficient for full activation. Moreover, the N- and C-terminal CaM lobes have distinct functions. Ca2+ binding to N lobe Ca2+ binding site 1 increases the turnover rate of the enzyme 5-fold, whereas the C lobe plays a dual role; it is required for full activity, but in addition, via Ca2+ binding site 3, it stabilizes ATP binding to αCaMKII 4-fold. Thr286 autophosphorylation is also dependent on Ca2+ binding sites on both the N and the C lobes of CaM. As the CaM C lobe sites are populated by low amplitude/low frequency (global) Ca2+ signals, but occupancy of N lobe site 1 and thus activation of αCaMKII requires high amplitude/high frequency (local) Ca2+ signals, lobe-specific sensing of Ca2+-signaling patterns by CaM is proposed to explain the requirement for both global and local Ca2+ signaling in the induction of LTP via αCaMKII.
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Affiliation(s)
- Abdirahman M Jama
- Division of Basic Medical Sciences, St. George's, University of London, Cranmer Terrace, London SW17 0RE, UK
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33
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Lobe specific Ca2+-calmodulin nano-domain in neuronal spines: a single molecule level analysis. PLoS Comput Biol 2010; 6:e1000987. [PMID: 21085618 PMCID: PMC2978734 DOI: 10.1371/journal.pcbi.1000987] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Accepted: 10/04/2010] [Indexed: 01/07/2023] Open
Abstract
Calmodulin (CaM) is a ubiquitous Ca2+ buffer and second messenger that affects cellular function as diverse as cardiac excitability, synaptic plasticity, and gene transcription. In CA1 pyramidal neurons, CaM regulates two opposing Ca2+-dependent processes that underlie memory formation: long-term potentiation (LTP) and long-term depression (LTD). Induction of LTP and LTD require activation of Ca2+-CaM-dependent enzymes: Ca2+/CaM-dependent kinase II (CaMKII) and calcineurin, respectively. Yet, it remains unclear as to how Ca2+ and CaM produce these two opposing effects, LTP and LTD. CaM binds 4 Ca2+ ions: two in its N-terminal lobe and two in its C-terminal lobe. Experimental studies have shown that the N- and C-terminal lobes of CaM have different binding kinetics toward Ca2+ and its downstream targets. This may suggest that each lobe of CaM differentially responds to Ca2+ signal patterns. Here, we use a novel event-driven particle-based Monte Carlo simulation and statistical point pattern analysis to explore the spatial and temporal dynamics of lobe-specific Ca2+-CaM interaction at the single molecule level. We show that the N-lobe of CaM, but not the C-lobe, exhibits a nano-scale domain of activation that is highly sensitive to the location of Ca2+ channels, and to the microscopic injection rate of Ca2+ ions. We also demonstrate that Ca2+ saturation takes place via two different pathways depending on the Ca2+ injection rate, one dominated by the N-terminal lobe, and the other one by the C-terminal lobe. Taken together, these results suggest that the two lobes of CaM function as distinct Ca2+ sensors that can differentially transduce Ca2+ influx to downstream targets. We discuss a possible role of the N-terminal lobe-specific Ca2+-CaM nano-domain in CaMKII activation required for the induction of synaptic plasticity. Calmodulin is a versatile Ca2+ signal mediator and a buffer in a wide variety of body organs including the heart and brain. In the brain, calmodulin regulates intracellular molecular processes that change the strength of connectivity between neurons, thus contributing to various brain functions including memory formation. The exact molecular mechanism as to how calmodulin regulates these processes is not yet known. Interestingly, in other excitable tissues, including the heart, each of two lobes of calmodulin responds differentially toward Ca2+ influx and toward its target molecules (e.g., ion channels). This way, calmodulin precisely controls the Ca2+ dynamics of the cell. We wish to test if a similar mechanism may be operational in neurons so that two lobes of calmodulin interact differentially with Ca2+ ions to activate different downstream molecules that control the strength of connections between neurons. We constructed a detailed simulation of calmodulin that allows us to keep track of its interactions with Ca2+ ions and target proteins at the single molecule level. The simulation predicts that two lobes of calmodulin respond differentially to Ca2+ influx both in space and in time. This work opens a door to future experimental testing of the lobe-specific control of neural function by calmodulin.
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34
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Pang ZP, Xu W, Cao P, Südhof TC. Calmodulin suppresses synaptotagmin-2 transcription in cortical neurons. J Biol Chem 2010; 285:33930-9. [PMID: 20729199 DOI: 10.1074/jbc.m110.150151] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Calmodulin (CaM) is a ubiquitous Ca(2+) sensor protein that plays a pivotal role in regulating innumerable neuronal functions, including synaptic transmission. In cortical neurons, most neurotransmitter release is triggered by Ca(2+) binding to synaptotagmin-1; however, a second delayed phase of release, referred to as asynchronous release, is triggered by Ca(2+) binding to an unidentified secondary Ca(2+) sensor. To test whether CaM could be the enigmatic Ca(2+) sensor for asynchronous release, we now use in cultured neurons short hairpin RNAs that suppress expression of ∼70% of all neuronal CaM isoforms. Surprisingly, we found that in synaptotagmin-1 knock-out neurons, the CaM knockdown caused a paradoxical rescue of synchronous release, instead of a block of asynchronous release. Gene and protein expression studies revealed that both in wild-type and in synaptotagmin-1 knock-out neurons, the CaM knockdown altered expression of >200 genes, including that encoding synaptotagmin-2. Synaptotagmin-2 expression was increased several-fold by the CaM knockdown, which accounted for the paradoxical rescue of synchronous release in synaptotagmin-1 knock-out neurons by the CaM knockdown. Interestingly, the CaM knockdown primarily activated genes that are preferentially expressed in caudal brain regions, whereas it repressed genes in rostral brain regions. Consistent with this correlation, quantifications of protein levels in adult mice uncovered an inverse relationship of CaM and synaptotagmin-2 levels in mouse forebrain, brain stem, and spinal cord. Finally, we employed molecular replacement experiments using a knockdown rescue approach to show that Ca(2+) binding to the C-lobe but not the N-lobe of CaM is required for suppression of synaptotagmin-2 expression in cortical neurons. Our data describe a previously unknown, Ca(2+)/CaM-dependent regulatory pathway that controls the expression of synaptic proteins in the rostral-caudal neuraxis.
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Affiliation(s)
- Zhiping P Pang
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, California 94304-5543, USA
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35
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Rellos P, Pike ACW, Niesen FH, Salah E, Lee WH, von Delft F, Knapp S. Structure of the CaMKIIdelta/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation. PLoS Biol 2010; 8:e1000426. [PMID: 20668654 PMCID: PMC2910593 DOI: 10.1371/journal.pbio.1000426] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 06/08/2010] [Indexed: 11/25/2022] Open
Abstract
Structural and biophysical studies reveal how CaMKII kinases, which are important for cellular learning and memory, are switched on by binding of Ca2+/calmodulin. Long-term potentiation (LTP), a long-lasting enhancement in communication between neurons, is considered to be the major cellular mechanism underlying learning and memory. LTP triggers high-frequency calcium pulses that result in the activation of Calcium/Calmodulin (CaM)-dependent kinase II (CaMKII). CaMKII acts as a molecular switch because it remains active for a long time after the return to basal calcium levels, which is a unique property required for CaMKII function. Here we describe the crystal structure of the human CaMKIIδ/Ca2+/CaM complex, structures of all four human CaMKII catalytic domains in their autoinhibited states, as well as structures of human CaMKII oligomerization domains in their tetradecameric and physiological dodecameric states. All four autoinhibited human CaMKIIs were monomeric in the determined crystal structures but associated weakly in solution. In the CaMKIIδ/Ca2+/CaM complex, the inhibitory region adopted an extended conformation and interacted with an adjacent catalytic domain positioning T287 into the active site of the interacting protomer. Comparisons with autoinhibited CaMKII structures showed that binding of calmodulin leads to the rearrangement of residues in the active site to a conformation suitable for ATP binding and to the closure of the binding groove for the autoinhibitory helix by helix αD. The structural data, together with biophysical interaction studies, reveals the mechanism of CaMKII activation by calmodulin and explains many of the unique regulatory properties of these two essential signaling molecules. Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3-D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the Web plugin are available in Text S1. CaMKII enzymes transmit calcium ion (Ca2+) signals released inside the cell by regulating signal transduction pathways through phosphorylation: Ca2+ first binds to the small regulatory protein CaM; this Ca2+/CaM complex then binds to and activates the kinase, which phosphorylates other proteins in the cell. Since CaMKs remain active long after rapid Ca2+ pulses have dropped they function as molecular switches that turn on or off crucial cell functions in response to Ca2+ levels. The multifunctional CaMKII forms of this enzyme – of which there are four in human – are important in many processes including signaling in neurons and controlling of the heart rate. They are particularly abundant in the brain where they probably play a role in memory. CaMKII forms an exceptionally large, dodecameric complex. Here, we describe the crystal structure of this complex for each of the four human CaMKII catalytic domains in their autoinhibited states, a complex of CaMKII with Ca2+/CaM, as well as the structure of the oligomerization domain (the part of the protein that mediates complex formation) in its physiological dodecameric state and in a tetradecameric state. Detailed comparison of this large body of structural data together with biophysical studies has allowed us to better understand the structural mechanisms of CaMKII activation by CaM and to explain many of the complex regulatory features of these essential enzymes.
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Affiliation(s)
- Peter Rellos
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Ashley C. W. Pike
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Frank H. Niesen
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Eidarus Salah
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Wen Hwa Lee
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Frank von Delft
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
| | - Stefan Knapp
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford, United Kingdom
- * E-mail:
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Byrne MJ, Putkey JA, Waxham MN, Kubota Y. Dissecting cooperative calmodulin binding to CaM kinase II: a detailed stochastic model. J Comput Neurosci 2009; 27:621-38. [PMID: 19609660 DOI: 10.1007/s10827-009-0173-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 05/28/2009] [Accepted: 07/01/2009] [Indexed: 12/11/2022]
Abstract
Calmodulin (CaM) is a major Ca(2+) binding protein involved in two opposing processes of synaptic plasticity of CA1 pyramidal neurons: long-term potentiation (LTP) and depression (LTD). The N- and C-terminal lobes of CaM bind to its target separately but cooperatively and introduce complex dynamics that cannot be well understood by experimental measurement. Using a detailed stochastic model constructed upon experimental data, we have studied the interaction between CaM and Ca(2+)-CaM-dependent protein kinase II (CaMKII), a key enzyme underlying LTP. The model suggests that the accelerated binding of one lobe of CaM to CaMKII, when the opposing lobe is already bound to CaMKII, is a critical determinant of the cooperative interaction between Ca(2+), CaM, and CaMKII. The model indicates that the target-bound Ca(2+) free N-lobe has an extended lifetime and may regulate the Ca(2+) response of CaMKII during LTP induction. The model also reveals multiple kinetic pathways which have not been previously predicted for CaM-dissociation from CaMKII.
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Affiliation(s)
- Michael J Byrne
- Department of Neurobiology and Anatomy, University of Texas Medical School, Houston, TX 77030, USA
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Evans TIA, Shea MA. Energetics of calmodulin domain interactions with the calmodulin binding domain of CaMKII. Proteins 2009; 76:47-61. [PMID: 19089983 DOI: 10.1002/prot.22317] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Calmodulin (CaM) is an essential eukaryotic calcium receptor that regulates many kinases, including CaMKII. Calcium-depleted CaM does not bind to CaMKII under physiological conditions. However, binding of (Ca(2+))(4)-CaM to a basic amphipathic helix in CaMKII releases auto-inhibition of the kinase. The crystal structure of CaM bound to CaMKIIp, a peptide representing the CaM-binding domain (CaMBD) of CaMKII, shows an antiparallel interface: the C-domain of CaM primarily contacts the N-terminal half of the CaMBD. The two domains of calcium-saturated CaM are believed to play distinct roles in releasing auto-inhibition. To investigate the underlying mechanism of activation, calcium-dependent titrations of isolated domains of CaM binding to CaMKIIp were monitored using fluorescence anisotropy. The binding affinity of CaMKIIp for the domains of CaM increased upon saturation with calcium, with the C-domain having a 35-fold greater affinity than the N-domain. Because the interdomain linker of CaM regulates calcium-binding affinity and contribute to conformational change, the role of each CaM domain was explored further by investigating effects of CaMKIIp on site-knockout mutants affecting the calcium-binding sites of a single domain. Investigation of the thermodynamic linkage between saturation of individual calcium-binding sites and CaM-domain binding to CaMKIIp showed that calcium binding to Sites III and IV was sufficient to recapitulate the behavior of (Ca(2+))(4)-CaM. The magnitude of favorable interdomain cooperativity varied depending on which of the four calcium-binding sites were mutated, emphasizing differential regulatory roles for the domains of CaM, despite the high degree of homology among the four EF-hands of CaM.
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Affiliation(s)
- T Idil Apak Evans
- Department of Biochemistry, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242-1109, USA
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