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Lisek M, Tomczak J, Boczek T, Zylinska L. Calcium-Associated Proteins in Neuroregeneration. Biomolecules 2024; 14:183. [PMID: 38397420 PMCID: PMC10887043 DOI: 10.3390/biom14020183] [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: 12/30/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The dysregulation of intracellular calcium levels is a critical factor in neurodegeneration, leading to the aberrant activation of calcium-dependent processes and, ultimately, cell death. Ca2+ signals vary in magnitude, duration, and the type of neuron affected. A moderate Ca2+ concentration can initiate certain cellular repair pathways and promote neuroregeneration. While the peripheral nervous system exhibits an intrinsic regenerative capability, the central nervous system has limited self-repair potential. There is evidence that significant variations exist in evoked calcium responses and axonal regeneration among neurons, and individual differences in regenerative capacity are apparent even within the same type of neurons. Furthermore, some studies have shown that neuronal activity could serve as a potent regulator of this process. The spatio-temporal patterns of calcium dynamics are intricately controlled by a variety of proteins, including channels, ion pumps, enzymes, and various calcium-binding proteins, each of which can exert either positive or negative effects on neural repair, depending on the cellular context. In this concise review, we focus on several calcium-associated proteins such as CaM kinase II, GAP-43, oncomodulin, caldendrin, calneuron, and NCS-1 in order to elaborate on their roles in the intrinsic mechanisms governing neuronal regeneration following traumatic damage processes.
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Affiliation(s)
| | | | | | - Ludmila Zylinska
- Department of Molecular Neurochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (M.L.); (J.T.); (T.B.)
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Mundhenk J, Fusi C, Kreutz MR. Caldendrin and Calneurons-EF-Hand CaM-Like Calcium Sensors With Unique Features and Specialized Neuronal Functions. Front Mol Neurosci 2019; 12:16. [PMID: 30787867 PMCID: PMC6372560 DOI: 10.3389/fnmol.2019.00016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/17/2019] [Indexed: 01/02/2023] Open
Abstract
The calmodulin (CaM)-like Ca2+-sensor proteins caldendrin, calneuron-1 and -2 are members of the neuronal calcium-binding protein (nCaBP)-family, a family that evolved relatively late during vertebrate evolution. All three proteins are abundant in brain but show a strikingly different subcellular localization. Whereas caldendrin is enriched in the postsynaptic density (PSD), calneuron-1 and -2 accumulate at the trans-Golgi-network (TGN). Caldendrin exhibit a unique bipartite structure with a basic and proline-rich N-terminus while calneurons are the only EF-Hand CaM-like transmembrane proteins. These uncommon structural features come along with highly specialized functions of calneurons in Golgi-to-plasma-membrane trafficking and for caldendrin in actin-remodeling in dendritic spine synapses. In this review article, we will provide a synthesis of available data on the structure and biophysical properties of all three proteins. We will then discuss their cellular function with special emphasis on synaptic neurotransmission. Finally, we will summarize the evidence for a role of these proteins in neuropsychiatric disorders.
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Affiliation(s)
- Jennifer Mundhenk
- RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Camilla Fusi
- RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Michael R Kreutz
- RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Leibniz Group "Dendritic Organelles and Synaptic Function", Center for Molecular Neurobiology, ZMNH, Hamburg, Germany
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Woolfrey KM, O'Leary H, Goodell DJ, Robertson HR, Horne EA, Coultrap SJ, Dell'Acqua ML, Bayer KU. CaMKII regulates the depalmitoylation and synaptic removal of the scaffold protein AKAP79/150 to mediate structural long-term depression. J Biol Chem 2017; 293:1551-1567. [PMID: 29196604 DOI: 10.1074/jbc.m117.813808] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/21/2017] [Indexed: 11/06/2022] Open
Abstract
Both long-term potentiation (LTP) and depression (LTD) of excitatory synapse strength require the Ca2+/calmodulin (CaM)-dependent protein kinase II (CaMKII) and its autonomous activity generated by Thr-286 autophosphorylation. Additionally, LTP and LTD are correlated with dendritic spine enlargement and shrinkage that are accompanied by the synaptic accumulation or removal, respectively, of the AMPA-receptor regulatory scaffold protein A-kinase anchoring protein (AKAP) 79/150. We show here that the spine shrinkage associated with LTD indeed requires synaptic AKAP79/150 removal, which in turn requires CaMKII activity. In contrast to normal CaMKII substrates, the substrate sites within the AKAP79/150 N-terminal polybasic membrane-cytoskeletal targeting domain were phosphorylated more efficiently by autonomous compared with Ca2+/CaM-stimulated CaMKII activity. This unusual regulation was mediated by Ca2+/CaM binding to the substrate sites resulting in protection from phosphorylation in the presence of Ca2+/CaM, a mechanism that favors phosphorylation by prolonged, weak LTD stimuli versus brief, strong LTP stimuli. Phosphorylation by CaMKII inhibited AKAP79/150 association with F-actin; it also facilitated AKAP79/150 removal from spines but was not required for it. By contrast, LTD-induced spine removal of AKAP79/150 required its depalmitoylation on two Cys residues within the N-terminal targeting domain. Notably, such LTD-induced depalmitoylation was also blocked by CaMKII inhibition. These results provide a mechanism how CaMKII can indeed mediate not only LTP but also LTD through regulated substrate selection; however, in the case of AKAP79/150, indirect CaMKII effects on palmitoylation are more important than the effects of direct phosphorylation. Additionally, our results provide the first direct evidence for a function of the well-described AKAP79/150 trafficking in regulating LTD-induced spine shrinkage.
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Affiliation(s)
- Kevin M Woolfrey
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Heather O'Leary
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Dayton J Goodell
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Holly R Robertson
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Eric A Horne
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Steven J Coultrap
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Mark L Dell'Acqua
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - K Ulrich Bayer
- From the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
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Seeger C, Talibov VO, Danielson UH. Biophysical analysis of the dynamics of calmodulin interactions with neurogranin and Ca 2+ /calmodulin-dependent kinase II. J Mol Recognit 2017; 30. [PMID: 28449373 PMCID: PMC5518211 DOI: 10.1002/jmr.2621] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/26/2016] [Accepted: 02/06/2017] [Indexed: 01/17/2023]
Abstract
Calmodulin (CaM) functions depend on interactions with CaM‐binding proteins, regulated by
Ca2+. Induced structural changes influence the affinity, kinetics, and specificities of the interactions. The dynamics of CaM interactions with neurogranin (Ng) and the CaM‐binding region of
Ca2+/calmodulin‐dependent kinase II (CaMKII290−309) have been studied using biophysical methods. These proteins have opposite
Ca2+ dependencies for CaM binding. Surface plasmon resonance biosensor analysis confirmed that
Ca2+ and CaM interact very rapidly, and with moderate affinity (
KDSPR=3μM). Calmodulin‐CaMKII290−309 interactions were only detected in the presence of
Ca2+, exhibiting fast kinetics and nanomolar affinity (
KDSPR=7.1nM). The CaM–Ng interaction had higher affinity under
Ca2+‐depleted (
KDSPR=480nM,k1=3.4×105M−1s−1 and k−1 = 1.6 × 10−1s−1) than
Ca2+‐saturated conditions (
KDSPR=19μM). The IQ motif of Ng (Ng27−50) had similar affinity for CaM as Ng under
Ca2+‐saturated conditions (
KDSPR=14μM), but no interaction was seen under
Ca2+‐depleted conditions. Microscale thermophoresis using fluorescently labeled CaM confirmed the surface plasmon resonance results qualitatively, but estimated lower affinities for the Ng (
KDMST=890nM) and CaMKII290−309(
KDMST=190nM) interactions. Although CaMKII290−309 showed expected interaction characteristics, they may be different for full‐length CaMKII. The data for full‐length Ng, but not Ng27−50, agree with the current model on Ng regulation of
Ca2+/CaM signaling.
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Affiliation(s)
- Christian Seeger
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.,Beactica AB, Uppsala, Sweden
| | | | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.,Beactica AB, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Fabini E, Zambelli B, Mazzei L, Ciurli S, Bertucci C. Surface plasmon resonance and isothermal titration calorimetry to monitor the Ni(II)-dependent binding of Helicobacter pylori NikR to DNA. Anal Bioanal Chem 2016; 408:7971-7980. [DOI: 10.1007/s00216-016-9894-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/28/2016] [Accepted: 08/17/2016] [Indexed: 02/03/2023]
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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Perna AM, Rodrigues T, Schmidt TP, Böhm M, Stutz K, Reker D, Pfeiffer B, Altmann KH, Backert S, Wessler S, Schneider G. Fragment-Based De Novo Design Reveals a Small-Molecule Inhibitor ofHelicobacter PyloriHtrA. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Perna AM, Rodrigues T, Schmidt TP, Böhm M, Stutz K, Reker D, Pfeiffer B, Altmann KH, Backert S, Wessler S, Schneider G. Fragment-Based De Novo Design Reveals a Small-Molecule Inhibitor of Helicobacter Pylori HtrA. Angew Chem Int Ed Engl 2015; 54:10244-8. [PMID: 26069090 DOI: 10.1002/anie.201504035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Indexed: 01/22/2023]
Abstract
Sustained identification of innovative chemical entities is key for the success of chemical biology and drug discovery. We report the fragment-based, computer-assisted de novo design of a small molecule inhibiting Helicobacter pylori HtrA protease. Molecular binding of the designed compound to HtrA was confirmed through biophysical methods, supporting its functional activity in vitro. Hit expansion led to the identification of the currently best-in-class HtrA inhibitor. The results obtained reinforce the validity of ligand-based de novo design and binding-kinetics-guided optimization for the efficient discovery of pioneering lead structures and prototyping drug-like chemical probes with tailored bioactivity.
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Affiliation(s)
- Anna M Perna
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Tiago Rodrigues
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | | | - Manja Böhm
- Department of Biology, Universität Erlangen-Nürnberg (Germany)
| | - Katharina Stutz
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Daniel Reker
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Bernhard Pfeiffer
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Steffen Backert
- Department of Biology, Universität Erlangen-Nürnberg (Germany)
| | - Silja Wessler
- Department of Molecular Biology, Universität Salzburg (Austria)
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland).
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