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Marino V, Cortivo GD, Dell'Orco D. Ionic displacement of Ca 2+ by Pb 2+ in calmodulin is affected by arrhythmia-associated mutations. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119490. [PMID: 37201768 DOI: 10.1016/j.bbamcr.2023.119490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/14/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Lead is a highly toxic metal that severely perturbs physiological processes even at sub-micromolar levels, often by disrupting the Ca2+ signaling pathways. Recently, Pb2+-associated cardiac toxicity has emerged, with potential involvement of both the ubiquitous Ca2+ sensor protein calmodulin (CaM) and ryanodine receptors. In this work, we explored the hypothesis that Pb2+ contributes to the pathological phenotype of CaM variants associated with congenital arrhythmias. We performed a thorough spectroscopic and computational characterization of CaM conformational switches in the co-presence of Pb2+ and four missense mutations associated with congenital arrhythmias, namely N53I, N97S, E104A and F141L, and analyzed their effects on the recognition of a target peptide of RyR2. When bound to any of the CaM variants, Pb2+ is difficult to displace even under equimolar Ca2+ concentrations, thus locking all CaM variants in a specific conformation, which exhibits characteristics of coiled-coil assemblies. All arrhythmia-associated variants appear to be more susceptible to Pb2+ than WT CaM, as the conformational transition towards the coiled-coil conformation occurs at lower Pb2+, regardless of the presence of Ca2+, with altered cooperativity. The presence of arrhythmia-associated mutations specifically alters the cation coordination of CaM variants, in some cases involving allosteric communication between the EF-hands in the two domains. Finally, while wild type CaM increases the affinity for the RyR2 target in the presence of Pb2+, no specific pattern could be detected for all other variants, ruling out a synergistic effect of Pb2+ and mutations in the recognition process.
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Affiliation(s)
- Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, I-37134 Verona, Italy
| | - Giuditta Dal Cortivo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, I-37134 Verona, Italy
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, I-37134 Verona, Italy.
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2
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Dobrovodský D, Di Primo C. Do conformational changes contribute to the surface plasmon resonance signal? Biosens Bioelectron 2023; 232:115296. [PMID: 37079993 DOI: 10.1016/j.bios.2023.115296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/23/2023] [Accepted: 04/02/2023] [Indexed: 04/09/2023]
Abstract
Surface plasmon resonance (SPR)-based biosensors are widely used instruments for characterizing molecular interactions. In theory the SPR signal depends only on mass changes for interacting molecules of same chemical nature. Whether conformational changes of interacting molecules also contribute to the SPR signal is still a subject of lively debates. Works have been published claiming that conformational changes were detected but all factors contributing to the SPR signal were not carefully considered, in addition to often using no or improper controls. In the present work we used a very well-characterized oligonucleotide, the thrombin-binding DNA aptamer (TBA), which upon binding of potassium ions folds into a two G-tetrad antiparallel G-quadruplex structure. All terms contributing to the maximal expected SPR response, Rmax, in particular the refractive index increment, RII, of both partners and the fraction of immobilized TBA target available, ca, were experimentally assessed. The resulting Rmax was then compared to the maximal experimental SPR response for potassium ions binding to TBA using appropriate controls. Regardless how the RIIs were measured, by SPR or refractometry, and how much TBA available for interacting with potassium ions was considered, the theoretical and the experimental SPR responses never matched, the former being always lower than the latter. Using a straightforward experimental model system and by thoroughly taking into account all contributing factors we therefore conclude that conformational changes can indeed contribute to the measured SPR signal.
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3
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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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4
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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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5
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Pons M, Perenon M, Bonnet H, Gillon E, Vallée C, Coche-Guérente L, Defrancq E, Spinelli N, Van der Heyden A, Dejeu J. Conformational transition in SPR experiments: impact of spacer length, immobilization mode and aptamer density on signal sign and amplitude. Analyst 2022; 147:4197-4205. [DOI: 10.1039/d2an00824f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The spacer length and immobilization mode impact the Surface plasmon resonance (SPR) signal and affinity measured for small target/aptamer recognition. The signal could be positive, negative or null explained by refractive index increment deviation.
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Affiliation(s)
- Marina Pons
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Marine Perenon
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Hugues Bonnet
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Emilie Gillon
- Univ. Grenoble Alpes, CERMAV-CNRS, 601 rue de la chimie, F-38610 Gières, France
| | - Celio Vallée
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Eric Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Nicolas Spinelli
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Jérôme Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
- FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
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6
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Marino V, Riva M, Zamboni D, Koch KW, Dell'Orco D. Bringing the Ca 2+ sensitivity of myristoylated recoverin into the physiological range. Open Biol 2021; 11:200346. [PMID: 33401992 PMCID: PMC7881174 DOI: 10.1098/rsob.200346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The prototypical Ca2+-sensor protein recoverin (Rec) is thought to regulate the activity of rhodopsin kinase (GRK1) in photoreceptors by switching from a relaxed (R) disc membrane-bound conformation in the dark to a more compact, cytosol-diffusing tense (T) conformation upon cell illumination. However, the apparent affinity for Ca2+ of its physiologically relevant form (myristoylated recoverin) is almost two orders of magnitude too low to support this mechanism in vivo. In this work, we compared the individual and synergistic roles of the myristic moiety, the GRK1 target and the disc membrane in modulating the calcium sensitivity of Rec. We show that the sole presence of the target or the disc membrane alone are not sufficient to achieve a physiological response to changes in intracellular [Ca2+]. Instead, the simultaneous presence of GRK1 and membrane allows the T to R transition to occur in a physiological range of [Ca2+] with high cooperativity via a conformational selection mechanism that drives the structural transitions of Rec in the presence of multiple ligands. Our conclusions may apply to other sensory transduction systems involving protein complexes and biological membranes.
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Affiliation(s)
- Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy
| | - Matteo Riva
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.,Department of Neuroscience, Division of Biochemistry, University of Oldenburg, 26111 Oldenburg, Germany
| | - Davide Zamboni
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.,Department of Neuroscience, Division of Biochemistry, University of Oldenburg, 26111 Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Division of Biochemistry, University of Oldenburg, 26111 Oldenburg, Germany
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy
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Abbas S, Koch KW. Quantitative Determination of Ca 2+-binding to Ca 2+-sensor Proteins by Isothermal Titration Calorimetry. Bio Protoc 2020; 10:e3580. [PMID: 33659550 DOI: 10.21769/bioprotoc.3580] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/19/2020] [Accepted: 01/21/2020] [Indexed: 01/29/2023] Open
Abstract
Diverse and complex molecular recognitions are central elements of signal transduction cascades. The strength and nature of these interaction modes can be determined by different experimental approaches. Among those, Isothermal titration calorimetry (ITC) offers certain advantages by providing binding constants and thermodynamic parameters from titration series without a need to label or immobilize one or more interaction partners. Furthermore, second messenger homeostasis involving Ca2+-ions requires in particular knowledge about stoichiometries and affinities of Ca2+-binding to Ca2+-sensor proteins or Ca2+-dependent regulators, which can be obtained by employing ITC. We used ITC to measure these parameters for a set of neuronal Ca2+-sensor proteins operating in photoreceptor cells. Here, we present a step wise protocol to (a) measure Ca2+ interaction with the Ca2+-sensor guanylate cyclase-activating protein 1, (b) to design an ITC experiment and prepare samples, (c) to remove Ca2+ nearly completely from Ca2+ binding proteins without using a chelating agent like EGTA.
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Affiliation(s)
- Seher Abbas
- Department of Neuroscience, Division of Biochemistry, University of Oldenburg, Oldenburg D-26129, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Division of Biochemistry, University of Oldenburg, Oldenburg D-26129, Germany
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Dal Cortivo G, Marino V, Iacobucci C, Vallone R, Arlt C, Rehkamp A, Sinz A, Dell'Orco D. Oligomeric state, hydrodynamic properties and target recognition of human Calcium and Integrin Binding protein 2 (CIB2). Sci Rep 2019; 9:15058. [PMID: 31636333 PMCID: PMC6803640 DOI: 10.1038/s41598-019-51573-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/12/2019] [Indexed: 11/23/2022] Open
Abstract
Calcium- and Integrin-Binding protein 2 (CIB2) is a small and ubiquitously expressed protein with largely unknown biological function but ascertained role in hearing physiology and disease. Recent studies found that CIB2 binds Ca2+ with moderate affinity and dimerizes under conditions mimicking the physiological ones. Here we provided new lines of evidence on CIB2 oligomeric state and the mechanism of interaction with the α7B integrin target. Based on a combination of native mass spectrometry, chemical cross-linking/mass spectrometry, analytical gel filtration, dynamic light scattering and molecular dynamics simulations we conclude that CIB2 is monomeric under all tested conditions and presents uncommon hydrodynamic properties, most likely due to the high content of hydrophobic solvent accessible surface. Surface plasmon resonance shows that the interaction with α7B occurs with relatively low affinity and is limited to the cytosolic region proximal to the membrane, being kinetically favored in the presence of physiological Mg2+ and in the absence of Ca2+. Although CIB2 binds to an α7B peptide in a 1:1 stoichiometry, the formation of the complex might induce binding of another CIB2 molecule.
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Affiliation(s)
- Giuditta Dal Cortivo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Rosario Vallone
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Anne Rehkamp
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy.
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9
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Abbas S, Marino V, Dell’Orco D, Koch KW. Molecular Recognition of Rhodopsin Kinase GRK1 and Recoverin Is Tuned by Switching Intra- and Intermolecular Electrostatic Interactions. Biochemistry 2019; 58:4374-4385. [DOI: 10.1021/acs.biochem.9b00846] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Seher Abbas
- Department of Neuroscience, Division of Biochemistry, University of Oldenburg, 26111 Oldenburg, Germany
| | - Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Daniele Dell’Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Division of Biochemistry, University of Oldenburg, 26111 Oldenburg, Germany
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Borsatto A, Marino V, Abrusci G, Lattanzi G, Dell'Orco D. Effects of Membrane and Biological Target on the Structural and Allosteric Properties of Recoverin: A Computational Approach. Int J Mol Sci 2019; 20:ijms20205009. [PMID: 31658639 PMCID: PMC6829511 DOI: 10.3390/ijms20205009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
Recoverin (Rec) is a prototypical calcium sensor protein primarily expressed in the vertebrate retina. The binding of two Ca2+ ions to the functional EF-hand motifs induces the extrusion of a myristoyl group that increases the affinity of Rec for the membrane and leads to the formation of a complex with rhodopsin kinase (GRK1). Here, unbiased all-atom molecular dynamics simulations were performed to monitor the spontaneous insertion of the myristoyl group into a model multicomponent biological membrane for both isolated Rec and for its complex with a peptide from the GRK1 target. It was found that the functional membrane anchoring of the myristoyl group is triggered by persistent electrostatic protein-membrane interactions. In particular, salt bridges between Arg43, Arg46 and polar heads of phosphatidylserine lipids are necessary to enhance the myristoyl hydrophobic packing in the Rec-GRK1 assembly. The long-distance communication between Ca2+-binding EF-hands and residues at the interface with GRK1 is significantly influenced by the presence of the membrane, which leads to dramatic changes in the connectivity of amino acids mediating the highest number of persistent interactions (hubs). In conclusion, specific membrane composition and allosteric interactions are both necessary for the correct assembly and dynamics of functional Rec-GRK1 complex.
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Affiliation(s)
- Alberto Borsatto
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.
- Department of Physics, University of Trento, 38123 Trento, Italy.
| | - Valerio Marino
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56026 Pisa, Italy.
| | - Gianfranco Abrusci
- Department of Physics, University of Trento, 38123 Trento, Italy.
- Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14, Povo, 38123 Trento, Italy.
| | - Gianluca Lattanzi
- Department of Physics, University of Trento, 38123 Trento, Italy.
- Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14, Povo, 38123 Trento, Italy.
| | - Daniele Dell'Orco
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy.
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Zang J, Neuhauss SCF. The Binding Properties and Physiological Functions of Recoverin. Front Mol Neurosci 2018; 11:473. [PMID: 30618620 PMCID: PMC6306944 DOI: 10.3389/fnmol.2018.00473] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Recoverin (Rcv) is a low molecular-weight, neuronal calcium sensor (NCS) primarily located in photoreceptor outer segments of the vertebrate retina. Calcium ions (Ca2+)-bound Rcv has been proposed to inhibit G-protein-coupled receptor kinase (GRKs) in darkness. During the light response, the Ca2+-free Rcv releases GRK, which in turn phosphorylates visual pigment, ultimately leading to the cessation of the visual transduction cascade. Technological advances over the last decade have contributed significantly to a deeper understanding of Rcv function. These include both biophysical and biochemical approaches that will be discussed in this review article. Furthermore, electrophysiological experiments uncovered additional functions of Rcv, such as regulation of the lifetime of Phosphodiesterase-Transducin complex. Recently, attention has been drawn to different roles in rod and cone photoreceptors.This review article focuses on Rcv binding properties to Ca2+, disc membrane and GRK, and its physiological functions in phototransduction and signal transmission.
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Affiliation(s)
- Jingjing Zang
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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12
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Elbers D, Scholten A, Koch KW. Zebrafish Recoverin Isoforms Display Differences in Calcium Switch Mechanisms. Front Mol Neurosci 2018; 11:355. [PMID: 30323742 PMCID: PMC6172410 DOI: 10.3389/fnmol.2018.00355] [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: 07/24/2018] [Accepted: 09/11/2018] [Indexed: 12/29/2022] Open
Abstract
Primary steps in vertebrate vision occur in rod and cone cells of the retina and require precise molecular switches in excitation, recovery, and adaptation. In particular, recovery of the photoresponse and light adaptation processes are under control of neuronal Ca2+ sensor (NCS) proteins. Among them, the Ca2+ sensor recoverin undergoes a pronounced Ca2+-dependent conformational change, a prototypical so-called Ca2+-myristoyl switch, which allows selective targeting of G protein-coupled receptor kinase. Zebrafish (Danio rerio) has gained attention as a model organism in vision research. It expresses four different recoverin isoforms (zRec1a, zRec1b, zRec2a, and zRec2b) that are orthologs to the one known mammalian variant. The expression pattern of the four isoforms cover both rod and cone cells, but the differential distribution in cones points to versatile functions of recoverin in these cell types. Initial functional studies on zebrafish larvae indicate different Ca2+-sensitive working modes for zebrafish recoverins, but experimental evidence is lacking so far. The aims of the present study are (1) to measure specific Ca2+-sensing properties of the different recoverin isoforms, (2) to ask whether switch mechanisms triggered by Ca2+ resemble that one observed with mammalian recoverin, and (3) to investigate a possible impact of an attached myristoyl moiety. For addressing these questions, we employ fluorescence spectroscopy, surface plasmon resonance (SPR), dynamic light scattering, and equilibrium centrifugation. Exposure of hydrophobic amino acids, due to the myristoyl switch, differed among isoforms and depended also on the myristoylation state of the particular recoverin. Ca2+-induced rearrangement of the protein-water shell was for all variants less pronounced than for the bovine ortholog indicating either a modified Ca2+-myristoyl switch or no switch. Our results have implications for a step-by-step response of recoverin isoforms to changing intracellular Ca2+ during illumination.
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Affiliation(s)
- Dana Elbers
- Department of Neuroscience, Biochemistry, University of Oldenburg, Oldenburg, Germany
| | - Alexander Scholten
- Department of Neuroscience, Biochemistry, University of Oldenburg, Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Biochemistry, University of Oldenburg, Oldenburg, Germany
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Dal Cortivo G, Wagner GE, Cortelletti P, Padmanabha Das KM, Zangger K, Speghini A, Dell'Orco D, Meyer NH. Luminescent and paramagnetic properties of nanoparticles shed light on their interactions with proteins. Sci Rep 2018; 8:3420. [PMID: 29467422 PMCID: PMC5821874 DOI: 10.1038/s41598-018-21571-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
Nanoparticles have been recognized as promising tools for targeted drug-delivery and protein therapeutics. However, the mechanisms of protein-nanoparticle interaction and the dynamics underlying the binding process are poorly understood. Here, we present a general methodology for the characterization of protein-nanoparticle interaction on a molecular level. To this end we combined biophysical techniques including nuclear magnetic resonance (NMR), circular dichroism (CD), resonance energy transfer (RET) and surface plasmon resonance (SPR). Particularly, we analyzed molecular mechanisms and dynamics of the interaction of CaF2 nanoparticles with the prototypical calcium sensor calmodulin (CaM). We observed the transient formation of an intermediate encounter complex involving the structural region linking the two domains. Specific interaction of CaM with CaF2 NPs is driven by the N-terminal EF-hands, which seem to recognize Ca2+ on the surface of the nanoparticle. We conclude that CaF2 NP-CaM interaction is fully compatible with potential applications in nanomedicine. Overall, the methods presented in this work can be extended to other systems and may be useful to quantitatively characterize structural and dynamic features of protein-NP interactions with important implications for nanomedicine and nano-biotechnology.
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Affiliation(s)
- Giuditta Dal Cortivo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, Strada le Grazie 8, Verona, Italy
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Paolo Cortelletti
- Nanomaterials Research Group, Department of Biotechnology, University of Verona and INSTM, UdR Verona, Strada Le Grazie 15, Verona, Italy
| | | | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010, Graz, Austria
| | - Adolfo Speghini
- Nanomaterials Research Group, Department of Biotechnology, University of Verona and INSTM, UdR Verona, Strada Le Grazie 15, Verona, Italy
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, Strada le Grazie 8, Verona, Italy.
| | - N Helge Meyer
- Department of Human Medicine and Department of Neuroscience, University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26131, Oldenburg, Germany.
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14
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Marino V, Borsatto A, Vocke F, Koch KW, Dell'Orco D. CaF 2 nanoparticles as surface carriers of GCAP1, a calcium sensor protein involved in retinal dystrophies. NANOSCALE 2017; 9:11773-11784. [PMID: 28785759 DOI: 10.1039/c7nr03288a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
CaF2-based nanoparticles (NP) are promising biocompatible tools for nanomedicine applications. The structure of the NP crystal lattice allows for specific interactions with Ca2+-binding proteins through their EF-hand cation binding motifs. Here we investigated the interaction of 23 nm citrate-coated CaF2 NP with a calcium sensor protein GCAP1 that is normally expressed in photoreceptor cells and involved in the regulation of the early steps of vision. Protein-NP interactions were thoroughly investigated for the wild type (WT) GCAP1 as well as for a variant carrying the Asp 100 to Glu mutation (D100E), which prevents the binding of Ca2+ to the highest affinity site and is linked to cone dystrophy. Circular dichroism and fluorescence spectroscopy showed that protein structure and Ca2+-sensing capability are conserved for both variants upon interaction with the NP surface, although the interaction mode depends on the specific occupation of Ca2+-binding sites. NP binding stabilizes the structure of the bound GCAP1 and occurs with nanomolar affinity, as probed by isothermal titration calorimetry. Surface plasmon resonance revealed a fully reversible binding compatible with physiologically relevant kinetics of protein release whereas biochemical assays indicated a residual capability for NP-dissociated GCAP1 to regulate the target retinal guanylate cyclase. Our study constitutes a proof of concept that CaF2 NP could be optimized to serve as biologically compatible carriers of high amounts of functional GCAP1 in photoreceptors affected by retinal dystrophies.
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Affiliation(s)
- Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy.
| | - Alberto Borsatto
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy.
| | - Farina Vocke
- Department of Neuroscience, Biochemistry Group, University of Oldenburg, Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Biochemistry Group, University of Oldenburg, Oldenburg, Germany
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy.
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Dell’Orco D, Koch KW. Fingerprints of Calcium-Binding Protein Conformational Dynamics Monitored by Surface Plasmon Resonance. ACS Chem Biol 2016; 11:2390-7. [PMID: 27380526 DOI: 10.1021/acschembio.6b00470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Surface plasmon resonance (SPR) spectroscopy is widely used to probe interactions involving biological macromolecules by detecting changes in the refractive index in a metal/dielectric interface following the dynamic formation of a molecular complex. In past years, SPR-based experimental approaches were developed to monitor conformational changes induced by the binding of small analytes to proteins coupled to the surface of commercially available sensor chips. A significant contribution to our understanding of the phenomenon came from the study of several Ca(2+)-sensor proteins operating in diverse cellular scenarios, in which the conformational switch is triggered by specific Ca(2+) signals. Structural and physicochemical analyses demonstrated that the SPR signal not only depends on the change in protein size upon Ca(2+)-binding but likely originates from variations in the hydration shell structure. The resulting changes in the dielectric properties of water or of the protein-water interface eventually reflect different crowding conditions on the SPR sensor chip, which mimic the cellular environment. SPR could hence be used to monitor conformational transitions in proteins, especially when a significant variation in the hydrophobicity of the solvent-exposed protein surface occurs, thus leading to changes in the dielectric milieu of the whole sensor chip surface. We review recent work in which SPR has been successfully employed to provide a fingerprint of the conformational change dynamics in proteins under native and altered conditions, which include post-translational modifications, copresence of competing analytes, and point mutations of single amino acids associated with genetic diseases.
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Affiliation(s)
- Daniele Dell’Orco
- Department
of Neurosciences, Biomedicine and Movement Sciences, Section of Biological
Chemistry, University of Verona, I-37134 Verona, Italy
| | - Karl-Wilhelm Koch
- Department
of Neurosciences, Biochemistry Group, University of Oldenburg, D-26111 Oldenburg, Germany
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Origin and prediction of free-solution interaction studies performed label-free. Proc Natl Acad Sci U S A 2016; 113:E1595-604. [PMID: 26960999 DOI: 10.1073/pnas.1515706113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Interaction/reaction assays have led to significant scientific discoveries in the biochemical, medical, and chemical disciplines. Several fundamental driving forces form the basis of intermolecular and intramolecular interactions in chemical and biochemical systems (London dispersion, hydrogen bonding, hydrophobic, and electrostatic), and in the past three decades the sophistication and power of techniques to interrogate these processes has developed at an unprecedented rate. In particular, label-free methods have flourished, such as NMR, mass spectrometry (MS), surface plasmon resonance (SPR), biolayer interferometry (BLI), and backscattering interferometry (BSI), which can facilitate assays without altering the participating components. The shortcoming of most refractive index (RI)-based label-free methods such as BLI and SPR is the requirement to tether one of the interaction entities to a sensor surface. This is not the case for BSI. Here, our hypothesis is that the signal origin for free-solution, label-free determinations can be attributed to conformation and hydration-induced changes in the solution RI. We propose a model for the free-solution response function (FreeSRF) and show that, when quality bound and unbound structural data are available, FreeSRF correlates well with the experiment (R(2)> 0.99, Spearman rank correlation coefficients >0.9) and the model is predictive within ∼15% of the experimental binding signal. It is also demonstrated that a simple mass-weighted dη/dC response function is the incorrect equation to determine that the change in RI is produced by binding or folding event in free solution.
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Astegno A, La Verde V, Marino V, Dell'Orco D, Dominici P. Biochemical and biophysical characterization of a plant calmodulin: Role of the N- and C-lobes in calcium binding, conformational change, and target interaction. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1864:297-307. [PMID: 26708477 DOI: 10.1016/j.bbapap.2015.12.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/29/2015] [Accepted: 12/09/2015] [Indexed: 12/22/2022]
Abstract
In plants, transient elevation of intracellular Ca(2+) concentration in response to abiotic stress is responsible for glutamate decarboxylase (GAD) activation via association with calmodulin (CaM), an EF-hand protein consisting of two homologous domains (N and C). An unusual 1:2 binding mode of CaM to CaM-binding domains of GAD has long been known, however the contribution of the two CaM domains in target recognition and activation remains to be clarified. Here, we explored the coupling between physicochemical properties of Arabidopsis CaM1 (AtCaM1) and Arabidopsis GAD1 activation, focusing on each AtCaM1 lobe. We found that the four EF-loops of AtCaM1 differently contribute to the ~20 μM apparent affinity for Ca(2+) and the C-lobe shows a ~6-fold higher affinity than N-lobe (Kd(app) 5.6 μM and 32 μM for C- and N-lobes, respectively). AtCaM1 responds structurally to Ca(2+) in a manner similar to vertebrate CaM based on comparison of Ca(2+)-induced changes in hydrophobicity exposure, secondary structure, and hydrodynamic behavior. Molecular dynamics simulations of AtCaM1 apo and Ca(2+)-bound reveal that the latter state is significantly less flexible, although regions of the N-lobe remain quite flexible; this suggests the importance of N-lobe for completing the transition to the extended structure of holoprotein, consistent with data from ANS fluorescence, CD spectroscopy, and SEC analysis. Moreover, enzymatic analysis reveal that mutations in the two lobes affect GAD1 activation in similar ways and only intact AtCaM1 can fully activate GAD1. Taken together, our data provide new insights into the CaM lobes role in interactions between CaM and plant GAD.
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Affiliation(s)
| | | | - Valerio Marino
- Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Daniele Dell'Orco
- Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Verona, Italy
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Sulmann S, Vocke F, Scholten A, Koch KW. Retina specific GCAPs in zebrafish acquire functional selectivity in Ca2+-sensing by myristoylation and Mg2+-binding. Sci Rep 2015; 5:11228. [PMID: 26061947 PMCID: PMC4462140 DOI: 10.1038/srep11228] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/18/2015] [Indexed: 11/09/2022] Open
Abstract
Zebrafish photoreceptor cells express six guanylate cyclase-activating proteins (zGCAPs) that share a high degree of amino acid sequence homology, but differ in Ca(2+)-binding properties, Ca(2+)-sensitive target regulation and spatial-temporal expression profiles. We here study a general problem in cellular Ca(2+)-sensing, namely how similar Ca(2+)-binding proteins achieve functional selectivity to control finely adjusted cellular responses. We investigated two parameters of critical importance for the trigger and switch function of guanylate cyclase-activating proteins: the myristoylation status and the occupation of Ca(2+)-binding sites with Mg(2+). All zGCAPs can be myristoylated in living cells using click chemistry. Myristoylation does not facilitate membrane binding of zGCAPs, but it significantly modified the regulatory properties of zGCAP2 and zGCAP5. We further determined for all zGCAPs at least two binding sites exhibiting high affinities for Ca(2+) with KD values in the submicromolar range, whereas for other zGCAPs (except zGCAP3) the affinity of the third binding site was in the micromolar range. Mg(2+) either occupied the low affinity Ca(2+)-binding site or it shifted the affinities for Ca(2+)-binding. Hydrodynamic properties of zGCAPs are more influenced by Ca(2+) than by Mg(2+), although to a different extent for each zGCAP. Posttranslational modification and competing ion-binding can tailor the properties of similar Ca(2+)-sensors.
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Affiliation(s)
- Stefan Sulmann
- Department of Neurosciences, Biochemistry Group, University of Oldenburg, D-26111-Oldenburg, Germany
| | - Farina Vocke
- Department of Neurosciences, Biochemistry Group, University of Oldenburg, D-26111-Oldenburg, Germany
| | - Alexander Scholten
- Department of Neurosciences, Biochemistry Group, University of Oldenburg, D-26111-Oldenburg, Germany
| | - Karl-Wilhelm Koch
- Department of Neurosciences, Biochemistry Group, University of Oldenburg, D-26111-Oldenburg, Germany
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19
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Chapleau RR, Frey JS, Riddle DS, Ruiz ON, Mauzy CA. Measuring Single-Domain Antibody Interactions with Epitopes in Jet Fuel Using Microscale Thermophoresis. ANAL LETT 2014. [DOI: 10.1080/00032719.2014.947535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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20
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Wu B, Liu G, Zhang G, Craig VSJ. Stiff chains inhibit and flexible chains promote protein adsorption to polyelectrolyte multilayers. SOFT MATTER 2014; 10:3806-3816. [PMID: 24718871 DOI: 10.1039/c4sm00413b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We tested the hypothesis that the level of protein adsorption onto polyelectrolyte multilayers (PEMs) is influenced by the chain stiffness of the polymers forming the multilayer. The implication being that by altering the chain stiffness, PEMs can be formed that promote or inhibit protein adsorption. Protein adsorption to PEMs consisting of flexible and semi-flexible polyelectrolytes was investigated. The flexible polyelectrolytes were poly(sodium 4-styrene sulfonate) (PSS) and poly(diallyldimethylammonium chloride) (PDDA) and the semi-flexible polyelectrolytes were sulfated chitosan (SC) and cationic guar gum (CGG). Polyelectrolytes were used in pairs to produce four types of polyelectrolyte multilayer films. Moreover, each of these films could be terminated with either of the polyelectrolytes resulting in protein adsorption being studied on 8 systems. Protein adsorption was investigated by optical reflectometry and quartz crystal microbalance with dissipation using bovine serum albumin as the test protein. We found that when a pair of semi-flexible polyelectrolytes was used very little protein adsorption took place, irrespective of which polyelectrolyte was used to terminate the film. When the film was formed by flexible polyelectrolytes, significant protein adsorption took place and the degree of adsorption depended strongly on which polyelectrolyte was used to terminate the film. We explain these observations by considering the conformation of the polyelectrolyte in the outermost region of the film and relate this to the flexibility of the polyelectrolyte chains employed to produce the polyelectrolyte multilayer.
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Affiliation(s)
- Bo Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, 230026, P. R. China.
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Invergo BM, Dell'Orco D, Montanucci L, Koch KW, Bertranpetit J. A comprehensive model of the phototransduction cascade in mouse rod cells. MOLECULAR BIOSYSTEMS 2014; 10:1481-9. [PMID: 24675755 DOI: 10.1039/c3mb70584f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Vertebrate visual phototransduction is perhaps the most well-studied G-protein signaling pathway. A wealth of available biochemical and electrophysiological data has resulted in a rich history of mathematical modeling of the system. However, while the most comprehensive models have relied upon amphibian biochemical and electrophysiological data, modern research typically employs mammalian species, particularly mice, which exhibit significantly faster signaling dynamics. In this work, we present an adaptation of a previously published, comprehensive model of amphibian phototransduction that can produce quantitatively accurate simulations of the murine photoresponse. We demonstrate the ability of the model to predict responses to a wide range of stimuli and under a variety of mutant conditions. Finally, we employ the model to highlight a likely unknown mechanism related to the interaction between rhodopsin and rhodopsin kinase.
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Affiliation(s)
- Brandon M Invergo
- IBE - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
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22
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Sulmann S, Dell'Orco D, Marino V, Behnen P, Koch KW. Conformational Changes in Calcium-Sensor Proteins under Molecular Crowding Conditions. Chemistry 2014; 20:6756-62. [DOI: 10.1002/chem.201402146] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Indexed: 11/05/2022]
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23
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Marino V, Astegno A, Pedroni M, Piccinelli F, Dell'Orco D. Nanodevice-induced conformational and functional changes in a prototypical calcium sensor protein. NANOSCALE 2014; 6:412-423. [PMID: 24213152 DOI: 10.1039/c3nr04978g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Calcium (Ca(2+)) plays a major role in a variety of cellular processes. Fine changes in its concentration are detected by calcium sensor proteins, which adopt specific conformations to regulate their molecular targets. Here, two distinct nanodevices were probed as biocompatible carriers of Ca(2+)-sensors and the structural and functional effects of protein-nanodevice interactions were investigated. The prototypical Ca(2+)-sensor recoverin (Rec) was incubated with 20-25 nm CaF2 nanoparticles (NPs) and 70-80 nm liposomes with lipid composition similar to that found in photoreceptor cells. Circular dichroism and fluorescence spectroscopy were used to characterize changes in the protein secondary and tertiary structure and in thermal stability upon interaction with the nanodevice, both in the presence and in the absence of free Ca(2+). Variations in the hydrodynamic diameter of the complex were measured by dynamic light scattering and the residual capability of the protein to act as a Ca(2+)-sensor in the presence of NPs was estimated spectroscopically. The conformation, thermal stability and Ca(2+)-sensing capability of Rec were all significantly affected by the presence of NPs, while liposomes did not significantly perturb Rec conformation and function, allowing reversible binding. NP-bound Rec maintained an all-helical fold but showed lower thermal stability and high cooperativity of unfolding. Our analysis can be proficiently used to validate the biocompatibility of other nanodevices intended for biomedical applications involving Ca(2+)-sensors.
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Affiliation(s)
- Valerio Marino
- Department of Life Sciences and Reproduction, Section of Biological Chemistry, University of Verona, Verona, Italy.
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24
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Palau W, Masante C, Ventura M, Di Primo C. Direct evidence for RNA-RNA interactions at the 3' end of the Hepatitis C virus genome using surface plasmon resonance. RNA (NEW YORK, N.Y.) 2013; 19:982-991. [PMID: 23651615 PMCID: PMC3683932 DOI: 10.1261/rna.037606.112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 03/11/2013] [Indexed: 06/02/2023]
Abstract
Surface plasmon resonance was used to investigate two previously described interactions analyzed by reverse genetics and complementation mutation experiments, involving 5BSL3.2, a stem-loop located in the NS5B coding region of HCV. 5BSL3.2 was immobilized on a sensor chip by streptavidin-biotin coupling, and its interaction either with the SL2 stem-loop of the 3' end or with an upstream sequence centered on nucleotide 9110 (referred to as Seq9110) was monitored in real-time. In contrast with previous results obtained by NMR assays with the same short RNA sequences that we used or SHAPE analysis with longer RNAs, we demonstrate that recognition between 5BSL3.2 and SL2 can occur in solution through a kissing-loop interaction. We show that recognition between Seq9110 and the internal loop of 5BSL3.2 does not prevent binding of SL2 on the apical loop of 5BSL3.2 and does not influence the rate constants of the SL2-5BSL3.2 complex. Therefore, the two binding sites of 5BSL3.2, the apical and internal loops, are structurally independent and both interactions can coexist. We finally show that the stem-loop SL2 is a highly dynamic RNA motif that fluctuates between at least two conformations: One is able to hybridize with 5BSL3.2 through loop-loop interaction, and the other one is capable of self-associating in the absence of protein, reinforcing the hypothesis of SL2 being a dimerization sequence. This result suggests also that the conformational dynamics of SL2 could play a crucial role for controlling the destiny of the genomic RNA.
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Affiliation(s)
- William Palau
- Université de Bordeaux, Laboratoire ARNA, F-33000 Bordeaux, France
- INSERM, U869, Laboratoire ARNA, F-33600 Pessac, France
| | - Cyril Masante
- Université de Bordeaux, Laboratoire MFP-UMR5234, F-33000 Bordeaux, France
- CNRS UMR 5234, Laboratoire MFP-UMR5234, F-33000 Bordeaux, France
| | - Michel Ventura
- Université de Bordeaux, Laboratoire MFP-UMR5234, F-33000 Bordeaux, France
- CNRS UMR 5234, Laboratoire MFP-UMR5234, F-33000 Bordeaux, France
| | - Carmelo Di Primo
- Université de Bordeaux, Laboratoire ARNA, F-33000 Bordeaux, France
- INSERM, U869, Laboratoire ARNA, F-33600 Pessac, France
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Invergo BM, Montanucci L, Koch KW, Bertranpetit J, Dell'orco D. Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling. Cell Commun Signal 2013; 11:36. [PMID: 23693153 PMCID: PMC3732082 DOI: 10.1186/1478-811x-11-36] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/09/2013] [Indexed: 01/20/2023] Open
Abstract
Background Phototransduction in vertebrate photoreceptor cells represents a paradigm of signaling pathways mediated by G-protein-coupled receptors (GPCRs), which share common modules linking the initiation of the cascade to the final response of the cell. In this work, we focused on the recovery phase of the visual photoresponse, which is comprised of several interacting mechanisms. Results We employed current biochemical knowledge to investigate the response mechanisms of a comprehensive model of the visual phototransduction pathway. In particular, we have improved the model by implementing a more detailed representation of the recoverin (Rec)-mediated calcium feedback on rhodopsin kinase and including a dynamic arrestin (Arr) oligomerization mechanism. The model was successfully employed to investigate the rate limiting steps in the recovery of the rod photoreceptor cell after illumination. Simulation of experimental conditions in which the expression levels of rhodospin kinase (RK), of the regulator of the G-protein signaling (RGS), of Arr and of Rec were altered individually or in combination revealed severe kinetic constraints to the dynamics of the overall network. Conclusions Our simulations confirm that RGS-mediated effector shutdown is the rate-limiting step in the recovery of the photoreceptor and show that the dynamic formation and dissociation of Arr homodimers and homotetramers at different light intensities significantly affect the timing of rhodopsin shutdown. The transition of Arr from its oligomeric storage forms to its monomeric form serves to temper its availability in the functional state. Our results may explain the puzzling evidence that overexpressing RK does not influence the saturation time of rod cells at bright light stimuli. The approach presented here could be extended to the study of other GPCR signaling pathways.
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Affiliation(s)
- Brandon M Invergo
- Department of Life Sciences and Reproduction, Section of Biological Chemistry and Center for BioMedical Computing (CBMC), University of Verona, Strada le Grazie 8, 37134, Verona, Italy.
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Fries R, Scholten A, Säftel W, Koch KW. Operation profile of zebrafish guanylate cyclase-activating protein 3. J Neurochem 2012; 121:54-65. [PMID: 22212098 DOI: 10.1111/j.1471-4159.2011.07643.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The expression pattern and property profile of the neuronal Ca(2+) sensor guanylate cyclase-activating protein 3 (zGCAP3) was studied by immunochemical approaches, biophysical methods and enzymatic assays. Using affinity purified antibodies immunoreactivity towards zGCAP3 was weakly detected in the outer and strongly in the inner segments of cone cells as well as in the outer plexiform layer, to a lesser degree also in the inner plexiform and ganglion cell layer of the zebrafish retina. This cellular distribution was independent of a dark/light cycle. Some neuronal Ca(2+) sensors are acylated (mainly myristoylated) at the amino-terminus. Probing larval and adult stages of the developing zebrafish retina indicated that zGCAP3 was first expressed in a non-myristoylated form, but was finally present in the adult retina as a myristoylated protein. While zGCAP3 did not undergo a classical Ca(2+) -myristoyl switch as investigated by surface plasmon resonance spectroscopy, myristoylation had two main other consequences: it enhanced the Ca(2+) -sensitivity of the Ca(2+) -induced conformational change and it stabilized the protein conformation. Differences between myristoylated and non-myristoylated zGCAP3 were also observed in modulating the kinetic and catalytic parameters of the GCAP-target, a membrane bound guanylate cyclase. Thus, the stabilizing effect of the myristoyl group is apparently less important in the larval than in the adult fish.
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Affiliation(s)
- Ramona Fries
- Biochemistry group, Institute of Biology and Environmental Science, Faculty V, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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Dell'Orco D, Sulmann S, Linse S, Koch KW. Dynamics of conformational Ca2+-switches in signaling networks detected by a planar plasmonic device. Anal Chem 2012; 84:2982-9. [PMID: 22404528 DOI: 10.1021/ac300213j] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ca(2+)-sensor proteins regulate a variety of intracellular processes by adopting specific conformations in response to finely tuned changes in Ca(2+)-concentration. Here we present a surface plasmon resonance (SPR)-based approach, which allows for simultaneous detection of conformational dynamics of four Ca(2+)-sensor proteins (calmodulin, recoverin, GCAP1, and GCAP2) operating in the vertebrate phototransduction cascade, over variations in Ca(2+) concentration in the 0.1-0.6 μM range. By working at conditions that quantitatively mimic those found in the cell, we show that the method is able to detect subtle differences in the dynamics of each Ca(2+)-sensor, which appear to be influenced by the presence of free Mg(2+) at physiological concentration and by posttranslational modifications such as myristoylation. Comparison between the macroscopic Ca(2+)-binding constants, directly measured by competition with a chromophoric chelator, and the concerted binding-conformational switch detected by SPR at equilibrium reveals the relative contribution of the conformational change process to the SPR signal. This process appears to be influenced by the presence of other cations that perturb Ca(2+)-binding and the conformational transition by competing with Ca(2+), or by pure electrostatic screening. In conclusion, the approach described here allows a comparative analysis of protein conformational changes occurring under physiologically relevant molecular crowding conditions in ultrathin biosensor layers.
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Affiliation(s)
- Daniele Dell'Orco
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany.
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Biophysical investigation of retinal calcium sensor function. Biochim Biophys Acta Gen Subj 2011; 1820:1228-33. [PMID: 22020050 DOI: 10.1016/j.bbagen.2011.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/05/2011] [Accepted: 10/06/2011] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neuronal calcium sensor proteins represent a subgroup of the family of EF-hand calcium binding proteins. Members of this subgroup are the guanylate cyclase-activating proteins and recoverin, which operate as important calcium sensors in retinal photoreceptor cells. Physiological and biochemical data indicate that these proteins participate in shaping the photoreceptor light response. SCOPE OF REVIEW Biophysical methods have been widely applied to investigate the molecular properties of retinal calcium binding proteins like the guanylate cyclase-activating proteins and recoverin. Properties include the determination of calcium affinities by isotope techniques and spectroscopical approaches. Conformational changes are investigated for example by tryptophan fluorescence emission. A special focus of this review is laid on a new experimental approach to study conformational changes in calcium binding proteins by surface plasmon resonance spectroscopy. In addition this technique has been employed for measuring the calcium-dependent binding of calcium sensors to membranes. MAJOR CONCLUSIONS Biophysical approaches provide valuable information about key properties of calcium sensor proteins involved in intracellular signalling. Parameters of their molecular properties like calcium binding and conformational changes help to define their physiological role derived from cellular, genetic or physiological studies. GENERAL SIGNIFICANCE Calcium is an important second messenger in intracellular signaling. Calcium signals are propagated via calcium binding proteins that are able to discriminate between incremental differences in intracellular calcium and that regulate their targets with high precision and specificity. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signalling.
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