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Cozzolino M, Panyi G. Intracellular acidity impedes KCa3.1 activation by Riluzole and SKA-31. Front Pharmacol 2024; 15:1380655. [PMID: 38638868 PMCID: PMC11024243 DOI: 10.3389/fphar.2024.1380655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/05/2024] [Indexed: 04/20/2024] Open
Abstract
Background The unique microenvironment in tumors inhibits the normal functioning of tumor-infiltrating lymphocytes, leading to immune evasion and cancer progression. Over-activation of KCa3.1 using positive modulators has been proposed to rescue the anti-tumor response. One of the key characteristics of the tumor microenvironment is extracellular acidity. Herein, we analyzed how intra- and extracellular pH affects K+ currents through KCa3.1 and if the potency of two of its positive modulators, Riluzole and SKA-31, is pH sensitive. Methods Whole-cell patch-clamp was used to measure KCa3.1 currents either in activated human peripheral lymphocytes or in CHO cells transiently transfected with either the H192A mutant or wild-type hKCa3.1 in combination with T79D-Calmodulin, or with KCa2.2. Results We found that changes in the intra- and extracellular pH minimally influenced the KCa3.1-mediated K+ current. Extracellular pH, in the range of 6.0-8.0, does not interfere with the capacity of Riluzole and SKA-31 to robustly activate the K+ currents through KCa3.1. Contrariwise, an acidic intracellular solution causes a slow, but irreversible loss of potency of both the activators. Using different protocols of perfusion and depolarization we demonstrated that the loss of potency is strictly time and pH-dependent and that this peculiar effect can be observed with a structurally similar channel KCa2.2. While two different point mutations of both KCa3.1 (H192A) and its associated protein Calmodulin (T79D) do not limit the effect of acidity, increasing the cytosolic Ca2+ concentration to saturating levels eliminated the loss-of-potency phenotype. Conclusion Based on our data we conclude that KCa3.1 currents are not sensitive the either the intracellular or the extracellular pH in the physiological and pathophysiological range. However, intracellular acidosis in T cells residing in the tumor microenvironment could hinder the potentiating effect of KCa3.1 positive modulators administered to boost their activity. Further research is warranted both to clarify the molecular interactions between the modulators and KCa3.1 at different intracellular pH conditions and to define whether this loss of potency can be observed in cancer models as well.
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Affiliation(s)
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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2
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Williams RB, Alam Afsar MN, Tikunova S, Kou Y, Fang X, Somarathne RP, Gyawu RF, Knotts GM, Agee TA, Garcia SA, Losordo LD, Fitzkee NC, Kekenes-Huskey PM, Davis JP, Johnson CN. Human disease-associated calmodulin mutations alter calcineurin function through multiple mechanisms. Cell Calcium 2023; 113:102752. [PMID: 37245392 PMCID: PMC10330910 DOI: 10.1016/j.ceca.2023.102752] [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: 12/17/2022] [Revised: 04/29/2023] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
Calmodulin (CaM) is a ubiquitous, calcium-sensing protein that regulates a multitude of processes throughout the body. In response to changes in [Ca2+], CaM modifies, activates, and deactivates enzymes and ion channels, as well as many other cellular processes. The importance of CaM is highlighted by the conservation of an identical amino acid sequence in all mammals. Alterations to CaM amino acid sequence were once thought to be incompatible with life. During the last decade modifications to the CaM protein sequence have been observed in patients suffering from life-threatening heart disease (calmodulinopathy). Thus far, inadequate or untimely interaction between mutant CaM and several proteins (LTCC, RyR2, and CaMKII) have been identified as mechanisms underlying calmodulinopathy. Given the extensive number of CaM interactions in the body, there are likely many consequences for altering CaM protein sequence. Here, we demonstrate that disease-associated CaM mutations alter the sensitivity and activity of the Ca2+-CaM-enhanced serine/threonine phosphatase calcineurin (CaN). Biophysical characterization by circular dichroism, solution NMR spectroscopy, stopped-flow kinetic measurements, and MD simulations provide mechanistic insight into mutation dysfunction as well as highlight important aspects of CaM Ca2+ signal transduction. We find that individual CaM point mutations (N53I, F89L, D129G, and F141L) impair CaN function, however, the mechanisms are not the same. Specifically, individual point mutations can influence or modify the following properties: CaM binding, Ca2+ binding, and/or Ca2+kinetics. Moreover, structural aspects of the CaNCaM complex can be altered in manners that indicate changes to allosteric transmission of CaM binding to the enzyme active site. Given that loss of CaN function can be fatal, as well as evidence that CaN modifies ion channels already associated with calmodulinopathy, our results raise the possibility that altered CaN function contributes to calmodulinopathy.
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Affiliation(s)
- Ryan B Williams
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Md Nure Alam Afsar
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Svetlana Tikunova
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A
| | - Yongjun Kou
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A
| | - Xuan Fang
- Department of Cell and Molecular Physiology, Loyola University of Chicago, Maywood Illinois 60153, U.S.A
| | - Radha P Somarathne
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Rita F Gyawu
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Garrett M Knotts
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Taylor A Agee
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Sara A Garcia
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Luke D Losordo
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University of Chicago, Maywood Illinois 60153, U.S.A
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus OH 43210, U.S.A.
| | - Christopher N Johnson
- Department of Chemistry, Mississippi State University, Starkville MS 39759, U.S.A; Vanderbilt Center for Arrhythmia Research and Therapeutics, Nashville TN 37232, U.S.A.
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3
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Orfali R, AlFaiz A, Rahman MA, Lau L, Nam YW, Zhang M. K Ca2 and K Ca3.1 Channels in the Airways: A New Therapeutic Target. Biomedicines 2023; 11:1780. [PMID: 37509419 PMCID: PMC10376499 DOI: 10.3390/biomedicines11071780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/30/2023] Open
Abstract
K+ channels are involved in many critical functions in lung physiology. Recently, the family of Ca2+-activated K+ channels (KCa) has received more attention, and a massive amount of effort has been devoted to developing selective medications targeting these channels. Within the family of KCa channels, three small-conductance Ca2+-activated K+ (KCa2) channel subtypes, together with the intermediate-conductance KCa3.1 channel, are voltage-independent K+ channels, and they mediate Ca2+-induced membrane hyperpolarization. Many KCa2 channel members are involved in crucial roles in physiological and pathological systems throughout the body. In this article, different subtypes of KCa2 and KCa3.1 channels and their functions in respiratory diseases are discussed. Additionally, the pharmacology of the KCa2 and KCa3.1 channels and the link between these channels and respiratory ciliary regulations will be explained in more detail. In the future, specific modulators for small or intermediate Ca2+-activated K+ channels may offer a unique therapeutic opportunity to treat muco-obstructive lung diseases.
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Affiliation(s)
- Razan Orfali
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
- Biomedical Research Administration, Research Centre, King Fahad Medical City, Riyadh Second Health Cluster, Riyadh 12231, Saudi Arabia
| | - Ali AlFaiz
- Biomedical Research Administration, Research Centre, King Fahad Medical City, Riyadh Second Health Cluster, Riyadh 12231, Saudi Arabia
| | - Mohammad Asikur Rahman
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Liz Lau
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Young-Woo Nam
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Miao Zhang
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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4
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Dal Cortivo G, Marino V, Bianconi S, Dell'Orco D. Calmodulin variants associated with congenital arrhythmia impair selectivity for ryanodine receptors. Front Mol Biosci 2023; 9:1100992. [PMID: 36685279 PMCID: PMC9849693 DOI: 10.3389/fmolb.2022.1100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Among its many molecular targets, the ubiquitous calcium sensor protein calmodulin (CaM) recognizes and regulates the activity of ryanodine receptors type 1 (RyR1) and 2 (RyR2), mainly expressed in skeletal and cardiac muscle, respectively. Such regulation is essential to achieve controlled contraction of muscle cells. To unravel the molecular mechanisms underlying the target recognition process, we conducted a comprehensive biophysical investigation of the interaction between two calmodulin variants associated with congenital arrhythmia, namely N97I and Q135P, and a highly conserved calmodulin-binding region in RyR1 and RyR2. The structural, thermodynamic, and kinetic properties of protein-peptide interactions were assessed together with an in-depth structural and topological investigation based on molecular dynamics simulations. This integrated approach allowed us to identify amino acids that are crucial in mediating allosteric processes, which enable high selectivity in molecular target recognition. Our results suggest that the ability of calmodulin to discriminate between RyR1 an RyR2 targets depends on kinetic discrimination and robust allosteric communication between Ca2+-binding sites (EF1-EF3 and EF3-EF4 pairs), which is perturbed in both N97I and Q135P arrhythmia-associated variants.
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5
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Chamorro-Garcia A, Parolo C, Ortega G, Idili A, Green J, Ricci F, Plaxco KW. The sequestration mechanism as a generalizable approach to improve the sensitivity of biosensors and bioassays. Chem Sci 2022; 13:12219-12228. [PMID: 36349092 PMCID: PMC9601244 DOI: 10.1039/d2sc03901j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/16/2022] [Indexed: 07/25/2023] Open
Abstract
Biosensors and bioassays, both of which employ proteins and nucleic acids to detect specific molecular targets, have seen significant applications in both biomedical research and clinical practice. This success is largely due to the extraordinary versatility, affinity, and specificity of biomolecular recognition. Nevertheless, these receptors suffer from an inherent limitation: single, saturable binding sites exhibit a hyperbolic relationship (the "Langmuir isotherm") between target concentration and receptor occupancy, which in turn limits the sensitivity of these technologies to small variations in target concentration. To overcome this and generate more responsive biosensors and bioassays, here we have used the sequestration mechanism to improve the steepness of the input/output curves of several bioanalytical methods. As our test bed for this we employed sensors and assays against neutrophil gelatinase-associated lipocalin (NGAL), a kidney biomarker for which enhanced sensitivity will improve the monitoring of kidney injury. Specifically, by introducing sequestration we have improved the responsiveness of an electrochemical aptamer based (EAB) biosensor, and two bioassays, a paper-based "dipstick" assay and an enzyme-linked immunosorbent assay (ELISA). Doing so we have narrowed the dynamic range of these sensors and assays several-fold, thus enhancing their ability to measure small changes in target concentration. Given that introducing sequestration requires only the addition of the appropriate concentration of a high-affinity "depletant," the mechanism appears simple and easily adaptable to tuning the binding properties of the receptors employed in a wide range of biosensors and bioassays.
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Affiliation(s)
- Alejandro Chamorro-Garcia
- Department of Chemistry and Biochemistry University of California Santa Barbara (UCSB) Santa Barbara CA 93106 USA
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133 Rome Italy
| | - Claudio Parolo
- ISGlobal-Barcelona Institute for Global Health Carrer del Rosselló 132 08036 Barcelona Spain
| | - Gabriel Ortega
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
- Precision Medicine and Metabolism Laboratory, CIC BioGUNE, Basque Research and Technology Alliance, Parque Tecnológico de Bizkaia 48160 Derio Spain
| | - Andrea Idili
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133 Rome Italy
| | - Joshua Green
- Department of Chemistry and Biochemistry University of California Santa Barbara (UCSB) Santa Barbara CA 93106 USA
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133 Rome Italy
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry University of California Santa Barbara (UCSB) Santa Barbara CA 93106 USA
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6
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Dal Cortivo G, Barracchia CG, Marino V, D'Onofrio M, Dell'Orco D. Alterations in calmodulin-cardiac ryanodine receptor molecular recognition in congenital arrhythmias. Cell Mol Life Sci 2022; 79:127. [PMID: 35133504 PMCID: PMC8825638 DOI: 10.1007/s00018-022-04165-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/27/2021] [Accepted: 01/23/2022] [Indexed: 12/03/2022]
Abstract
Calmodulin (CaM), a ubiquitous and highly conserved Ca2+-sensor protein involved in the regulation of over 300 molecular targets, has been recently associated with severe forms of lethal arrhythmia. Here, we investigated how arrhythmia-associated mutations in CaM localized at the C-terminal lobe alter the molecular recognition with Ryanodine receptor 2 (RyR2), specifically expressed in cardiomyocytes. We performed an extensive structural, thermodynamic, and kinetic characterization of the variants D95V/H in the EF3 Ca2+-binding motif and of the D129V and D131H/E variants in the EF4 motif, and probed their interaction with RyR2. Our results show that the specific structural changes observed for individual CaM variants do not extend to the complex with the RyR2 target. Indeed, some common alterations emerge at the protein–protein interaction level, suggesting the existence of general features shared by the arrhythmia-associated variants. All mutants showed a faster rate of dissociation from the target peptide than wild-type CaM. Integration of spectroscopic data with exhaustive molecular dynamics simulations suggests that, in the presence of Ca2+, functional recognition involves allosteric interactions initiated by the N-terminal lobe of CaM, which shows a lower affinity for Ca2+ compared to the C-terminal lobe in the isolated protein.
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Affiliation(s)
- Giuditta Dal Cortivo
- Department of Neurosciences Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | | | - Valerio Marino
- Department of Neurosciences Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy.
| | - Daniele Dell'Orco
- Department of Neurosciences Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada le Grazie 8, 37134, Verona, Italy.
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7
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Simultaneous detection of reciprocal interactions between calmodulin, Ca2+ and molecular targets: a focus on the calmodulin-RyR2 complex. Biochem J 2021; 478:487-491. [PMID: 33544125 DOI: 10.1042/bcj20200818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 01/22/2023]
Abstract
In a recent issue of Biochemical Journal, Brohus et al. (Biochem. J.476, 193-209) investigated the interaction between the ubiquitous intracellular Ca2+-sensor calmodulin (CaM) and peptides that mimic different structural regions of the cardiac ryanodine receptor (RyR2) at different Ca2+ concentrations. For the purpose, a novel bidimensional titration assay based on changes in fluorescence anisotropy was designed. The study identified the CaM domains that selectively bind to a specific CaM-binding domain in RyR2 and demonstrated that the interaction occurs essentially under Ca2+-saturating conditions. This study provides an elegant and experimentally accessible framework for detailed molecular investigations of the emerging life-threatening arrhythmia diseases associated with mutations in the genes encoding CaM. Furthermore, by allowing the measurement of the equilibrium dissociation constant in a protein-protein complex as a function of [Ca2+], the methodology presented by Brohus et al. may have broad applicability to the study of Ca2+ signalling.
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8
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Nelson SED, Weber DK, Rebbeck RT, Cornea RL, Veglia G, Thomas DD. Met125 is essential for maintaining the structural integrity of calmodulin's C-terminal domain. Sci Rep 2020; 10:21320. [PMID: 33288831 PMCID: PMC7721703 DOI: 10.1038/s41598-020-78270-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/17/2020] [Indexed: 11/09/2022] Open
Abstract
We have used NMR and circular dichroism spectroscopy to investigate the structural and dynamic effects of oxidation on calmodulin (CaM), using peroxide and the Met to Gln oximimetic mutations. CaM is a Ca2+-sensitive regulatory protein that interacts with numerous targets. Due to its high methionine content, CaM is highly susceptible to oxidation by reactive oxygen species under conditions of cell stress and age-related muscle degeneration. CaM oxidation alters regulation of a host of CaM's protein targets, emphasizing the importance of understanding the mechanism of CaM oxidation in muscle degeneration and overall physiology. It has been shown that the M125Q CaM mutant can mimic the functional effects of methionine oxidation on CaM's regulation of the calcium release channel, ryanodine receptor (RyR). We report here that the M125Q mutation causes a localized unfolding of the C-terminal lobe of CaM, preventing the formation of a hydrophobic cluster of residues near the EF-hand Ca2+ binding sites. NMR analysis of CaM oxidation by peroxide offers further insights into the susceptibility of CaM's Met residues to oxidation and the resulting structural effects. These results further resolve oxidation-driven structural perturbation of CaM, with implications for RyR regulation and the decay of muscle function in aging.
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Affiliation(s)
- Sarah E D Nelson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
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9
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Liu J, Lenzoni G, Knight MR. Design Principle for Decoding Calcium Signals to Generate Specific Gene Expression Via Transcription. PLANT PHYSIOLOGY 2020; 182:1743-1761. [PMID: 31744935 PMCID: PMC7140924 DOI: 10.1104/pp.19.01003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/31/2019] [Indexed: 05/18/2023]
Abstract
The second messenger calcium plays a key role in conveying specificity of signaling pathways in plant cells. Specific calcium signatures are decoded to generate correct gene expression responses and amplification of calcium signatures is vital to this process. (1) It is not known if this amplification is an intrinsic property of all calcium-regulated gene expression responses and whether all calcium signatures have the potential to be amplified, or (2) how a given calcium signature maintains specificity in cells containing a great number of transcription factors (TFs) and other proteins with the potential to be calcium-regulated. The work presented here uncovers the design principle by which it is possible to decode calcium signals into specific changes in gene transcription in plant cells. Regarding the first question, we found that the binding mechanism between protein components possesses an intrinsic property that will nonlinearly amplify any calcium signal. This nonlinear amplification allows plant cells to effectively distinguish the kinetics of different calcium signatures to produce specific and appropriate changes in gene expression. Regarding the second question, we found that the large number of calmodulin (CaM)-binding TFs or proteins in plant cells form a buffering system such that the concentration of an active CaM-binding TF is insensitive to the concentration of any other CaM-binding protein, thus maintaining specificity. The design principle revealed by this work can be used to explain how any CaM-binding TF decodes calcium signals to generate specific gene expression responses in plant cells via transcription.
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Affiliation(s)
- Junli Liu
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Gioia Lenzoni
- School of Pharmaceutical Sciences, University of Geneva, Geneva CH-1211, Switzerland
| | - Marc R Knight
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
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10
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Calmodulin Mutations Associated with Heart Arrhythmia: A Status Report. Int J Mol Sci 2020; 21:ijms21041418. [PMID: 32093079 PMCID: PMC7073091 DOI: 10.3390/ijms21041418] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Calmodulin (CaM) is a ubiquitous intracellular Ca2+ sensing protein that modifies gating of numerous ion channels. CaM has an extraordinarily high level of evolutionary conservation, which led to the fundamental assumption that mutation would be lethal. However, in 2012, complete exome sequencing of infants suffering from recurrent cardiac arrest revealed de novo mutations in the three human CALM genes. The correlation between mutations and pathophysiology suggests defects in CaM-dependent ion channel functions. Here, we review the current state of the field for all reported CaM mutations associated with cardiac arrhythmias, including knowledge of their biochemical and structural characteristics, and progress towards understanding how these mutations affect cardiac ion channel function.
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11
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Ohadi D, Schmitt DL, Calabrese B, Halpain S, Zhang J, Rangamani P. Computational Modeling Reveals Frequency Modulation of Calcium-cAMP/PKA Pathway in Dendritic Spines. Biophys J 2019; 117:1963-1980. [PMID: 31668749 PMCID: PMC7031750 DOI: 10.1016/j.bpj.2019.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/30/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022] Open
Abstract
Dendritic spines are the primary excitatory postsynaptic sites that act as subcompartments of signaling. Ca2+ is often the first and most rapid signal in spines. Downstream of calcium, the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) pathway plays a critical role in the regulation of spine formation, morphological modifications, and ultimately, learning and memory. Although the dynamics of calcium are reasonably well-studied, calcium-induced cAMP/PKA dynamics, particularly with respect to frequency modulation, are not fully explored. In this study, we present a well-mixed model for the dynamics of calcium-induced cAMP/PKA dynamics in dendritic spines. The model is constrained using experimental observations in the literature. Further, we measured the calcium oscillation frequency in dendritic spines of cultured hippocampal CA1 neurons and used these dynamics as model inputs. Our model predicts that the various steps in this pathway act as frequency modulators for calcium, and the high frequency of calcium input is filtered by adenylyl cyclase 1 and phosphodiesterases in this pathway such that cAMP/PKA only responds to lower frequencies. This prediction has important implications for noise filtering and long-timescale signal transduction in dendritic spines. A companion manuscript presents a three-dimensional spatial model for the same pathway.
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Affiliation(s)
- Donya Ohadi
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California
| | - Danielle L Schmitt
- Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Barbara Calabrese
- Division of Biological Sciences and Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, California
| | - Shelley Halpain
- Division of Biological Sciences and Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, California
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California.
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Restoration of cytosolic calcium inhibits Mycobacterium tuberculosis intracellular growth: Theoretical evidence and experimental observation. J Theor Biol 2019; 472:110-123. [DOI: 10.1016/j.jtbi.2019.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 01/05/2023]
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13
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Martins TV, Hammelman J, Marinova S, Ding CO, Morris RJ. An Information-Theoretical Approach for Calcium Signaling Specificity. IEEE Trans Nanobioscience 2018; 18:93-100. [PMID: 30561348 DOI: 10.1109/tnb.2018.2882223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Calcium is a key signaling agent in animals and plants. Its involvement in the regulation of a wide range of processes has led to the question of how calcium signals can activate stimulus-specific responses. We introduce a computational framework for studying intracellular calcium signaling using elements of information theory. We use mutual information to quantify the differential activation of proteins in response to different calcium signals to provide an operational definition of specificity. Using optimization procedures this framework allows us to explore the biochemical determinants of calcium decoding. We explore simple toy models and general binding kinetics approaches to demonstrate the utility and limitations of the proposed framework. Unravelling signaling specificity is key for understanding information processing within cells and for the future design of synthetic nanodevices for molecular communications.
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14
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Badone B, Ronchi C, Kotta MC, Sala L, Ghidoni A, Crotti L, Zaza A. Calmodulinopathy: Functional Effects of CALM Mutations and Their Relationship With Clinical Phenotypes. Front Cardiovasc Med 2018; 5:176. [PMID: 30619883 PMCID: PMC6297375 DOI: 10.3389/fcvm.2018.00176] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/22/2018] [Indexed: 12/16/2022] Open
Abstract
In spite of the widespread role of calmodulin (CaM) in cellular signaling, CaM mutations lead specifically to cardiac manifestations, characterized by remarkable electrical instability and a high incidence of sudden death at young age. Penetrance of the mutations is surprisingly high, thus postulating a high degree of functional dominance. According to the clinical patterns, arrhythmogenesis in CaM mutations can be attributed, in the majority of cases, to either prolonged repolarization (as in long-QT syndrome, LQTS phenotype), or to instability of the intracellular Ca2+ store (as in catecholamine-induced tachycardias, CPVT phenotype). This review discusses how mutations affect CaM signaling function and how this may relate to the distinct arrhythmia phenotypes/mechanisms observed in patients; this involves mechanistic interpretation of negative dominance and mutation-specific CaM-target interactions. Knowledge of the mechanisms involved may allow critical approach to clinical manifestations and aid in the development of therapeutic strategies for "calmodulinopathies," a recently identified nosological entity.
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Affiliation(s)
- Beatrice Badone
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Carlotta Ronchi
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Maria-Christina Kotta
- Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Luca Sala
- Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Alice Ghidoni
- Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Lia Crotti
- Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Istituto Auxologico Italiano, IRCCS, Milan, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
- Department of Cardiovascular, Neural and Metabolic Sciences, San Luca Hospital, Istituto Auxologico Italiano, IRCCS, Milan, Italy
| | - Antonio Zaza
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
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15
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Kotta MC, Sala L, Ghidoni A, Badone B, Ronchi C, Parati G, Zaza A, Crotti L. Calmodulinopathy: A Novel, Life-Threatening Clinical Entity Affecting the Young. Front Cardiovasc Med 2018; 5:175. [PMID: 30574507 PMCID: PMC6291462 DOI: 10.3389/fcvm.2018.00175] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/22/2018] [Indexed: 01/31/2023] Open
Abstract
Sudden cardiac death (SCD) in the young may often be the first manifestation of a genetic arrythmogenic disease that had remained undiagnosed. Despite the significant discoveries of the genetic bases of inherited arrhythmia syndromes, there remains a measurable fraction of cases where in-depth clinical and genetic investigations fail to identify the underlying SCD etiology. A few years ago, 2 cases of infants with recurrent cardiac arrest episodes, due to what appeared to be as a severe form of long QT syndrome (LQTS), came to our attention. These prompted a number of clinical and genetic research investigations that allowed us to identify a novel, closely associated to LQTS but nevertheless distinct, clinical entity that is now known as calmodulinopathy. Calmodulinopathy is a life-threatening arrhythmia syndrome, affecting mostly young individuals, caused by mutations in any of the 3 genes encoding calmodulin (CaM). Calmodulin is a ubiquitously expressed Ca2+ signaling protein that, in the heart, modulates several ion channels and participates in a plethora of cellular processes. We will hereby provide an overview of CaM's structure and function under normal and disease states, highlighting the genetic etiology of calmodulinopathy and the related disease mechanisms. We will also discuss the phenotypic spectrum of patients with calmodulinopathy and present state-of-the art approaches with patient-derived induced pluripotent stem cells that have been thus far adopted in order to accurately model calmodulinopathy in vitro, decipher disease mechanisms and identify novel therapies.
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Affiliation(s)
- Maria-Christina Kotta
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
| | - Luca Sala
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
| | - Alice Ghidoni
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy
| | - Beatrice Badone
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Carlotta Ronchi
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Gianfranco Parati
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy.,Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular, Neural and Metabolic Sciences, San Luca Hospital, Milan, Italy
| | - Antonio Zaza
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Lia Crotti
- Istituto Auxologico Italiano, IRCCS, Center for Cardiac Arrhythmias of Genetic Origin and Laboratory of Cardiovascular Genetics, Milan, Italy.,Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy.,Istituto Auxologico Italiano, IRCCS, Department of Cardiovascular, Neural and Metabolic Sciences, San Luca Hospital, Milan, Italy
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16
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Zhou W, Saran R, Huang PJJ, Ding J, Liu J. An Exceptionally Selective DNA Cooperatively Binding Two Ca2+Ions. Chembiochem 2017; 18:518-522. [PMID: 28087991 DOI: 10.1002/cbic.201600708] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Runjhun Saran
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
| | - Juewen Liu
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
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17
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Lee K, Alphonse S, Piserchio A, Tavares CDJ, Giles DH, Wellmann RM, Dalby KN, Ghose R. Structural Basis for the Recognition of Eukaryotic Elongation Factor 2 Kinase by Calmodulin. Structure 2016; 24:1441-51. [PMID: 27499441 DOI: 10.1016/j.str.2016.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/06/2016] [Accepted: 06/10/2016] [Indexed: 12/25/2022]
Abstract
Binding of Ca(2+)-loaded calmodulin (CaM) activates eukaryotic elongation factor 2 kinase (eEF-2K) that phosphorylates eEF-2, its only known cellular target, leading to a decrease in global protein synthesis. Here, using an eEF-2K-derived peptide (eEF-2KCBD) that encodes the region necessary for its CaM-mediated activation, we provide a structural basis for their interaction. The striking feature of this association is the absence of Ca(2+) from the CaM C-lobe sites, even under high Ca(2+) conditions. eEF-2KCBD engages CaM largely through the C lobe of the latter in an anti-parallel 1-5-8 hydrophobic mode reinforced by a pair of unique electrostatic contacts. Sparse interactions of eEF-2KCBD with the CaM N lobe results in persisting inter-lobe mobility. A conserved eEF-2K residue (W85) anchors it to CaM by inserting into a deep hydrophobic cavity within the CaM C lobe. Mutation of this residue (W85S) substantially weakens interactions between full-length eEF-2K and CaM in vitro and reduces eEF-2 phosphorylation in cells.
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Affiliation(s)
- Kwangwoon Lee
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Sébastien Alphonse
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Clint D J Tavares
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - David H Giles
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, TX 78712, USA
| | - Rebecca M Wellmann
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, TX 78712, USA
| | - Kevin N Dalby
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; Division of Chemical Biology and Medicinal Chemistry, 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; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA.
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18
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Salakhieva DV, Sadreev II, Chen MZQ, Umezawa Y, Evstifeev AI, Welsh GI, Kotov NV. Kinetic regulation of multi-ligand binding proteins. BMC SYSTEMS BIOLOGY 2016; 10:32. [PMID: 27090530 PMCID: PMC4835871 DOI: 10.1186/s12918-016-0277-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/13/2016] [Indexed: 12/24/2022]
Abstract
BACKGROUND Second messengers, such as calcium, regulate the activity of multisite binding proteins in a concentration-dependent manner. For example, calcium binding has been shown to induce conformational transitions in the calcium-dependent protein calmodulin, under steady state conditions. However, intracellular concentrations of these second messengers are often subject to rapid change. The mechanisms underlying dynamic ligand-dependent regulation of multisite proteins require further elucidation. RESULTS In this study, a computational analysis of multisite protein kinetics in response to rapid changes in ligand concentrations is presented. Two major physiological scenarios are investigated: i) Ligand concentration is abundant and the ligand-multisite protein binding does not affect free ligand concentration, ii) Ligand concentration is of the same order of magnitude as the interacting multisite protein concentration and does not change. Therefore, buffering effects significantly influence the amounts of free ligands. For each of these scenarios the influence of the number of binding sites, the temporal effects on intermediate apo- and fully saturated conformations and the multisite regulatory effects on target proteins are investigated. CONCLUSIONS The developed models allow for a novel and accurate interpretation of concentration and pressure jump-dependent kinetic experiments. The presented model makes predictions for the temporal distribution of multisite protein conformations in complex with variable numbers of ligands. Furthermore, it derives the characteristic time and the dynamics for the kinetic responses elicited by a ligand concentration change as a function of ligand concentration and the number of ligand binding sites. Effector proteins regulated by multisite ligand binding are shown to depend on ligand concentration in a highly nonlinear fashion.
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Affiliation(s)
- Diana V. Salakhieva
- />Kazan (Volga Region) Federal University, 18 Kremlyovskaya St., 420008 Kazan, Russia
| | - Ildar I. Sadreev
- />Centre for Systems, Dynamics and Control, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Harrison Building, North Park Road, Exeter, EX4 4QF UK
| | - Michael Z. Q. Chen
- />Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yoshinori Umezawa
- />Department of Dermatology, The Jikei University School of Medicine, 3-25-8 Nishishimbashi, Minato-ku, Tokyo, 105-8461 Japan
| | - Aleksandr I. Evstifeev
- />Biophysics & Bionics Lab, Institute of Physics, Kazan Federal University, Kazan, 420008 Russia
| | - Gavin I. Welsh
- />Academic Renal Unit, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY UK
| | - Nikolay V. Kotov
- />Biophysics & Bionics Lab, Institute of Physics, Kazan Federal University, Kazan, 420008 Russia
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19
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Guo Z, Johnston WA, Stein V, Kalimuthu P, Perez-Alcala S, Bernhardt PV, Alexandrov K. Engineering PQQ-glucose dehydrogenase into an allosteric electrochemical Ca2+ sensor. Chem Commun (Camb) 2016; 52:485-8. [DOI: 10.1039/c5cc07824e] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Electrochemical biosensors convert biological events to an electrical current.
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Affiliation(s)
- Zhong Guo
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane
- Australia
| | - Wayne A. Johnston
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane
- Australia
| | - Viktor Stein
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane
- Australia
| | - Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | | | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane
- Australia
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20
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Osman R, Mezei M, Engel S. The role of protein “Stability patches” in molecular recognition: A case study of the human growth hormone-receptor complex. J Comput Chem 2015; 37:913-9. [DOI: 10.1002/jcc.24276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Roman Osman
- Department of Structural and Chemical Biology; Icahn School of Medicine at Mount Sinai; New York
| | - Mihaly Mezei
- Department of Structural and Chemical Biology; Icahn School of Medicine at Mount Sinai; New York
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev; Beer-Sheva Israel
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21
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Budu A, Gomes MM, Melo PM, El Chamy Maluf S, Bagnaresi P, Azevedo MF, Carmona AK, Gazarini ML. Calmidazolium evokes high calcium fluctuations in Plasmodium falciparum. Cell Signal 2015; 28:125-135. [PMID: 26689736 DOI: 10.1016/j.cellsig.2015.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/30/2015] [Accepted: 12/07/2015] [Indexed: 10/22/2022]
Abstract
Calcium and calmodulin (CaM) are important players in eukaryote cell signaling. In the present study, by using a knockin approach, we demonstrated the expression and localization of CaM in all erythrocytic stages of Plasmodium falciparum. Under extracellular Ca(2+)-free conditions, calmidazolium (CZ), a potent CaM inhibitor, promoted a transient cytosolic calcium ([Ca(2+)]cyt) increase in isolated trophozoites, indicating that CZ mobilizes intracellular sources of calcium. In the same extracellular Ca(2+)-free conditions, the [Ca(2+)]cyt rise elicited by CZ treatment was ~3.5 fold higher when the endoplasmic reticulum (ER) calcium store was previously depleted ruling out the mobilization of calcium from the ER by CZ. The effects of the Ca(2+)/H(+) ionophore ionomycin (ION) and the Na(+)/H(+) ionophore monensin (MON) suggest that the [Ca(2+)]cyt-increasing effect of CZ is driven by the removal of Ca(2+) from at least one Ca(2+)-CaM-related (CaMR) protein as well as by the mobilization of Ca(2+) from intracellular acidic calcium stores. Moreover, we showed that the mitochondrion participates in the sequestration of the cytosolic Ca(2+) elicited by CZ. Finally, the modulation of membrane Ca(2+) channels by CZ and thapsigargin (THG) was demonstrated. The opened channels were blocked by the unspecific calcium channel blocker Co(2+) but not by 2-APB (capacitative calcium entry inhibitor) or nifedipine (L-type Ca(2+) channel inhibitor). Taken together, the results suggested that one CaMR protein is an important modulator of calcium signaling and homeostasis during the Plasmodium intraerythrocytic cell cycle, working as a relevant intracellular Ca(2+) reservoir in the parasite.
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Affiliation(s)
- Alexandre Budu
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Mayrim M Gomes
- Departamento de Biociências, Universidade Federal de São Paulo, Santos, SP, Brazil
| | - Pollyana M Melo
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Sarah El Chamy Maluf
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Piero Bagnaresi
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Mauro F Azevedo
- Instituto de Ciências Biomédicas, Universidade de São Paulo, SP, Brazil
| | - Adriana K Carmona
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
| | - Marcos L Gazarini
- Departamento de Biociências, Universidade Federal de São Paulo, Santos, SP, Brazil.
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22
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Liu J, Whalley HJ, Knight MR. Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses. THE NEW PHYTOLOGIST 2015; 208:174-87. [PMID: 25917109 PMCID: PMC4832281 DOI: 10.1111/nph.13428] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/26/2015] [Indexed: 05/23/2023]
Abstract
Experimental data show that Arabidopsis thaliana is able to decode different calcium signatures to produce specific gene expression responses. It is also known that calmodulin-binding transcription activators (CAMTAs) have calmodulin (CaM)-binding domains. Therefore, the gene expression responses regulated by CAMTAs respond to calcium signals. However, little is known about how different calcium signatures are decoded by CAMTAs to produce specific gene expression responses. A dynamic model of Ca(2+) -CaM-CAMTA binding and gene expression responses is developed following thermodynamic and kinetic principles. The model is parameterized using experimental data. Then it is used to analyse how different calcium signatures are decoded by CAMTAs to produce specific gene expression responses. Modelling analysis reveals that: calcium signals in the form of cytosolic calcium concentration elevations are nonlinearly amplified by binding of Ca(2+) , CaM and CAMTAs; amplification of Ca(2+) signals enables calcium signatures to be decoded to give specific CAMTA-regulated gene expression responses; gene expression responses to a calcium signature depend upon its history and accumulate all the information during the lifetime of the calcium signature. Information flow from calcium signatures to CAMTA-regulated gene expression responses has been established by combining experimental data with mathematical modelling.
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Affiliation(s)
- Junli Liu
- School of Biological and Biomedical SciencesDurham Centre for Crop Improvement TechnologyDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Helen J. Whalley
- Cell Signalling GroupCancer Research UK Manchester InstituteThe University of ManchesterManchesterM20 4BXUK
| | - Marc R. Knight
- School of Biological and Biomedical SciencesDurham Centre for Crop Improvement TechnologyDurham UniversitySouth RoadDurhamDH1 3LEUK
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23
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Hou W, Izadi M, Nemitz S, Haag N, Kessels MM, Qualmann B. The Actin Nucleator Cobl Is Controlled by Calcium and Calmodulin. PLoS Biol 2015; 13:e1002233. [PMID: 26334624 PMCID: PMC4559358 DOI: 10.1371/journal.pbio.1002233] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 07/23/2015] [Indexed: 01/10/2023] Open
Abstract
Actin nucleation triggers the formation of new actin filaments and has the power to shape cells but requires tight control in order to bring about proper morphologies. The regulation of the members of the novel class of WASP Homology 2 (WH2) domain-based actin nucleators, however, thus far has largely remained elusive. Our study reveals signal cascades and mechanisms regulating Cordon-Bleu (Cobl). Cobl plays some, albeit not fully understood, role in early arborization of neurons and nucleates actin by a mechanism that requires a combination of all three of its actin monomer–binding WH2 domains. Our experiments reveal that Cobl is regulated by Ca2+ and multiple, direct associations of the Ca2+ sensor Calmodulin (CaM). Overexpression analyses and rescue experiments of Cobl loss-of-function phenotypes with Cobl mutants in primary neurons and in tissue slices demonstrated the importance of CaM binding for Cobl’s functions. Cobl-induced dendritic branch initiation was preceded by Ca2+ signals and coincided with local F-actin and CaM accumulations. CaM inhibitor studies showed that Cobl-mediated branching is strictly dependent on CaM activity. Mechanistic studies revealed that Ca2+/CaM modulates Cobl’s actin binding properties and furthermore promotes Cobl’s previously identified interactions with the membrane-shaping F-BAR protein syndapin I, which accumulated with Cobl at nascent dendritic protrusion sites. The findings of our study demonstrate a direct regulation of an actin nucleator by Ca2+/CaM and reveal that the Ca2+/CaM-controlled molecular mechanisms we discovered are crucial for Cobl’s cellular functions. By unveiling the means of Cobl regulation and the mechanisms, by which Ca2+/CaM signals directly converge on a cellular effector promoting actin filament formation, our work furthermore sheds light on how local Ca2+ signals steer and power branch initiation during early arborization of nerve cells—a key process in neuronal network formation. The calcium sensor calmodulin directly regulates the actin filament-promoting factor Cobl to help shape the complex architecture of neurons underlying neuronal network formation. The organization and the formation of new actin filaments by polymerization of actin monomers has the power to shape cells. The rate-limiting step in actin polymerization is “nucleation”—a process during which the first actin monomers are assembled with the help of actin nucleators. This nucleation step requires tight temporal and spatial control in order to achieve proper cell morphologies. Here, we analyse signaling cascades and mechanisms regulating the actin nucleator Cobl, which is crucial for the formation of dendritic arbors of nerve cells—a key process in neuronal network formation. We show that the calcium (Ca2+)-binding signaling component calmodulin (CaM) binds to Cobl and regulates its functions. Using 3-D time-lapse analyses of developing neurons, we visualized how Cobl works. We observed local accumulation of CaM, Cobl, actin, and syndapin I—a membrane-shaping protein—at dendritic branch initiation sites. We find that Ca2+/CaM modulates Cobl’s actin-binding properties and promotes its interactions with syndapin I, which then serves as a membrane anchor for Cobl. In summary, we i) show a direct regulation of the actin nucleator Cobl by Ca2+/CaM, ii) demonstrate that the molecular mechanisms we discovered are crucial for shaping nerve cells, and iii) underscore how local Ca2+ signals steer and power branch initiation during early arborization of neurons.
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Affiliation(s)
- Wenya Hou
- Institute of Biochemistry I, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - Maryam Izadi
- Institute of Biochemistry I, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - Sabine Nemitz
- Institute of Biochemistry I, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - Natja Haag
- Institute of Biochemistry I, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
| | - Michael M. Kessels
- Institute of Biochemistry I, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
- * E-mail: (BQ); (MMK)
| | - Britta Qualmann
- Institute of Biochemistry I, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany
- * E-mail: (BQ); (MMK)
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24
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Tong M, Wang Q, Wang Y, Chen G. Structures and energies of the transition between two conformations of the alternate frame folding calbindin-D9k protein: a theoretical study. RSC Adv 2015. [DOI: 10.1039/c5ra11234f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We carried out molecular dynamics simulations and energy calculations for the two states of the alternate frame folding (AFF) calbindin-D9k protein and their conformational transition in Ca2+-free form to address their dynamical transition mechanism.
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Affiliation(s)
- Mingqiong Tong
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Qing Wang
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry
- Ministry of Education
- College of Chemistry
- Beijing Normal University
- Beijing 100875
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25
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Zhang Q, Bhattacharya S, Andersen ME. Ultrasensitive response motifs: basic amplifiers in molecular signalling networks. Open Biol 2013; 3:130031. [PMID: 23615029 PMCID: PMC3718334 DOI: 10.1098/rsob.130031] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multi-component signal transduction pathways and gene regulatory circuits underpin integrated cellular responses to perturbations. A recurring set of network motifs serve as the basic building blocks of these molecular signalling networks. This review focuses on ultrasensitive response motifs (URMs) that amplify small percentage changes in the input signal into larger percentage changes in the output response. URMs generally possess a sigmoid input–output relationship that is steeper than the Michaelis–Menten type of response and is often approximated by the Hill function. Six types of URMs can be commonly found in intracellular molecular networks and each has a distinct kinetic mechanism for signal amplification. These URMs are: (i) positive cooperative binding, (ii) homo-multimerization, (iii) multistep signalling, (iv) molecular titration, (v) zero-order covalent modification cycle and (vi) positive feedback. Multiple URMs can be combined to generate highly switch-like responses. Serving as basic signal amplifiers, these URMs are essential for molecular circuits to produce complex nonlinear dynamics, including multistability, robust adaptation and oscillation. These dynamic properties are in turn responsible for higher-level cellular behaviours, such as cell fate determination, homeostasis and biological rhythm.
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Affiliation(s)
- Qiang Zhang
- Center for Dose Response Modeling, Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences, Research Triangle Park, NC 27709, USA.
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Kuttner YY, Nagar T, Engel S. Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+. PLoS Comput Biol 2013; 9:e1003028. [PMID: 23592972 PMCID: PMC3617199 DOI: 10.1371/journal.pcbi.1003028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 02/25/2013] [Indexed: 11/19/2022] Open
Abstract
Knowledge of the structural basis of protein-protein interactions (PPI) is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s) orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD) to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM), whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+). Calmodulin is a regulatory protein that acts as an intracellular Ca(2+) sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+) and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+) binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.
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Affiliation(s)
- Yosef Y. Kuttner
- Bioinformatics Core Facility, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tal Nagar
- Bioinformatics Core Facility, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Genetically encoded Ca(2+) indicators: properties and evaluation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:1787-97. [PMID: 23352808 DOI: 10.1016/j.bbamcr.2013.01.011] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/02/2013] [Accepted: 01/10/2013] [Indexed: 02/04/2023]
Abstract
Genetically encoded calcium ion (Ca(2+)) indicators have become very useful and widely used tools for Ca(2+) imaging, not only in cellular models, but also in living organisms. However, the in vivo and in situ characterization of these indicators is tedious and time consuming, and it does not provide information regarding the suitability of an indicator for particular experimental environments. Thus, initial in vitro evaluation of these tools is typically performed to determine their properties. In this review, we examined the properties of dynamic range, affinity, selectivity, and kinetics for Ca(2+) indicators. Commonly used strategies for evaluating these properties are presented. This article is part of a Special Issue entitled: 12th European Symposium on Calcium.
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Ovchinnikov V, Karplus M. Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin. J Phys Chem B 2012; 116:8584-603. [PMID: 22409258 PMCID: PMC3406239 DOI: 10.1021/jp212634z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The popular targeted molecular dynamics (TMD) method for generating transition paths in complex biomolecular systems is revisited. In a typical TMD transition path, the large-scale changes occur early and the small-scale changes tend to occur later. As a result, the order of events in the computed paths depends on the direction in which the simulations are performed. To identify the origin of this bias, and to propose a method in which the bias is absent, variants of TMD in the restraint formulation are introduced and applied to the complex open ↔ closed transition in the protein calmodulin. Due to the global best-fit rotation that is typically part of the TMD method, the simulated system is guided implicitly along the lowest-frequency normal modes, until the large spatial scales associated with these modes are near the target conformation. The remaining portion of the transition is described progressively by higher-frequency modes, which correspond to smaller-scale rearrangements. A straightforward modification of TMD that avoids the global best-fit rotation is the locally restrained TMD (LRTMD) method, in which the biasing potential is constructed from a number of TMD potentials, each acting on a small connected portion of the protein sequence. With a uniform distribution of these elements, transition paths that lack the length-scale bias are obtained. Trajectories generated by steered MD in dihedral angle space (DSMD), a method that avoids best-fit rotations altogether, also lack the length-scale bias. To examine the importance of the paths generated by TMD, LRTMD, and DSMD in the actual transition, we use the finite-temperature string method to compute the free energy profile associated with a transition tube around a path generated by each algorithm. The free energy barriers associated with the paths are comparable, suggesting that transitions can occur along each route with similar probabilities. This result indicates that a broad ensemble of paths needs to be calculated to obtain a full description of conformational changes in biomolecules. The breadth of the contributing ensemble suggests that energetic barriers for conformational transitions in proteins are offset by entropic contributions that arise from a large number of possible paths.
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Kotov NV, Bates DG, Gizatullina AN, Gilaziev B, Khairullin RN, Chen MZQ, Drozdov I, Umezawa Y, Hundhausen C, Aleksandrov A, Yan XG, Spurgeon SK, Smales CM, Valeyev NV. Computational modelling elucidates the mechanism of ciliary regulation in health and disease. BMC SYSTEMS BIOLOGY 2011; 5:143. [PMID: 21920041 PMCID: PMC3224258 DOI: 10.1186/1752-0509-5-143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 09/15/2011] [Indexed: 12/23/2022]
Abstract
Background Ciliary dysfunction leads to a number of human pathologies, including primary ciliary dyskinesia, nephronophthisis, situs inversus pathology or infertility. The mechanism of cilia beating regulation is complex and despite extensive experimental characterization remains poorly understood. We develop a detailed systems model for calcium, membrane potential and cyclic nucleotide-dependent ciliary motility regulation. Results The model describes the intimate relationship between calcium and potassium ionic concentrations inside and outside of cilia with membrane voltage and, for the first time, describes a novel type of ciliary excitability which plays the major role in ciliary movement regulation. Our model describes a mechanism that allows ciliary excitation to be robust over a wide physiological range of extracellular ionic concentrations. The model predicts the existence of several dynamic modes of ciliary regulation, such as the generation of intraciliary Ca2+ spike with amplitude proportional to the degree of membrane depolarization, the ability to maintain stable oscillations, monostable multivibrator regimes, all of which are initiated by variability in ionic concentrations that translate into altered membrane voltage. Conclusions Computational investigation of the model offers several new insights into the underlying molecular mechanisms of ciliary pathologies. According to our analysis, the reported dynamic regulatory modes can be a physiological reaction to alterations in the extracellular environment. However, modification of the dynamic modes, as a result of genetic mutations or environmental conditions, can cause a life threatening pathology.
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Affiliation(s)
- Nikolay V Kotov
- Centre for Molecular Processing, School of Biosciences, University of Kent, Canterbury, Kent, UK
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Mori MX, Imai Y, Itsuki K, Inoue R. Quantitative measurement of Ca(2+)-dependent calmodulin-target binding by Fura-2 and CFP and YFP FRET imaging in living cells. Biochemistry 2011; 50:4685-96. [PMID: 21517110 DOI: 10.1021/bi200287x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Calcium dynamics and its linked molecular interactions cause a variety of biological responses; thus, exploiting techniques for detecting both concurrently is essential. Here we describe a method for measuring the cytosolic Ca(2+) concentration ([Ca(2+)](i)) and protein-protein interactions within the same cell, using Fura-2 and superenhanced cyan and yellow fluorescence protein (seCFP and seYFP, respectively) FRET imaging techniques. Concentration-independent corrections for bleed-through of Fura-2 into FRET cubes across different time points and [Ca(2+)](i) values allowed for an effective separation of Fura-2 cross-talk signals and seCFP and seYFP cross-talk signals, permitting calculation of [Ca(2+)](i) and FRET with high fidelity. This correction approach was particularly effective at lower [Ca(2+)](i) levels, eliminating bleed-through signals that resulted in an artificial enhancement of FRET. By adopting this correction approach combined with stepwise [Ca(2+)](i) increases produced in living cells, we successfully elucidated steady-state relationships between [Ca(2+)](i) and FRET derived from the interaction of seCFP-tagged calmodulin (CaM) and the seYFP-fused CaM binding domain of myosin light chain kinase. The [Ca(2+)](i) versus FRET relationship for voltage-gated sodium, calcium, and TRPC6 channel CaM binding domains (IQ domain or CBD) revealed distinct sensitivities for [Ca(2+)](i). Moreover, the CaM binding strength at basal or subbasal [Ca(2+)](i) levels provided evidence of CaM tethering or apoCaM binding in living cells. Of the ion channel studies, apoCaM binding was weakest for the TRPC6 channel, suggesting that more global Ca(2+) and CaM changes rather than the local CaM-channel interface domain may be involved in Ca(2+)CaM-mediated regulation of this channel. This simultaneous Fura-2 and CFP- and YFP-based FRET imaging system will thus serve as a simple but powerful means of quantitatively elucidating cellular events associated with Ca(2+)-dependent functions.
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Affiliation(s)
- Masayuki X Mori
- Department of Physiology, School of Medicine, Fukuoka University, 7-45-1 Nanakuma, Fukuoka, Japan.
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Laine E, Martínez L, Blondel A, Malliavin TE. Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding. Biophys J 2011; 99:2264-72. [PMID: 20923661 DOI: 10.1016/j.bpj.2010.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 07/14/2010] [Accepted: 07/23/2010] [Indexed: 11/19/2022] Open
Abstract
Calmodulin (CaM) is a remarkably flexible protein which can bind multiple targets in response to changes in intracellular calcium concentration. It contains four calcium-binding sites, arranged in two globular domains. The calcium affinity of CaM N-terminal domain (N-CaM) is dramatically reduced when the complex with the edema factor (EF) of Bacillus anthracis is formed. Here, an atomic explanation for this reduced affinity is proposed through molecular dynamics simulations and free energy perturbation calculations of the EF-CaM complex starting from different crystallographic models. The simulations show that electrostatic interactions between CaM and EF disfavor the opening of N-CaM domains usually induced by calcium binding. Relative calcium affinities of the N-CaM binding sites are probed by free energy perturbation, and dissociation probabilities are evaluated with locally enhanced sampling simulations. We show that EF impairs calcium binding on N-CaM through a direct conformational restraint on Site 1, by an indirect destabilization of Site 2, and by reducing the cooperativity between the two sites.
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Affiliation(s)
- Elodie Laine
- Unité de Bioinformatique Structurale, Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France.
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Abstract
Systems Biology approaches to drug discovery largely focus on the increasing understanding of intracellular and cellular circuits, by computational representation of a molecular system followed by parameter validation against experimental data. This chapter outlines a universal approach to systems biology that allows the linking of intracellular molecular machinery and cellular activity. This procedure is achieved by applying mathematical modeling to molecular modules of a cell in the light of systems biology techniques.
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Valeyev NV, Kim JS, Heslop-Harrison JSP, Postlethwaite I, Kotov NV, Bates DG. Computational modelling suggests dynamic interactions between Ca2+, IP3 and G protein-coupled modules are key to robust Dictyostelium aggregation. MOLECULAR BIOSYSTEMS 2009; 5:612-28. [PMID: 19462019 DOI: 10.1039/b822074c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Under conditions of starvation, Dictyostelium cells begin a programme of development during which they aggregate to form a multicellular structure by chemotaxis, guided by propagating waves of cyclic AMP that are relayed robustly from cell to cell. In this paper, we develop and analyse a new model for the intracellular and extracellular cAMP dependent processes that regulate Dictyostelium migration. The model allows, for the first time, a quantitative analysis of the dynamic interactions between calcium, IP(3) and G protein-dependent modules that are shown to be key to the generation of robust cAMP oscillations in Dictyostelium cells. The model provides a mechanistic explanation for the transient increase in cytosolic free Ca(2+) concentration seen in recent experiments with the application of the calmodulin inhibitor calmidazolium (R24571) to Dictyostelium cells, and also allows elucidation of the effects of varying both the conductivity of stretch-activated channels and the concentration of external phosphodiesterase on the oscillatory regime of an individual cell. A rigorous analysis of the robustness of the new model shows that interactions between the different modules significantly reduce the sensitivity of the resulting cAMP oscillations to variations in the kinetics of different Dictyostelium cells, an essential requirement for the generation of the spatially and temporally synchronised chemoattractant cAMP waves that guide Dictyostelium aggregation.
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Affiliation(s)
- Najl V Valeyev
- Systems Biology Lab, Department of Engineering, University of Leicester, University Road, Leicester, UK.
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