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Zeng C, Lu Y, Wei X, Sun L, Wei L, Ou S, Huang Q, Wu Y. Parvalbumin Regulates GAD Expression through Calcium Ion Concentration to Affect the Balance of Glu-GABA and Improve KA-Induced Status Epilepticus in PV-Cre Transgenic Mice. ACS Chem Neurosci 2024; 15:1951-1966. [PMID: 38696478 DOI: 10.1021/acschemneuro.3c00600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024] Open
Abstract
Aims: the study aimed to (i) use adeno-associated virus technology to modulate parvalbumin (PV) gene expression, both through overexpression and silencing, within the hippocampus of male mice and (ii) assess the impact of PV on the metabolic pathway of glutamate and γ-aminobutyric acid (GABA). Methods: a status epilepticus (SE) mouse model was established by injecting kainic acid into the hippocampus of transgenic mice. When the seizures of mice reached SE, the mice were killed at that time point and 30 min after the onset of SE. Hippocampal tissues were extracted and the mRNA and protein levels of PV and the 65 kDa (GAD65) and 67 kDa (GAD67) isoforms of glutamate decarboxylase were assessed using real-time quantitative polymerase chain reaction and Western blot, respectively. The concentrations of glutamate and GABA were detected with high-performance liquid chromatography (HPLC), and the intracellular calcium concentration was detected using flow cytometry. Results: we demonstrate that the expression of PV is associated with GAD65 and GAD67 and that PV regulates the levels of GAD65 and GAD67. PV was correlated with calcium concentration and GAD expression. Interestingly, PV overexpression resulted in a reduction in calcium ion concentration, upregulation of GAD65 and GAD67, elevation of GABA concentration, reduction in glutamate concentration, and an extension of seizure latency. Conversely, PV silencing induced the opposite effects. Conclusion: parvalbumin may affect the expression of GAD65 and GAD67 by regulating calcium ion concentration, thereby affecting the metabolic pathways associated with glutamate and GABA. In turn, this contributes to the regulation of seizure activity.
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Affiliation(s)
- Chunmei Zeng
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, #6 Shuangyong Road,Nanning, Guangxi 530021, China
| | - Yuling Lu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, #6 Shuangyong Road,Nanning, Guangxi 530021, China
| | - Xing Wei
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, #6 Shuangyong Road,Nanning, Guangxi 530021, China
| | - Lanfeng Sun
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, #6 Shuangyong Road,Nanning, Guangxi 530021, China
| | - Lei Wei
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, #6 Shuangyong Road,Nanning, Guangxi 530021, China
| | - Sijie Ou
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, #6 Shuangyong Road,Nanning, Guangxi 530021, China
| | - Qi Huang
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, #6 Shuangyong Road,Nanning, Guangxi 530021, China
| | - Yuan Wu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, #6 Shuangyong Road,Nanning, Guangxi 530021, China
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2
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Saridakis E, Donta K. Protein Thermodynamic Properties, Crystallisation, and the Hofmeister Series. Chempluschem 2024:e202300733. [PMID: 38702291 DOI: 10.1002/cplu.202300733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
The Hofmeister series is a series of ions ordered according to their ability to precipitate proteins. It has also been linked to a host of (bio)chemical phenomena. Several attempts over the years to correlate the series to the varying success of different salts in crystallising proteins have been largely inconclusive. A correlation, based on published data and crystallisation conditions for several proteins, is proposed here between some thermodynamic properties of proteins and the position in the Hofmeister series of the salts from which they preferentially crystallise. Namely, a high ratio between the entropic or enthalpic protein-solvent interactions contribution to thermodynamic stability and the total thermodynamic stability of a given protein, indicate the protein's high propensity to crystallise in solutions of highly kosmotropic salts. Low such ratios on the other hand, indicate that chaotropic salts can be equally successful, i. e. that the protein in question is rather indifferent to the Hofmeister character of the salt. Testing various model proteins for crystallisation against screens containing salts found at different points on the Hofmeister series, as well as further bibliographic analysis, have yielded results that appear to largely corroborate this hypothesis. These conclusions may conceivably be used as a crystallisation predictive tool.
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Affiliation(s)
- Emmanuel Saridakis
- Institute of Nanoscience & Nanotechnology, National Centre for Scientific Research "Demokritos", Neapoleos 27, Ag. Paraskevi, Athens, 15341, Greece
| | - Katerina Donta
- Institute of Nanoscience & Nanotechnology, National Centre for Scientific Research "Demokritos", Neapoleos 27, Ag. Paraskevi, Athens, 15341, Greece
- Department of Chemistry, University of Athens, Panepistimiopolis, Athens, 15771, Greece
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3
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Lai R, Li G, Cui Q. Flexibility of Binding Site is Essential to the Ca 2+ Selectivity in EF-Hand Calcium-Binding Proteins. J Am Chem Soc 2024; 146:7628-7639. [PMID: 38456823 PMCID: PMC11102802 DOI: 10.1021/jacs.3c13981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
High binding affinity and selectivity of metal ions are essential to the function of metalloproteins. Thus, understanding the factors that determine these binding characteristics is of major interest for both fundamental mechanistic investigations and guiding of the design of novel metalloproteins. In this work, we perform QM cluster model calculations and quantum mechanics/molecular mechanics (QM/MM) free energy simulations to understand the binding selectivity of Ca2+ and Mg2+ in the wild-type carp parvalbumin and its mutant. While a nonpolarizable MM model (CHARMM36) does not lead to the correct experimental trend, treatment of the metal binding site with the DFTB3 model in a QM/MM framework leads to relative binding free energies (ΔΔGbind) comparable with experimental data. For the wild-type (WT) protein, the calculated ΔΔGbind is ∼6.6 kcal/mol in comparison with the experimental value of 5.6 kcal/mol. The good agreement highlights the value of a QM description of the metal binding site and supports the role of electronic polarization and charge transfer to metal binding selectivity. For the D51A/E101D/F102W mutant, different binding site models lead to considerable variations in computed binding affinities. With a coordination number of seven for Ca2+, which is shown by QM/MM metadynamics simulations to be the dominant coordination number for the mutant, the calculated relative binding affinity is ∼4.8 kcal/mol, in fair agreement with the experimental value of 1.6 kcal/mol. The WT protein is observed to feature a flexible binding site that accommodates a range of coordination numbers for Ca2+, which is essential to the high binding selectivity for Ca2+ over Mg2+. In the mutant, the E101D mutation reduces the flexibility of the binding site and limits the dominant coordination number of Ca2+ to be seven, thereby leading to reduced binding selectivity against Mg2+. Our results highlight that the binding selectivity of metal ions depends on both the structural and dynamical properties of the protein binding site.
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Affiliation(s)
- Rui Lai
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Guohui Li
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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4
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Ino Y, Ohira T, Kumagai K, Nakai Y, Akiyama T, Moriyama K, Takeda Y, Saito T, Ryo A, Inaba Y, Hirano H, Kimura Y. Identification of mouse soleus muscle proteins altered in response to changes in gravity loading. Sci Rep 2023; 13:15768. [PMID: 37737267 PMCID: PMC10517164 DOI: 10.1038/s41598-023-42875-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023] Open
Abstract
Gravity-dependent physical processes strongly affect the ability of elderly people to maintain musculoskeletal health by reducing muscle atrophy and increasing bone mineral density, thereby increasing quality of life. A need therefore exists to identify molecules in the musculoskeletal system that are responsive to gravitational loading and to establish an objective indicator for the maintenance of healthy musculoskeletal systems. Here, we performed an integrated assessment of the results of soleus muscle proteomic analyses in three model mouse experiments under different gravity environments (hypergravity, hindlimb unloading, and spaceflight). Myl6b, Gpd1, Fbp2, Pvalb, and Actn3 were shown to be gravity-responsive muscle proteins, and alterations in the levels of these proteins indicated changes in muscle fiber type to slow-twitch type due to gravity loading. In addition, immunoblotting and enzyme-linked immunosorbent assays revealed that Pvalb levels in the sera of hindlimb-unloaded mice and osteoporosis patients were higher than in control subjects, suggesting that Pvalb levels might be useful to objectively evaluate soleus muscle atrophy and bone loss.
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Affiliation(s)
- Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Takashi Ohira
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-Ku, Yokohama, 236-0004, Japan.
- Department of Physiology and Regenerative Medicine, Kindai University Faculty of Medicine, Ohno-Higashi 377-2, Osaka-Sayama, Osaka, Japan.
| | - Ken Kumagai
- Department of Orthopaedic Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Yusuke Nakai
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Tomoko Akiyama
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Kayano Moriyama
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Yuriko Takeda
- Department of Biostatistics, Yokohama City University School of Medicine, Yokohama, Japan
| | | | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Yutaka Inaba
- Department of Orthopaedic Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-Ku, Yokohama, 236-0004, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-Ku, Yokohama, 236-0004, Japan.
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5
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Mazumder M, Kumar S, Kumar D, Bhattacharya A, Gourinath S. Machine learning-based modulation of Ca 2+-binding affinity in EF-hand proteins and comparative structural insights into site-specific cooperative binding. Int J Biol Macromol 2023; 248:125866. [PMID: 37473887 DOI: 10.1016/j.ijbiomac.2023.125866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
Ca2+-binding proteins are present in almost all living organisms and different types display different levels of binding affinities for the cation. Here, we report two new scoring schemes enabling the user to estimate and manipulate the calcium binding affinities in EF hand containing proteins. To validate this, we designed a unique EF-hand loop capable of binding calcium with high affinity by altering five residues. The N-terminal domain of Entamoeba histolytica calcium-binding protein1 (NtEhCaBP1) is used for site-directed mutagenesis to incorporate the designed loop sequence into the second EF-hand motif of this protein, referred as Nt-EhCaBP1-EF2 mutant. The binding isotherms calculated using ITC calorimetry showed that Nt-EhCaBP1-EF2 mutant site binds Ca2+ with higher affinity than Wt-Nt-EhCaBP1, by ∼600 times. The crystal structure of the mutant displayed more compact Ca2+-coordination spheres in both of its EF loops than the structure of the wildtype protein. The compact coordination sphere of EF-2 causes the bend in the helix-3, which leads to the formation of unexpected hexamer of NtEhCaBP1-EF2 mutant structure. Further dynamic correlation analysis revealed that the mutation in the second EF loop changed the entire residue network of the monomer, resulting in stronger coordination of Ca2+ even in another EF-hand loop.
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Affiliation(s)
- Mohit Mazumder
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Pine Biotech, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Sanjeev Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, Nashville, TN 37232-0146, USA
| | - Devbrat Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - S Gourinath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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6
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Hao F, Bu Y, Huang S, Li W, Feng H, Wang Y. Effects of pyrethroids on the cerebellum and related mechanisms: a narrative review. Crit Rev Toxicol 2023; 53:229-243. [PMID: 37417402 DOI: 10.1080/10408444.2023.2229384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023]
Abstract
Pyrethroids (PYRs) are a group of synthetic organic chemicals that mimic natural pyrethrins. Due to their low toxicity and persistence in mammals, they are widely used today. PYRs exhibit higher lipophilicity than other insecticides, which allows them to easily penetrate the blood-brain barrier and directly induce toxic effects on the central nervous system. Several studies have shown that the cerebellum appears to be one of the regions with the largest changes in biomarkers. The cerebellum, which is extremely responsive to PYRs, functions as a crucial region for storing motor learning memories. Exposure to low doses of various types of PYRs during rat development resulted in diverse long-term effects on motor activity and coordination functions. Reduced motor activity may result from developmental exposure to PYRs in rats, as indicated by delayed cerebellar morphogenesis and maturation. PYRs also caused adverse histopathological and biochemical changes in the cerebellum of mothers and their offspring. By some studies, PYRs may affect granule cells and Purkinje cells, causing damage to cerebellar structures. Destruction of cerebellar structures and morphological defects in Purkinje cells are known to be directly related to functional impairment of motor coordination. Although numerous data support that PYRs cause damage to cerebellar structures, function and development, the mechanisms are not completely understood and require further in-depth studies. This paper reviews the available evidence on the relationship between the use of PYRs and cerebellar damage and discusses the mechanisms of PYRs.
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Affiliation(s)
- Fei Hao
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education, China Medical University, Shenyang, P.R. China
- Department of Occupational and Environmental Health, School of Public Health, China Medical University, Shenyang, P.R. China
| | - Ye Bu
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education, China Medical University, Shenyang, P.R. China
- Department of Occupational and Environmental Health, School of Public Health, China Medical University, Shenyang, P.R. China
| | - Shasha Huang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education, China Medical University, Shenyang, P.R. China
- Department of Occupational and Environmental Health, School of Public Health, China Medical University, Shenyang, P.R. China
| | - Wanqi Li
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education, China Medical University, Shenyang, P.R. China
- Department of Occupational and Environmental Health, School of Public Health, China Medical University, Shenyang, P.R. China
| | - Huiwen Feng
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education, China Medical University, Shenyang, P.R. China
- Department of Occupational and Environmental Health, School of Public Health, China Medical University, Shenyang, P.R. China
| | - Yuan Wang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention, Ministry of Education, China Medical University, Shenyang, P.R. China
- Department of Occupational and Environmental Health, School of Public Health, China Medical University, Shenyang, P.R. China
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7
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Nikolova V, Kircheva N, Dobrev S, Angelova S, Dudev T. Lanthanides as Calcium Mimetic Species in Calcium-Signaling/Buffering Proteins: The Effect of Lanthanide Type on the Ca2+/Ln3+ Competition. Int J Mol Sci 2023; 24:ijms24076297. [PMID: 37047269 PMCID: PMC10094714 DOI: 10.3390/ijms24076297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Lanthanides, the 14 4f-block elements plus Lanthanum, have been extensively used to study the structure and biochemical properties of metalloproteins. The characteristics of lanthanides within the lanthanide series are similar, but not identical. The present research offers a systematic investigation of the ability of the entire Ln3+ series to substitute for Ca2+ in biological systems. A well-calibrated DFT/PCM protocol is employed in studying the factors that control the metal selectivity in biological systems by modeling typical calcium signaling/buffering binding sites and elucidating the thermodynamic outcome of the competition between the “alien” La3+/Ln3+ and “native” Ca2+, and La3+ − Ln3+ within the lanthanide series. The calculations performed reveal that the major determinant of the Ca2+/Ln3+ selectivity in calcium proteins is the net charge of the calcium binding pocket; the more negative the charge, the higher the competitiveness of the trivalent Ln3+ with respect to its Ca2+ contender. Solvent exposure of the binding site also influences the process; buried active centers with net charge of −4 or −3 are characterized by higher Ln3+ over Ca2+ selectivity, whereas it is the opposite for sites with overall charge of −1. Within the series, the competition between La3+ and its fellow lanthanides is determined by the balance between two competing effects: electronic (favoring heavier lanthanides) and solvation (generally favoring the lighter lanthanides).
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Affiliation(s)
- Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1164 Sofia, Bulgaria
| | - Nikoleta Kircheva
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1164 Sofia, Bulgaria
- Correspondence:
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Retinoic Acid Prevents the Neuronal Damage Through the Regulation of Parvalbumin in an Ischemic Stroke Model. Neurochem Res 2023; 48:487-501. [PMID: 36245066 DOI: 10.1007/s11064-022-03769-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 02/04/2023]
Abstract
Ischemic stroke is a neurological disease that causes brain damage by increasing oxidative stress and ion imbalance. Retinoic acid is a major metabolite of vitamin A and regulates oxidative stress, calcium homeostasis, and cell death. Intracellular calcium is involved in neuronal growth and synaptic plasticity. Parvalbumin is a calcium-binding protein that is mainly expressed in brain. In this study, we investigated whether retinoic acid has neuroprotective effects by controlling intracellular calcium concentration and parvalbumin expression in ischemic brain damage. Middle cerebral artery occlusion (MCAO) was performed to induce cerebral ischemia. Retinoic acid (5 mg/kg) or vehicle was injected into the abdominal cavity for four days before surgery and cerebral cortices were collected 24 h after MCAO for further studies. MCAO damage induced neurological deficits and histopathological changes and decreased parvalbumin expression. However, retinoic acid treatment alleviated these changes. In cultured neurons, glutamate (5 mM) exposure induced neuronal cell death, increased intracellular calcium concentration, and decreased parvalbumin expression. Retinoic acid treatment attenuated these changes against glutamate toxicity in a dose-dependent manner. It also regulates glutamate induced change in bcl-2 and bax expression. The mitigation effects of retinoic acid were greater under non-transfection conditions than under parvalbumin siRNA transfection conditions. Our findings showed that retinoic acid modulates intracellular calcium concentration and parvalbumin expression and prevents apoptosis in ischemic brain injury. In conclusion, retinoic acid contributes to the preservation of neurons from ischemic stroke by controlling parvalbumin expression and apoptosis-related proteins.
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9
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Identification of radiation responsive RBC membrane associated proteins (RMAPs) in whole-body γ-irradiated New Zealand white rabbits. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2023; 37:e00783. [PMID: 36718137 PMCID: PMC9883204 DOI: 10.1016/j.btre.2023.e00783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/27/2022] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
This study is aimed to identify radiation-responsive RBC Membrane Associated Proteins (RMAPs) in Rabbits in vivo. Male New Zealand White rabbits were exposed to a single acute total body γ-radiation dose of 2 Gy at a dose rate of 0.746 Gy/min. Following this, at early time points of 6 h till the 7 d, RMAPs were collected and analyzed by MALDI-TOF-MS. Bioinformatics analysis was conducted to explore the biological functions of these proteins. Based on fold change, radiation responsiveness, GO, pathway enrichment, and hub position in the PPI network, we identified seven RMAPs as potential biomarker candidates viz., PVALB, PRKCB, GPD1, CP2G1, CSNK2B, ATP1B1, TPI1. As per KEGG enrichment, most of the proteins were implicated in cellular radiation response, oxidative damage, DNA repair, apoptosis, immune response, and cell signaling. This study forms the foundation for RMAPs-based Proteomic strategies for high throughput radiation bio-dosimetry for triage in the case of a radiological/nuclear incident.
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10
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Zeng C, Lei D, Lu Y, Huang Q, Wu Y, Yang S, Wu Y. Parvalbumin in the metabolic pathway of glutamate and γ-aminobutyric acid: Influence on expression of GAD65 and GAD67. Arch Biochem Biophys 2023; 734:109499. [PMID: 36587827 DOI: 10.1016/j.abb.2022.109499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Parvalbumin-expressing neurons are a type of inhibitory intermediate neuron that play an important role in terminating seizures. The aim of the present study was to use lentiviral construction and packaging technology to overexpress and silence the parvalbumin gene in pheochromocytoma (PC12) cells, and to evaluate how parvalbumin influences the metabolic pathway involving glutamate and γ-aminobutyric acid (GABA). In this work, Immunofluorescence staining was used to verify the differentiation of PC12 cells into neurons after adding nerve growth factor (NGF). Western blotting and real-time quantitative polymerase chain reaction (qRT-PCR) were used to confirm lentivirus-mediated knockdown or overexpression of parvalbumin. Expression of parvalbumin, the 65-kDa GAD isoform (GAD65), and the 67-kDa GAD isoform (GAD67) in neuronal cells was examined at the mRNA and protein levels using qRT-PCR, western blotting and immunofluorescence staining, while intracellular glutamate and GABA levels were determined by high performance liquid chromatography (HPLC). We demonstrate that the expression of parvalbumin is associated with GAD65 and GAD67. Interestingly, overexpression of parvalbumin up-regulated GAD65 and GAD67, increased GABA concentration, and decreased glutamate concentration. Silencing of parvalbumin led to the opposite effects. Altogether, parvalbumin affected the expression of GAD65 and GAD67, thereby influencing the metabolic pathway involving glutamate and GABA.
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Affiliation(s)
- Chunmei Zeng
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, #6 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Danqing Lei
- Experimental Center of Life Sciences Institutes, Guangxi Medical University, #22 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Yuling Lu
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, #6 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Qi Huang
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, #6 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Ying Wu
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, #6 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Shengyu Yang
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, #6 Shuangyong Road, Nanning, 530021, Guangxi, China
| | - Yuan Wu
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, #6 Shuangyong Road, Nanning, 530021, Guangxi, China.
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11
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Parvalbumin: A Major Fish Allergen and a Forensically Relevant Marker. Genes (Basel) 2023; 14:genes14010223. [PMID: 36672964 PMCID: PMC9858982 DOI: 10.3390/genes14010223] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Parvalbumins (PVALBs) are low molecular weight calcium-binding proteins. In addition to their role in many biological processes, PVALBs play an important role in regulating Ca2+ switching in muscles with fast-twitch fibres in addition to their role in many biological processes. The PVALB gene family is divided into two gene types, alpha (α) and beta (β), with the β gene further divided into two gene types, beta1 (β1) and beta2 (β2), carrying traces of whole genome duplication. A large variety of commonly consumed fish species contain PVALB proteins which are known to cause fish allergies. More than 95% of all fish-induced food allergies are caused by PVALB proteins. The authentication of fish species has become increasingly important as the seafood industry continues to grow and the growth brings with it many cases of food fraud. Since the PVALB gene plays an important role in the initiation of allergic reactions, it has been used for decades to develop alternate assays for fish identification. A brief review of the significance of the fish PVALB genes is presented in this article, which covers evolutionary diversity, allergic properties, and potential use as a forensic marker.
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12
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Studying Peptide-Metal Ion Complex Structures by Solution-State NMR. Int J Mol Sci 2022; 23:ijms232415957. [PMID: 36555599 PMCID: PMC9782655 DOI: 10.3390/ijms232415957] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Metal chelation can provide structural stability and form reactive centers in metalloproteins. Approximately one third of known protein structures are metalloproteins, and metal binding, or the lack thereof, is often implicated in disease, making it necessary to be able to study these systems in detail. Peptide-metal complexes are both present in nature and can provide a means to focus on the binding region of a protein and control experimental variables to a high degree. Structural studies of peptide complexes with metal ions by nuclear magnetic resonance (NMR) were surveyed for all the essential metal complexes and many non-essential metal complexes. The various methods used to study each metal ion are presented together with examples of recent research. Many of these metal systems have been individually reviewed and this current overview of NMR studies of metallopeptide complexes aims to provide a basis for inspiration from structural studies and methodology applied in the field.
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13
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Dijkstra JM, Kondo Y. Comprehensive Sequence Analysis of Parvalbumins in Fish and Their Comparison with Parvalbumins in Tetrapod Species. BIOLOGY 2022; 11:biology11121713. [PMID: 36552222 PMCID: PMC9774829 DOI: 10.3390/biology11121713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022]
Abstract
Parvalbumins are small molecules with important functions in Ca2+ signaling, but their sequence comparisons to date, especially in fish, have been relatively poor. We here, characterize sequence motifs that distinguish parvalbumin subfamilies across vertebrate species, as well as those that distinguish individual parvalbumins (orthologues) in fish, and map them to known parvalbumin structures. As already observed by others, all classes of jawed vertebrates possess parvalbumins of both the α-parvalbumin and oncomodulin subfamilies. However, we could not find convincing phylogenetic support for the common habit of classifying all non-α-parvalbumins together as "β-parvalbumins." In teleost (modern bony) fish, we here distinguish parvalbumins 1-to-10, of which the gene copy number can differ between species. The genes for α-parvalbumins (pvalb6 and pvalb7) and oncomodulins (pvalb8 and pvalb9) are well conserved between teleost species, but considerable variation is observed in their copy numbers of the non-α/non-oncomodulin genes pvalb1-to-5 and pvalb10. Teleost parvalbumins 1-to-4 are hardly distinguishable from each other and are highly expressed in muscle, and described allergens belong to this subfamily. However, in some fish species α-parvalbumin expression is also high in muscle. Pvalb5 and pvalb10 molecules form distinct lineages, the latter even predating the origin of teleosts, but have been lost in some teleost species. The present study aspires to be a frame of reference for future studies trying to compare different parvalbumins.
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Affiliation(s)
- Johannes M. Dijkstra
- Center for Medical Science, Fujita Health University, Dengaku-gakubo 1-98, Toyoake 470-1192, Japan
| | - Yasuto Kondo
- Department of Pediatrics, Fujita Health University Bantane Hospital, Otobashi 3-6-10, Nakagawa, Nagoya 454-8509, Japan
- Correspondence:
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Kayastha BB, Kubo A, Burch-Konda J, Dohmen RL, McCoy JL, Rogers RR, Mares S, Bevere J, Huckaby A, Witt W, Peng S, Chaudhary B, Mohanty S, Barbier M, Cook G, Deng J, Patrauchan MA. EF-hand protein, EfhP, specifically binds Ca 2+ and mediates Ca 2+ regulation of virulence in a human pathogen Pseudomonas aeruginosa. Sci Rep 2022; 12:8791. [PMID: 35614085 PMCID: PMC9132961 DOI: 10.1038/s41598-022-12584-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/09/2022] [Indexed: 11/30/2022] Open
Abstract
Calcium (Ca2+) is well known as a second messenger in eukaryotes, where Ca2+ signaling controls life-sustaining cellular processes. Although bacteria produce the components required for Ca2+ signaling, little is known about the mechanisms of bacterial Ca2+ signaling. Previously, we have identified a putative Ca2+-binding protein EfhP (PA4107) with two canonical EF-hand motifs and reported that EfhP mediates Ca2+ regulation of virulence factors production and infectivity in Pseudomonas aeruginosa, a human pathogen causing life-threatening infections. Here, we show that EfhP selectively binds Ca2+ with 13.7 µM affinity, and that mutations at the +X and -Z positions within each or both EF-hand motifs abolished Ca2+ binding. We also show that the hydrophobicity of EfhP increased in a Ca2+-dependent manner, however no such response was detected in the mutated proteins. 15 N-NMR showed Ca2+-dependent chemical shifts in EfhP confirming Ca2+-binding triggered structural rearrangements in the protein. Deletion of efhP impaired P. aeruginosa survival in macrophages and virulence in vivo. Disabling EfhP Ca2+ binding abolished Ca2+ induction of pyocyanin production in vitro. These data confirm that EfhP selectively binds Ca2+, which triggers its structural changes required for the Ca2+ regulation of P. aeruginosa virulence, thus establishing the role of EfhP as a Ca2+ sensor.
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Affiliation(s)
- Biraj B Kayastha
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Aya Kubo
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Jacob Burch-Konda
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Rosalie L Dohmen
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Jacee L McCoy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Rendi R Rogers
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Sergio Mares
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Justin Bevere
- Vaccine Development Center at West Virginia University, Morgantown, WV, 26506, USA
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Annalisa Huckaby
- Vaccine Development Center at West Virginia University, Morgantown, WV, 26506, USA
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - William Witt
- Vaccine Development Center at West Virginia University, Morgantown, WV, 26506, USA
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Shuxia Peng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Bharat Chaudhary
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Smita Mohanty
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Mariette Barbier
- Vaccine Development Center at West Virginia University, Morgantown, WV, 26506, USA
- Department of Microbiology, Immunology and Cell Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Gabriel Cook
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Junpeng Deng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
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15
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Jin S, Wang JN, Xue Y, Li P, Mei Y. Selectivity of parvalbumin B protein binding to Ca2+ and Mg2+ at an ab initio QM/MM level using the reference-potential method. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2109176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Shuwei Jin
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Jia-Ning Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Yuanfei Xue
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- Silicon Therapeutics (Suzhou) Co., Ltd., Suzhou 215000, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, China
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16
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Wesley T, Berzins S, Kannourakis G, Ahmed N. The attributes of plakins in cancer and disease: perspectives on ovarian cancer progression, chemoresistance and recurrence. Cell Commun Signal 2021; 19:55. [PMID: 34001250 PMCID: PMC8127266 DOI: 10.1186/s12964-021-00726-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
The plakin family of cytoskeletal proteins play an important role in cancer progression yet are under-studied in cancer, especially ovarian cancer. These large cytoskeletal proteins have primary roles in the maintenance of cytoskeletal integrity but are also associated with scaffolds of intermediate filaments and hemidesmosomal adhesion complexes mediating signalling pathways that regulate cellular growth, migration, invasion and differentiation as well as stress response. Abnormalities of plakins, and the closely related spectraplakins, result in diseases of the skin, striated muscle and nervous tissue. Their prevalence in epithelial cells suggests that plakins may play a role in epithelial ovarian cancer progression and recurrence. In this review article, we explore the roles of plakins, particularly plectin, periplakin and envoplakin in disease-states and cancers with emphasis on ovarian cancer. We discuss the potential role the plakin family of proteins play in regulating cancer cell growth, survival, migration, invasion and drug resistance. We highlight potential relationships between plakins, epithelial-mesenchymal transition (EMT) and cancer stem cells (CSCs) and discuss how interaction of these processes may affect ovarian cancer progression, chemoresistance and ultimately recurrence. We propose that molecular changes in the expression of plakins leads to the transition of benign ovarian tumours to carcinomas, as well as floating cellular aggregates (commonly known as spheroids) in the ascites microenvironment, which may contribute to the sustenance and progression of the disease. In this review, attempts have been made to understand the crucial changes in plakin expression in relation to progression and recurrence of ovarian cancer. Video Abstract
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Affiliation(s)
- Tamsin Wesley
- Fiona Elsey Cancer Research Institute, Ballarat Technology Central Park, Suites 23-26, 106-110 Lydiard Street South, Ballarat, VIC, 3353, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, 3010, Australia
| | - Stuart Berzins
- Fiona Elsey Cancer Research Institute, Ballarat Technology Central Park, Suites 23-26, 106-110 Lydiard Street South, Ballarat, VIC, 3353, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, 3010, Australia
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Ballarat Technology Central Park, Suites 23-26, 106-110 Lydiard Street South, Ballarat, VIC, 3353, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, 3010, Australia
| | - Nuzhat Ahmed
- Fiona Elsey Cancer Research Institute, Ballarat Technology Central Park, Suites 23-26, 106-110 Lydiard Street South, Ballarat, VIC, 3353, Australia. .,School of Science, Psychology and Sport, Federation University Australia, Ballarat, VIC, 3010, Australia. .,Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, VIC, 3052, Australia. .,Centre for Reproductive Health, The Hudson Institute of Medical Research and Department of Translational Medicine, Monash University, Melbourne, VIC, 3168, Australia.
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17
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Rayani K, Seffernick J, Li AY, Davis JP, Spuches AM, Van Petegem F, Solaro RJ, Lindert S, Tibbits GF. Binding of calcium and magnesium to human cardiac troponin C. J Biol Chem 2021; 296:100350. [PMID: 33548225 PMCID: PMC7961095 DOI: 10.1016/j.jbc.2021.100350] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
Cardiac muscle thin filaments are composed of actin, tropomyosin, and troponin that change conformation in response to Ca2+ binding, triggering muscle contraction. Human cardiac troponin C (cTnC) is the Ca2+-sensing component of the thin filament. It contains structural sites (III/IV) that bind both Ca2+ and Mg2+ and a regulatory site (II) that has been thought to bind only Ca2+. Binding of Ca2+ at this site initiates a series of conformational changes that culminate in force production. However, the mechanisms that underpin the regulation of binding at site II remain unclear. Here, we have quantified the interaction between site II and Ca2+/Mg2+ through isothermal titration calorimetry and thermodynamic integration simulations. Direct and competitive binding titrations with WT N-terminal cTnC and full-length cTnC indicate that physiologically relevant concentrations of both Ca2+/Mg2+ interacted with the same locus. Moreover, the D67A/D73A N-terminal cTnC construct in which two coordinating residues within site II were removed was found to have significantly reduced affinity for both cations. In addition, 1 mM Mg2+ caused a 1.4-fold lower affinity for Ca2+. These experiments strongly suggest that cytosolic-free Mg2+ occupies a significant population of the available site II. Interaction of Mg2+ with site II of cTnC likely has important functional consequences for the heart both at baseline as well as in diseased states that decrease or increase the availability of Mg2+, such as secondary hyperparathyroidism or ischemia, respectively.
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Affiliation(s)
- Kaveh Rayani
- Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Justin Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA
| | - Alison Yueh Li
- Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio, USA
| | - Anne Marie Spuches
- Department of Chemistry, East Carolina University, 300 Science and Technology Building, Greenville, North Carolina, USA
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - R John Solaro
- Department of Physiology and Biophysics and the Center for Cardiovascular Research, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio, USA
| | - Glen F Tibbits
- Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Cardiac Group, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
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18
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Lee IG, Cason SE, Alqassim SS, Holzbaur ELF, Dominguez R. A tunable LIC1-adaptor interaction modulates dynein activity in a cargo-specific manner. Nat Commun 2020; 11:5695. [PMID: 33173051 PMCID: PMC7655957 DOI: 10.1038/s41467-020-19538-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/16/2020] [Indexed: 01/07/2023] Open
Abstract
Cytoplasmic dynein-1 (dynein) is the motor responsible for most retrograde transport of cargoes along microtubules in eukaryotic cells, including organelles, mRNA and viruses. Cargo selectivity and activation of processive motility depend on a group of so-called "activating adaptors" that link dynein to its general cofactor, dynactin, and cargoes. The mechanism by which these adaptors regulate dynein transport is poorly understood. Here, based on crystal structures, quantitative binding studies, and in vitro motility assays, we show that BICD2, CRACR2a, and HOOK3, representing three subfamilies of unrelated adaptors, interact with the same amphipathic helix of the dynein light intermediate chain-1 (LIC1). While the hydrophobic character of the interaction is conserved, the three adaptor subfamilies use different folds (coiled-coil, EF-hand, HOOK domain) and different surface contacts to bind the LIC1 helix with affinities ranging from 1.5 to 15.0 μM. We propose that a tunable LIC1-adaptor interaction modulates dynein's motility in a cargo-specific manner.
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Affiliation(s)
- In-Gyun Lee
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.35541.360000000121053345Present Address: Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-Gil, Seongbuk-Gu, Seoul, 02792 Republic of Korea
| | - Sydney E. Cason
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Neuroscience Graduate Group, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Saif S. Alqassim
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,Present Address: College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Erika L. F. Holzbaur
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Neuroscience Graduate Group, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Roberto Dominguez
- grid.25879.310000 0004 1936 8972Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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19
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Matsarskaia O, Roosen‐Runge F, Schreiber F. Multivalent ions and biomolecules: Attempting a comprehensive perspective. Chemphyschem 2020; 21:1742-1767. [PMID: 32406605 PMCID: PMC7496725 DOI: 10.1002/cphc.202000162] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/13/2020] [Indexed: 12/13/2022]
Abstract
Ions are ubiquitous in nature. They play a key role for many biological processes on the molecular scale, from molecular interactions, to mechanical properties, to folding, to self-organisation and assembly, to reaction equilibria, to signalling, to energy and material transport, to recognition etc. Going beyond monovalent ions to multivalent ions, the effects of the ions are frequently not only stronger (due to the obviously higher charge), but qualitatively different. A typical example is the process of binding of multivalent ions, such as Ca2+ , to a macromolecule and the consequences of this ion binding such as compaction, collapse, potential charge inversion and precipitation of the macromolecule. Here we review these effects and phenomena induced by multivalent ions for biological (macro)molecules, from the "atomistic/molecular" local picture of (potentially specific) interactions to the more global picture of phase behaviour including, e. g., crystallisation, phase separation, oligomerisation etc. Rather than attempting an encyclopedic list of systems, we rather aim for an embracing discussion using typical case studies. We try to cover predominantly three main classes: proteins, nucleic acids, and amphiphilic molecules including interface effects. We do not cover in detail, but make some comparisons to, ion channels, colloidal systems, and synthetic polymers. While there are obvious differences in the behaviour of, and the relevance of multivalent ions for, the three main classes of systems, we also point out analogies. Our attempt of a comprehensive discussion is guided by the idea that there are not only important differences and specific phenomena with regard to the effects of multivalent ions on the main systems, but also important similarities. We hope to bridge physico-chemical mechanisms, concepts of soft matter, and biological observations and connect the different communities further.
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Affiliation(s)
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms-Research Center for Biointerfaces (BRCB), Faculty of Health and SocietyMalmö UniversitySweden
- Division of Physical ChemistryLund UniversitySweden
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20
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Glutamatergic fast-spiking parvalbumin neurons in the lateral hypothalamus: Electrophysiological properties to behavior. Physiol Behav 2020; 221:112912. [PMID: 32289319 DOI: 10.1016/j.physbeh.2020.112912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/14/2020] [Accepted: 04/06/2020] [Indexed: 01/10/2023]
Abstract
Throughout the central nervous system, neurons expressing the calcium-binding protein parvalbumin have been typically classified as GABAergic with fast-spiking characteristics. However, new methods that allow systematic characterization of the cytoarchitectural organization, connectivity, activity patterns, neurotransmitter nature, and function of genetically-distinct cell types have revealed populations of parvalbumin-positive neurons that are glutamatergic. Remarkably, such findings challenge longstanding concepts that fast-spiking neurons are exclusively GABAergic, suggesting conservation of the fast-spiking phenotype across at least two neurotransmitter systems. This review focuses on the recent advancements that have begun to reveal the functional roles of lateral hypothalamic parvalbumin-positive neurons in regulating behaviors essential for survival.
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21
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Litman J, Thiel AC, Schnieders MJ. Scalable Indirect Free Energy Method Applied to Divalent Cation-Metalloprotein Binding. J Chem Theory Comput 2019; 15:4602-4614. [DOI: 10.1021/acs.jctc.9b00147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jacob Litman
- University of Iowa, Department of Biochemistry, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, Iowa 52242, United States
| | - Andrew C. Thiel
- University of Iowa, Department of Biomedical Engineering, 103 South Capitol Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
| | - Michael J. Schnieders
- University of Iowa, Department of Biochemistry, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, Iowa 52242, United States
- University of Iowa, Department of Biomedical Engineering, 103 South Capitol Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States
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Breed, Diet, and Interaction Effects on Adipose Tissue Transcriptome in Iberian and Duroc Pigs Fed Different Energy Sources. Genes (Basel) 2019; 10:genes10080589. [PMID: 31382709 PMCID: PMC6723240 DOI: 10.3390/genes10080589] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 12/14/2022] Open
Abstract
In this study, we analyzed the effects of breed, diet energy source, and their interaction on adipose tissue transcriptome in growing Iberian and Duroc pigs. The study comprised 29 Iberian and 19 Duroc males, which were kept under identical management conditions except the nutritional treatment. Two isoenergetic diets were used with 6% high oleic sunflower oil (HO) or carbohydrates (CH) as energy sources. All animals were slaughtered after 47 days of treatment at an average live weight of 51.2 kg. Twelve animals from each breed (six fed each diet) were employed for ham subcutaneous adipose tissue RNA-Seq analysis. The data analysis was performed using two different bioinformatic pipelines. We detected 837 and 1456 differentially expressed genes (DEGs) according to breed, depending on the pipeline. Due to the strong effect of breed on transcriptome, the effect of the diet was separately evaluated in the two breeds. We identified 207 and 57 DEGs depending on diet in Iberian and Duroc pigs, respectively. A joint analysis of both effects allowed the detection of some breed–diet interactions on transcriptome, which were inferred from RNA-Seq and quantitative PCR data. The functional analysis showed the enrichment of functions related to growth and tissue development, inflammatory response, immune cell trafficking, and carbohydrate and lipid metabolism, and allowed the identification of potential regulators. The results indicate different effects of diet on adipose tissue gene expression between breeds, affecting relevant biological pathways.
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23
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Fu L, Wang C, Zhu Y, Wang Y. Seafood allergy: Occurrence, mechanisms and measures. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.03.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Hoyer E, Knöppel J, Liebmann M, Steppert M, Raiwa M, Herczynski O, Hanspach E, Zehner S, Göttfert M, Tsushima S, Fahmy K, Oertel J. Calcium binding to a disordered domain of a type III-secreted protein from a coral pathogen promotes secondary structure formation and catalytic activity. Sci Rep 2019; 9:7115. [PMID: 31068617 PMCID: PMC6506597 DOI: 10.1038/s41598-019-42898-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/10/2019] [Indexed: 01/05/2023] Open
Abstract
Strains of the Gram-negative bacterium Vibrio coralliilyticus cause the bleaching of corals due to decomposition of symbiotic microalgae. The V. coralliilyticus strain ATCC BAA-450 (Vc450) encodes a type III secretion system (T3SS). The gene cluster also encodes a protein (locus tag VIC_001052) with sequence homology to the T3SS-secreted nodulation proteins NopE1 and NopE2 of Bradyrhizobium japonicum (USDA110). VIC_001052 has been shown to undergo auto-cleavage in the presence of Ca2+ similar to the NopE proteins. We have studied the hitherto unknown secondary structure, Ca2+-binding affinity and stoichiometry of the “metal ion-inducible autocleavage” (MIIA) domain of VIC_001052 which does not possess a classical Ca2+-binding motif. CD and fluorescence spectroscopy revealed that the MIIA domain is largely intrinsically disordered. Binding of Ca2+ and other di- and trivalent cations induced secondary structure and hydrophobic packing after partial neutralization of the highly negatively charged MIIA domain. Mass spectrometry and isothermal titration calorimetry showed two Ca2+-binding sites which promote structure formation with a total binding enthalpy of −110 kJ mol−1 at a low micromolar Kd. Putative binding motifs were identified by sequence similarity to EF-hand domains and their structure analyzed by molecular dynamics simulations. The stoichiometric Ca2+-dependent induction of structure correlated with catalytic activity and may provide a “host-sensing” mechanism that is shared among pathogens that use a T3SS for efficient secretion of disordered proteins.
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Affiliation(s)
- Elisabeth Hoyer
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany.,Ludwig-Maximilians-Universität München, Department of Biology I, Microbiology, Großhaderner Str. 2, D-82152, Planegg-Martinsried, Germany
| | - Julius Knöppel
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Martina Liebmann
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Michael Steppert
- Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Manuel Raiwa
- Leibniz University Hannover, Institute of Radioecology and Radiation Protection, Herrenhäuser Str. 2, D-30419, Hannover, Germany
| | - Olivia Herczynski
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Erik Hanspach
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Susanne Zehner
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Michael Göttfert
- Technische Universität Dresden, Institute of Genetics, Zellescher Weg 20b, D-01217, Dresden, Germany
| | - Satoru Tsushima
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany
| | - Jana Oertel
- Helmholtz-Zentrum Dresden - Rossendorf, Bautzner Landstrasse 400, D-01328, Dresden, Germany.
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Molakarimi M, Gorman MA, Mohseni A, Pashandi Z, Taghdir M, Naderi-Manesh H, Sajedi RH, Parker MW. Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations. J Biol Chem 2019; 294:20-27. [PMID: 30420427 PMCID: PMC6322872 DOI: 10.1074/jbc.ra118.006053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Indexed: 11/06/2022] Open
Abstract
Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca2+-dependent photoproteins. The mechanism of light emission operates via the same reaction in both animal families. Despite numerous studies on the ctenophore photoprotein family, the detailed catalytic mechanism and arrangement of amino acid residues surrounding the chromophore in this family are a mystery. Here, we report the crystal structure of Cd2+-loaded apo-mnemiopsin1, a member of the ctenophore family, at 2.15 Å resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction mechanism. The simulations suggested that an Asp-156-Arg-39-Tyr-202 triad creates a hydrogen-bonded network to facilitate the transfer of a proton from the 2-hydroperoxy group of the chromophore coelenterazine to bulk solvent. We identified a water molecule in the coelenteramide-binding cavity that forms a hydrogen bond with the amide nitrogen atom of coelenteramide, which, in turn, is hydrogen-bonded via another water molecule to Tyr-131. This observation supports the hypothesis that the function of the coelenteramide-bound water molecule is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion, thereby triggering the bioluminescence reaction in the ctenophore photoprotein family.
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Affiliation(s)
- Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Michael A Gorman
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Zaiddodine Pashandi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.
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26
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Tsvetkov PO, Roman AY, Baksheeva VE, Nazipova AA, Shevelyova MP, Vladimirov VI, Buyanova MF, Zinchenko DV, Zamyatnin AA, Devred F, Golovin AV, Permyakov SE, Zernii EY. Functional Status of Neuronal Calcium Sensor-1 Is Modulated by Zinc Binding. Front Mol Neurosci 2018; 11:459. [PMID: 30618610 PMCID: PMC6302015 DOI: 10.3389/fnmol.2018.00459] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/28/2018] [Indexed: 11/29/2022] Open
Abstract
Neuronal calcium sensor-1 (NCS-1) protein is abundantly expressed in the central nervous system and retinal neurons, where it regulates many vital processes such as synaptic transmission. It coordinates three calcium ions by EF-hands 2-4, thereby transducing Ca2+ signals to a wide range of protein targets, including G protein-coupled receptors and their kinases. Here, we demonstrate that NCS-1 also has Zn2+-binding sites, which affect its structural and functional properties upon filling. Fluorescence and circular dichroism experiments reveal the impact of Zn2+ binding on NCS-1 secondary and tertiary structure. According to atomic absorption spectroscopy and isothermal titration calorimetry studies, apo-NCS-1 has two high-affinity (4 × 106 M-1) and one low-affinity (2 × 105 M-1) Zn2+-binding sites, whereas Mg2+-loaded and Ca2+-loaded forms (which dominate under physiological conditions) bind two zinc ions with submicromolar affinity. Metal competition analysis and circular dichroism studies suggest that Zn2+-binding sites of apo- and Mg2+-loaded NCS-1 overlap with functional EF-hands of the protein. Consistently, high Zn2+ concentrations displace Mg2+ from the EF-hands and decrease the stoichiometry of Ca2+ binding. Meanwhile, one of the EF-hands of Zn2+-saturated NCS-1 exhibits a 14-fold higher calcium affinity, which increases the overall calcium sensitivity of the protein. Based on QM/MM molecular dynamics simulations, Zn2+ binding to Ca2+-loaded NCS-1 could occur at EF-hands 2 and 4. The high-affinity zinc binding increases the thermal stability of Ca2+-free NCS-1 and favours the interaction of its Ca2+-loaded form with target proteins, such as dopamine receptor D2R and GRK1. In contrast, low-affinity zinc binding promotes NCS-1 aggregation accompanied by the formation of twisted rope-like structures. Altogether, our findings suggest a complex interplay between magnesium, calcium and zinc binding to NCS-1, leading to the appearance of multiple conformations of the protein, in turn modulating its functional status.
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Affiliation(s)
- Philipp O Tsvetkov
- Aix-Marseille University, CNRS, INP, Institute of Neurophysiopathology, Faculty of Pharmacy, Marseille, France
| | - Andrei Yu Roman
- Institute of Physiologically Active Compounds (RAS), Chernogolovka, Russia
| | - Viktoriia E Baksheeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aliya A Nazipova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Marina P Shevelyova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Vasiliy I Vladimirov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
| | - Michelle F Buyanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
| | - Andrey A Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - François Devred
- Aix-Marseille University, CNRS, INP, Institute of Neurophysiopathology, Faculty of Pharmacy, Marseille, France
| | - Andrey V Golovin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russia
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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27
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Jing Z, Liu C, Qi R, Ren P. Many-body effect determines the selectivity for Ca 2+ and Mg 2+ in proteins. Proc Natl Acad Sci U S A 2018; 115:E7495-E7501. [PMID: 30038003 PMCID: PMC6094099 DOI: 10.1073/pnas.1805049115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Calcium ion is a versatile messenger in many cell-signaling processes. To achieve their functions, calcium-binding proteins selectively bind Ca2+ against a background of competing ions such as Mg2+ The high specificity of calcium-binding proteins has been intriguing since Mg2+ has a higher charge density than Ca2+ and is expected to bind more tightly to the carboxylate groups in calcium-binding pockets. Here, we showed that the specificity for Ca2+ is dictated by the many-body polarization effect, which is an energetic cost arising from the dense packing of multiple residues around the metal ion. Since polarization has stronger distance dependence compared with permanent electrostatics, the cost associated with the smaller Mg2+ is much higher than that with Ca2+ and outweighs the electrostatic attraction favorable for Mg2+ With the AMOEBA (atomic multipole optimized energetics for biomolecular simulation) polarizable force field, our simulations captured the relative binding free energy between Ca2+ and Mg2+ for proteins with various types of binding pockets and explained the nonmonotonic size dependence of the binding free energy in EF-hand proteins. Without electronic polarization, the smaller ions are always favored over larger ions and the relative binding free energy is roughly proportional to the net charge of the pocket. The many-body effect depends on both the number and the arrangement of charged residues. Fine-tuning of the ion selectivity could be achieved by combining the many-body effect and geometric constraint.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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28
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Seafood allergy: A comprehensive review of fish and shellfish allergens. Mol Immunol 2018; 100:28-57. [PMID: 29858102 DOI: 10.1016/j.molimm.2018.04.008] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 11/23/2022]
Abstract
Seafood refers to several distinct groups of edible aquatic animals including fish, crustacean, and mollusc. The two invertebrate groups of crustacean and mollusc are, for culinary reasons, often combined as shellfish but belong to two very different phyla. The evolutionary and taxonomic diversity of the various consumed seafood species poses a challenge in the identification and characterisation of the major and minor allergens critical for reliable diagnostics and therapeutic treatments. Many allergenic proteins are very different between these groups; however, some pan-allergens, including parvalbumin, tropomyosin and arginine kinase, seem to induce immunological and clinical cross-reactivity. This extensive review details the advances in the bio-molecular characterisation of 20 allergenic proteins within the three distinct seafood groups; fish, crustacean and molluscs. Furthermore, the structural and biochemical properties of the major allergens are described to highlight the immunological and subsequent clinical cross-reactivities. A comprehensive list of purified and recombinant allergens is provided, and the applications of component-resolved diagnostics and current therapeutic developments are discussed.
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29
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Cook AA, Deng W, Ren J, Li R, Sondek J, Bergmeier W. Calcium-induced structural rearrangements release autoinhibition in the Rap-GEF CalDAG-GEFI. J Biol Chem 2018; 293:8521-8529. [PMID: 29622678 DOI: 10.1074/jbc.ra118.002712] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/22/2018] [Indexed: 11/06/2022] Open
Abstract
Platelets are recruited to sites of vascular injury, where they are activated and aggregate to form a hemostatic plug. This process requires the activation of the small GTPase Rap1B by its cognate guanine nucleotide exchange factor CalDAG-GEFI. Studies on platelet function suggest that CalDAG-GEFI activity is regulated by changes in cytosolic calcium, but the exact molecular mechanism is poorly understood. Here we show that purified CalDAG-GEFI is autoinhibited and directly regulated by calcium. Substitutions of putative calcium-binding residues within the canonical EF hands of CalDAG-GEFI diminish its capacity to activate Rap1B. Structural differences between active (WT) and inactive (EF hand variant) CalDAG-GEFI protein were determined by hydrogen-deuterium exchange MS. The highest differential rates of deuterium uptake in WT over EF hand variant CalDAG-GEFI were observed in regions within the catalytic Cdc25 domain and a putative autoinhibitory linker connecting the Cdc25 and EF hand domains. Exchange activity in the EF hand variant was fully restored by an additional substitution, valine 406 to glutamate, which is thought to disrupt the interface between the autoinhibitory linker and the Cdc25 domain. Overall, our results suggest a model for how CalDAG-GEFI remains in an autoinhibited state when levels of cytosolic calcium in resting platelets are low. In response to cellular stimulation, calcium mobilization and binding to the EF hands causes conformational rearrangements within CalDAG-GEFI, including the autoinhibitory linker that frees the catalytic surface of CalDAG-GEFI to engage and activate Rap1B. The data from this study are the first evidence linking CalDAG-GEFI activity directly to calcium.
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Affiliation(s)
- Aaron A Cook
- From the Departments of Biochemistry and Biophysics and
| | - Wei Deng
- the Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, and
| | | | - Renhao Li
- the Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, and
| | - John Sondek
- From the Departments of Biochemistry and Biophysics and.,Pharmacology and.,the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Wolfgang Bergmeier
- From the Departments of Biochemistry and Biophysics and .,the McAllister Heart Institute, University of North Carolina, Chapel Hill, North Carolina 27516
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30
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Lopez AJ, Martínez L. Parametric models to compute tryptophan fluorescence wavelengths from classical protein simulations. J Comput Chem 2018; 39:1249-1258. [PMID: 29484676 DOI: 10.1002/jcc.25188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/22/2017] [Accepted: 01/28/2018] [Indexed: 12/21/2022]
Abstract
Fluorescence spectroscopy is an important method to study protein conformational dynamics and solvation structures. Tryptophan (Trp) residues are the most important and practical intrinsic probes for protein fluorescence due to the variability of their fluorescence wavelengths: Trp residues emit in wavelengths ranging from 308 to 360 nm depending on the local molecular environment. Fluorescence involves electronic transitions, thus its computational modeling is a challenging task. We show that it is possible to predict the wavelength of emission of a Trp residue from classical molecular dynamics simulations by computing the solvent-accessible surface area or the electrostatic interaction between the indole group and the rest of the system. Linear parametric models are obtained to predict the maximum emission wavelengths with standard errors of the order 5 nm. In a set of 19 proteins with emission wavelengths ranging from 308 to 352 nm, the best model predicts the maximum wavelength of emission with a standard error of 4.89 nm and a quadratic Pearson correlation coefficient of 0.81. These models can be used for the interpretation of fluorescence spectra of proteins with multiple Trp residues, or for which local Trp environmental variability exists and can be probed by classical molecular dynamics simulations. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Alvaro J Lopez
- Institute of Chemistry and Center for Computational Engineering & Sciences, University of Campinas, Campinas, SP, Brazil
| | - Leandro Martínez
- Institute of Chemistry and Center for Computational Engineering & Sciences, University of Campinas, Campinas, SP, Brazil
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31
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Revisiting paradigms of Ca2+ signaling protein kinase regulation in plants. Biochem J 2018; 475:207-223. [DOI: 10.1042/bcj20170022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/15/2022]
Abstract
Calcium (Ca2+) serves as a universal second messenger in eukaryotic signal transduction. Understanding the Ca2+ activation kinetics of Ca2+ sensors is critical to understanding the cellular signaling mechanisms involved. In this review, we discuss the regulatory properties of two sensor classes: the Ca2+-dependent protein kinases (CPKs/CDPKs) and the calcineurin B-like (CBL) proteins that control the activity of CBL-interacting protein kinases (CIPKs) and identify emerging topics and some foundational points that are not well established experimentally. Most plant CPKs are activated by physiologically relevant Ca2+ concentrations except for those with degenerate EF hands, and new results suggest that the Ca2+-dependence of kinase activation may be modulated by both protein–protein interactions and CPK autophosphorylation. Early results indicated that activation of plant CPKs by Ca2+ occurred by relief of autoinhibition. However, recent studies of protist CDPKs suggest that intramolecular interactions between CDPK domains contribute allosteric control to CDPK activation. Further studies are required to elucidate the mechanisms regulating plant CPKs. With CBL–CIPKs, the two major activation mechanisms are thought to be (i) binding of Ca2+-bound CBL to the CIPK and (ii) phosphorylation of residues in the CIPK activation loop. However, the relative importance of these two mechanisms in regulating CIPK activity is unclear. Furthermore, information detailing activation by physiologically relevant [Ca2+] is lacking, such that the paradigm of CBLs as Ca2+ sensors still requires critical, experimental validation. Developing models of CPK and CIPK regulation is essential to understand how these kinases mediate Ca2+ signaling and to the design of experiments to test function in vivo.
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32
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Asp ML, Sjaastad FV, Siddiqui JK, Davis JP, Metzger JM. Effects of Modified Parvalbumin EF-Hand Motifs on Cardiac Myocyte Contractile Function. Biophys J 2017; 110:2094-105. [PMID: 27166817 DOI: 10.1016/j.bpj.2016.03.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 10/21/2022] Open
Abstract
Cardiac gene delivery of parvalbumin (Parv), an EF-hand Ca(2+) buffer, has been studied as a therapeutic strategy for diastolic heart failure, in which slow Ca(2+) reuptake is an important contributor. A limitation of wild-type (WT) Parv is the significant trade-off between faster relaxation and blunted contraction amplitude, occurring because WT-Parv sequesters Ca(2+) too early in the cardiac cycle and prematurely truncates sarcomere shortening in the facilitation of rapid relaxation. We recently demonstrated that an E → Q substitution (ParvE101Q) at amino acid 12 of the EF-hand Ca(2+)/Mg(2+) binding loop disrupts bidentate Ca(2+) binding, reducing Ca(2+) affinity by 99-fold and increasing Mg(2+) affinity twofold. ParvE101Q caused faster relaxation and not only preserved contractility, but unexpectedly increased it above untreated myocytes. To gain mechanistic insight into the increased contractility, we focused here on amino acid 12 of the EF-hand motif. We introduced an E → D substitution (ParvE101D) at this site, which converts bidentate Ca(2+) coordination to monodentate coordination. ParvE101D decreased Ca(2+) affinity by 114-fold and increased Mg(2+) affinity 28-fold compared to WT-Parv. ParvE101D increased contraction amplitude compared to both untreated myocytes and myocytes with ParvE101Q, with limited improvement in relaxation. Additionally, ParvE101D increased spontaneous contractions after pacing stress. ParvE101D also increased Ca(2+) transient peak height and was diffusely localized around the Z-line of the sarcomere, suggesting a Ca(2+)-dependent mechanism of enhanced contractility. Sarcoplasmic reticulum Ca(2+) load was not changed with ParvE101D, but postpacing Ca(2+) waves were increased. Together, these data show that inverted Ca(2+)/Mg(2+) binding affinities of ParvE101D increase myocyte contractility through a Ca(2+)-dependent mechanism without altering sarcoplasmic reticulum Ca(2+) load and by increasing unstimulated contractions and Ca(2+) waves. ParvE101D provides mechanistic insight into how changes in the Ca(2+)/Mg(2+) binding affinities of parvalbumin's EF-hand motif alter function of cardiac myocytes. These data are informative in developing new Ca(2+) buffering strategies for the failing heart.
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Affiliation(s)
- Michelle L Asp
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Frances V Sjaastad
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Jalal K Siddiqui
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Jonathan P Davis
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Joseph M Metzger
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota.
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33
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Structural implications of Ca 2+-dependent actin-bundling function of human EFhd2/Swiprosin-1. Sci Rep 2016; 6:39095. [PMID: 27974828 PMCID: PMC5156911 DOI: 10.1038/srep39095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/17/2016] [Indexed: 01/20/2023] Open
Abstract
EFhd2/Swiprosin-1 is a cytoskeletal Ca2+-binding protein implicated in Ca2+-dependent cell spreading and migration in epithelial cells. EFhd2 domain architecture includes an N-terminal disordered region, a PxxP motif, two EF-hands, a ligand mimic helix and a C-terminal coiled-coil domain. We reported previously that EFhd2 displays F-actin bundling activity in the presence of Ca2+ and this activity depends on the coiled-coil domain and direct interaction of the EFhd2 core region. However, the molecular mechanism for the regulation of F-actin binding and bundling by EFhd2 is unknown. Here, the Ca2+-bound crystal structure of the EFhd2 core region is presented and structures of mutants defective for Ca2+-binding are also described. These structures and biochemical analyses reveal that the F-actin bundling activity of EFhd2 depends on the structural rigidity of F-actin binding sites conferred by binding of the EF-hands to Ca2+. In the absence of Ca2+, the EFhd2 core region exhibits local conformational flexibility around the EF-hand domain and C-terminal linker, which retains F-actin binding activity but loses the ability to bundle F-actin. In addition, we establish that dimerisation of EFhd2 via the C-terminal coiled-coil domain, which is necessary for F-actin bundling, occurs through the parallel coiled-coil interaction.
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34
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Springer TI, Emerson CC, Johns CW, Finley NL. Interaction with adenylate cyclase toxin from Bordetella pertussis affects the metal binding properties of calmodulin. FEBS Open Bio 2016; 7:25-34. [PMID: 28097085 PMCID: PMC5221433 DOI: 10.1002/2211-5463.12138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022] Open
Abstract
Adenylate cyclase toxin domain (CyaA‐ACD) is a calmodulin (CaM)‐dependent adenylate cyclase involved in Bordetella pertussis pathogenesis. Calcium (Ca2+) and magnesium (Mg2+) concentrations impact CaM‐dependent CyaA‐ACD activation, but the structural mechanisms remain unclear. In this study, NMR, dynamic light scattering, and native PAGE were used to probe Mg2+‐induced transitions in CaM's conformation in the presence of CyaA‐ACD. Mg2+ binding was localized to sites I and II, while sites III and IV remained Ca2+ loaded when CaM was bound to CyaA‐ACD. 2Mg2+/2Ca2+‐loaded CaM/CyaA‐ACD was elongated, whereas mutation of site I altered global complex conformation. These data suggest that CyaA‐ACD interaction moderates CaM's Ca2+‐ and Mg2+‐binding capabilities, which may contribute to pathobiology.
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Affiliation(s)
| | - Corey C Emerson
- Department of Microbiology Miami University Oxford OH USA; Present address: Department of Pharmacology Cleveland Center for Membrane and Structural Biology Case Western Reserve University Cleveland OH 44106 USA
| | - Christian W Johns
- Cell, Molecular, and Structural Biology Program Miami University Oxford OH USA
| | - Natosha L Finley
- Department of Microbiology Miami University Oxford OH USA; Cell, Molecular, and Structural Biology Program Miami University Oxford OH USA
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35
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Kobayashi A, Ichimura A, Kobayashi Y, Shiomi K. IgE-binding epitopes of various fish parvalbumins exist in a stereoscopic conformation maintained by Ca(2+) binding. Allergol Int 2016; 65:345-8. [PMID: 27184826 DOI: 10.1016/j.alit.2016.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 01/28/2016] [Accepted: 02/08/2016] [Indexed: 11/28/2022] Open
Affiliation(s)
- Ayako Kobayashi
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ayako Ichimura
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yukihiro Kobayashi
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan; Course of Safety Management in Food Supply Chain, Tokyo University of Marine Science and Technology, Tokyo, Japan.
| | - Kazuo Shiomi
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
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36
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Chataigner L, Guo J, Erskine PT, Coker AR, Wood SP, Gombos Z, Cooper JB. Binding of Gd(3+) to the neuronal signalling protein calexcitin identifies an exchangeable Ca(2+)-binding site. Acta Crystallogr F Struct Biol Commun 2016; 72:276-81. [PMID: 27050260 PMCID: PMC4822983 DOI: 10.1107/s2053230x16003526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/29/2016] [Indexed: 11/11/2022] Open
Abstract
Calexcitin was first identified in the marine snail Hermissenda crassicornis as a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg(2+) and Ca(2+), while EF-3 is likely to bind only Ca(2+). The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of calexcitin is most readily replaced by exogenous metal ions, potentially shedding light on which of the EF-hands play a `sensory' role in neuronal calcium signalling. By co-crystallizing recombinant calexcitin with equimolar Gd(3+) in the presence of trace Ca(2+), EF-1 was shown to become fully occupied by Gd(3+) ions, while the other two sites remain fully occupied by Ca(2+). The structure of the Gd(3+)-calexcitin complex has been refined to an R factor of 21.5% and an Rfree of 30.4% at 2.2 Å resolution. These findings suggest that EF-1 of calexcitin is the Ca(2+)-binding site with the lowest selectivity for Ca(2+), and the implications of this finding for calcium sensing in neuronal signalling pathways are discussed.
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Affiliation(s)
- Lucas Chataigner
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Jingxu Guo
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Peter T. Erskine
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
| | - Alun R. Coker
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Steve P. Wood
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Zoltan Gombos
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Jonathan B. Cooper
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
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37
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Srivastava SS, Mishra A, Krishnan B, Sharma Y. Ca2+-binding motif of βγ-crystallins. J Biol Chem 2014; 289:10958-10966. [PMID: 24567326 DOI: 10.1074/jbc.o113.539569] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
βγ-Crystallin-type double clamp (N/D)(N/D)XX(S/T)S motif is an established but sparsely investigated motif for Ca(2+) binding. A βγ-crystallin domain is formed of two Greek key motifs, accommodating two Ca(2+)-binding sites. βγ-Crystallins make a separate class of Ca(2+)-binding proteins (CaBP), apparently a major group of CaBP in bacteria. Paralleling the diversity in βγ-crystallin domains, these motifs also show great diversity, both in structure and in function. Although the expression of some of them has been associated with stress, virulence, and adhesion, the functional implications of Ca(2+) binding to βγ-crystallins in mediating biological processes are yet to be elucidated.
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Affiliation(s)
- Shanti Swaroop Srivastava
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Uppal Road, Hyderabad-500 007, India
| | - Amita Mishra
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Uppal Road, Hyderabad-500 007, India
| | - Bal Krishnan
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Uppal Road, Hyderabad-500 007, India
| | - Yogendra Sharma
- Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR), Uppal Road, Hyderabad-500 007, India.
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38
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Somkuti J, Smeller L. High pressure effects on allergen food proteins. Biophys Chem 2013; 183:19-29. [DOI: 10.1016/j.bpc.2013.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
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39
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Das A, Chakrabarti J, Ghosh M. Conformational thermodynamics of metal-ion binding to a protein. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Wang W, Barnabei MS, Asp ML, Heinis FI, Arden E, Davis J, Braunlin E, Li Q, Davis JP, Potter JD, Metzger JM. Noncanonical EF-hand motif strategically delays Ca2+ buffering to enhance cardiac performance. Nat Med 2013; 19:305-12. [PMID: 23396207 DOI: 10.1038/nm.3079] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/21/2012] [Indexed: 12/26/2022]
Abstract
EF-hand proteins are ubiquitous in cell signaling. Parvalbumin (Parv), the archetypal EF-hand protein, is a high-affinity Ca(2+) buffer in many biological systems. Given the centrality of Ca(2+) signaling in health and disease, EF-hand motifs designed to have new biological activities may have widespread utility. Here, an EF-hand motif substitution that had been presumed to destroy EF-hand function, that of glutamine for glutamate at position 12 of the second cation binding loop domain of Parv (ParvE101Q), markedly inverted relative cation affinities: Mg(2+) affinity increased, whereas Ca(2+) affinity decreased, forming a new ultra-delayed Ca(2+) buffer with favorable properties for promoting cardiac relaxation. In therapeutic testing, expression of ParvE101Q fully reversed the severe myocyte intrinsic contractile defect inherent to expression of native Parv and corrected abnormal myocardial relaxation in diastolic dysfunction disease models in vitro and in vivo. Strategic design of new EF-hand motif domains to modulate intracellular Ca(2+) signaling could benefit many biological systems with abnormal Ca(2+) handling, including the diseased heart.
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Affiliation(s)
- Wang Wang
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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41
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Chen ML. Two-dimensional gel electrophoresis revealed antipsychotic drugs induced protein expression modulations in C6 glioma cells. Prog Neuropsychopharmacol Biol Psychiatry 2013; 40:1-11. [PMID: 22960606 DOI: 10.1016/j.pnpbp.2012.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/22/2012] [Accepted: 08/22/2012] [Indexed: 01/13/2023]
Abstract
The efficacy and side effects of long-term administration of antipsychotic drugs (APDs) may be attributed to drug-induced change in protein expression in brain cells. Glial cells are non-neuronal cells that can provide nutrients and physiological support to neuronal cells. Glial cells are believed to participate in neurotransmission, neurons' early development, and guiding migration of neurons. Accumulated clinical data also indicate relationships between disturbance of glial cells' function and various psychotic diseases including schizophrenia. We used two-dimensional gel electrophoresis coupled with MALDI-TOF/TOF mass spectrometry protein identification to analyze differentially expressed proteins in haloperidol-, risperidone-, and clozapine-treated C6 glioma cells. We found that the expression of pericentrin, glial fibrillary acidic protein, Rho GDP-dissociation inhibitor 1, anionic trypsin-1, peroxiredoxin-1, and parvalbumin were regulated by each of the three APDs. Western blot analysis supported the findings. Real-time quantitative PCR detected changed transcriptions of those proteins. Protein and gene expression of N-cadherin in C6 cells were affected by haloperidol and clozapine but not risperidone. In addition, regulatory effects of clozapine on the glyceraldehyde 3-phosphate dehydrogenase gene were observed in C6 cells. This may be the first study to uncover how APD-modulated genes may cause protein expression changes and affect ARHGDIA-mediated regulation of Rho GTPase family proteins in glial cells.
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Affiliation(s)
- Mao-Liang Chen
- Department of Research, Buddhist Tzu Chi General Hospital, Taipei Branch, New Taipei City, Taiwan, ROC.
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42
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Asp ML, Martindale JJ, Heinis FI, Wang W, Metzger JM. Calcium mishandling in diastolic dysfunction: mechanisms and potential therapies. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:895-900. [PMID: 23022395 DOI: 10.1016/j.bbamcr.2012.09.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 01/11/2023]
Abstract
Diastolic dysfunction is characterized by slow or incomplete relaxation of the ventricles during diastole, and is an important contributor to heart failure pathophysiology. Clinical symptoms include fatigue, shortness of breath, and pulmonary and peripheral edema, all contributing to decreased quality of life and poor prognosis. There are currently no therapies available that directly target the heart pump defects in diastolic function. Calcium mishandling is a hallmark of heart disease and has been the subject of a large body of research. Efforts are ongoing in a number of gene therapy approaches to normalize the function of calcium handling proteins such as sarcoplasmic reticulum calcium ATPase. An alternative approach to address calcium mishandling in diastolic dysfunction is to introduce calcium buffers to facilitate relaxation of the heart. Parvalbumin is a calcium binding protein found in fast-twitch skeletal muscle and not normally expressed in the heart. Gene transfer of parvalbumin into normal and diseased cardiac myocytes increases relaxation rate but also markedly decreases contraction amplitude. Although parvalbumin binds calcium in a delayed manner, it is not delayed enough to preserve full contractility. Factors contributing to the temporal nature of calcium buffering by parvalbumin are discussed in relation to remediation of diastolic dysfunction. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction.
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Affiliation(s)
- Michelle L Asp
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
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43
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Whittington AC, Moerland TS. Resurrecting prehistoric parvalbumins to explore the evolution of thermal compensation in extant Antarctic fish parvalbumins. J Exp Biol 2012; 215:3281-92. [PMID: 22693024 DOI: 10.1242/jeb.070615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Parvalbumins (PVs) from Antarctic notothenioid fishes display a pattern of thermal adaptation that likely reflects evolutionary changes in protein conformational flexibility. We have used ancestral sequence reconstruction and homology modeling to identify two amino acid changes that could potentially account for the present thermal sensitivity pattern of Antarctic fish PVs compared with a PV from a theoretical warm-adapted ancestral fish. To test this hypothesis, ancient PVs were resurrected in the lab using PV from the notothenioid Gobionotothen gibberifrons as a platform for introducing mutations comparable to the reconstructed ancestral PV sequences. The wild-type PV (WT) as well as three mutant expression constructs were engineered: lysine 8 to asparagine (K8N), lysine 26 to asparagine (K26N) and a double mutant (DM). Calcium equilibrium dissociation constants (K(d)) versus temperature curves for all mutants were right-shifted, as predicted, relative to that of WT PV. The K(d) values for the K8N and K26N single mutants were virtually identical at all temperatures and showed an intermediate level of thermal sensitivity. The DM construct displayed a full conversion of thermal sensitivity pattern to that of a PV from a warm/temperate-adapted fish. Additionally, the K(d) versus temperature curve for the WT construct revealed greater thermal sensitivity compared with the mutant constructs. Measurements of the rates of Ca(2+) dissociation (k(off)) showed that all mutants generally had slower k(off) values than WT at all temperatures. Calculated rates of Ca(2+) binding (k(on)) for the K8N and K26N mutants were similar to values for the WT PV at all temperatures. In contrast, the calculated k(on) values for the DM PV were faster, providing mechanistic insights into the nature of potentially adaptive changes in Ca(2+) binding in this PV. The overall results suggest that the current thermal phenotype of Antarctic PVs can be recapitulated by just two amino acid substitutions.
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Affiliation(s)
- A Carl Whittington
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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44
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Senguen FT, Grabarek Z. X-ray structures of magnesium and manganese complexes with the N-terminal domain of calmodulin: insights into the mechanism and specificity of metal ion binding to an EF-hand. Biochemistry 2012; 51:6182-94. [PMID: 22803592 DOI: 10.1021/bi300698h] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Calmodulin (CaM), a member of the EF-hand superfamily, regulates many aspects of cell function by responding specifically to micromolar concentrations of Ca(2+) in the presence of an ~1000-fold higher concentration of cellular Mg(2+). To explain the structural basis of metal ion binding specificity, we have determined the X-ray structures of the N-terminal domain of calmodulin (N-CaM) in complexes with Mg(2+), Mn(2+), and Zn(2+). In contrast to Ca(2+), which induces domain opening in CaM, octahedrally coordinated Mg(2+) and Mn(2+) stabilize the closed-domain, apo-like conformation, while tetrahedrally coordinated Zn(2+) ions bind at the protein surface and do not compete with Ca(2+). The relative positions of bound Mg(2+) and Mn(2+) within the EF-hand loops are similar to those of Ca(2+); however, the Glu side chain at position 12 of the loop, whose bidentate interaction with Ca(2+) is critical for domain opening, does not bind directly to either Mn(2+) or Mg(2+), and the vacant ligand position is occupied by a water molecule. We conclude that this critical interaction is prevented by specific stereochemical constraints imposed on the ligands by the EF-hand β-scaffold. The structures suggest that Mg(2+) contributes to the switching off of calmodulin activity and possibly other EF-hand proteins at the resting levels of Ca(2+). The Mg(2+)-bound N-CaM structure also provides a unique view of a transiently bound hydrated metal ion and suggests a role for the hydration water in the metal-induced conformational change.
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Affiliation(s)
- F Timur Senguen
- Boston Biomedical Research Institute, Watertown, MA 02472, USA
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45
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Junctate is a Ca2+-sensing structural component of Orai1 and stromal interaction molecule 1 (STIM1). Proc Natl Acad Sci U S A 2012; 109:8682-7. [PMID: 22586105 DOI: 10.1073/pnas.1200667109] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Orai1 and stromal interaction molecule (STIM)1 are critical components of Ca(2+) release-activated Ca(2+) (CRAC) channels. Orai1 is a pore subunit of CRAC channels, and STIM1 acts as an endoplasmic reticulum (ER) Ca(2+) sensor that detects store depletion. Upon store depletion after T-cell receptor stimulation, STIM1 translocates and coclusters with Orai1 at sites of close apposition of the plasma membrane (PM) and the ER membrane. However, the molecular components of these ER-PM junctions remain poorly understood. Using affinity protein purification, we uncovered junctate as an interacting partner of Orai1-STIM1 complex. Furthermore, we identified a Ca(2+)-binding EF-hand motif in the ER-luminal region of junctate. Mutation of this EF-hand domain of junctate impaired its Ca(2+) binding and resulted in partial activation of CRAC channels and clustering of STIM1 independently of store depletion. In addition to the known mechanisms of STIM1 clustering (i.e., phosphoinositide and Orai1 binding), our study identifies an alternate mechanism to recruit STIM1 into the ER-PM junctions via binding to junctate. We propose that junctate, a Ca(2+)-sensing ER protein, is a structural component of the ER-PM junctions where Orai1 and STIM1 cluster and interact in T cells.
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46
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Schulze C, Sticht H, Meyerhoff P, Dietrich P. Differential contribution of EF-hands to the Ca²⁺-dependent activation in the plant two-pore channel TPC1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 68:424-32. [PMID: 21736651 DOI: 10.1111/j.1365-313x.2011.04697.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Two-pore channels (TPC) have been established as components of calcium signalling networks in plants and animals. In plants, TPC1 in the vacuolar membrane is gated open upon binding of calcium in a voltage-dependent manner. Here, we analyzed the molecular mechanism of the Ca²⁺-dependent activity of TPC1 from Arabidopsis thaliana, using site-directed mutagenesis of its two canonical EF-hands. Wild-type TPC1 and TPC1-D335A with a mutated first Ca²⁺ ligand in EF-hand 1 produced channels that retained their voltage- and Ca²⁺-dependent gating characteristics, but were less sensitive at Ca²⁺ concentrations < 200 μm. Additional mutation of the first Ca²⁺ ligand in EF-hand 2 resulted in silent TPC1-D335A/D376A channels. Similarly, the single mutant TPC1-D376A could not be activated up to 1 mm Ca²⁺, indicating that the second EF-hand is essential for the Ca²⁺-dependent channel gating. Molecular modeling suggests that EF-hand 1 displays a low-affinity Ca²⁺/Mg²⁺-binding site, while EF-hand 2 represents a high-affinity Ca²⁺-binding site. Together, our data prove that EF-hand 2 is responsible for the Ca²⁺-receptor characteristics of TPC1, while EF-hand 1 is a structural site required to enable channel responses at physiological changes in Ca²⁺ concentration.
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Affiliation(s)
- Christina Schulze
- Department Biology, Molecular Plant Physiology, and Erlangen Centre of Plant Science, Staudtstraße 5, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
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47
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Zhang J, Shettigar V, Zhang GC, Kindell DG, Liu X, López JJ, Yerrimuni V, Davis GA, Davis JP. Engineering Parvalbumin for the Heart: Optimizing the Mg Binding Properties of Rat β-Parvalbumin. Front Physiol 2011; 2:77. [PMID: 22059076 PMCID: PMC3204457 DOI: 10.3389/fphys.2011.00077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 10/10/2011] [Indexed: 01/01/2023] Open
Abstract
Parvalbumin (PV), an EF-hand protein family member, is a delayed calcium buffer that exchanges magnesium for calcium to facilitate fast skeletal muscle relaxation. Genetic approaches that express parvalbumin in the heart also enhance relaxation and show promise of being therapeutic against various cardiac diseases where relaxation is compromised. Unfortunately, skeletal muscle PVs have very slow rates of Ca2+ dissociation and are prone to becoming saturated with Ca2+, eventually losing their buffering capability within the constantly beating heart. In order for PV to have a more therapeutic potential in the heart, a PV with faster rates of calcium dissociation and high Mg2+ affinity is needed. We demonstrate that at 35°C, rat β-PV has an ~30-fold faster rate of Ca2+ dissociation compared to rat skeletal muscle α-PV, and still possesses a physiologically relevant Ca2+ affinity (~100 nM). However, rat β-PV will not be a delayed Ca2+ buffer since its Mg2+ affinity is too low (~1 mM). We have engineered two mutations into rat β-PV, S55D and E62D, when observed alone increase Mg2+ affinity up to fivefold, but when combined increase Mg2+ affinity ~13-fold, well within a physiologically relevant affinity. Furthermore, the Mg2+ dissociation rate (172/s) from the engineered S55D, E62D PV is slow enough for delayed Ca2+ buffering. Additionally, the engineered PV retains a high Ca2+ affinity (132 nM) and fast rate of Ca2+ dissociation (64/s). These PV design strategies hold promise for the development of new therapies to remediate relaxation abnormalities in different heart diseases and heart failure.
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Affiliation(s)
- Jianchao Zhang
- Department of Physiology and Cell Biology, The Ohio State University Columbus, OH, USA
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48
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Ohashi W, Hirota H, Yamazaki T. Solution structure and fluctuation of the Mg(2+)-bound form of calmodulin C-terminal domain. Protein Sci 2011; 20:690-701. [PMID: 21312310 DOI: 10.1002/pro.598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Calmodulin (CaM) is a Ca(2+)-binding protein that functions as a ubiquitous Ca(2+)-signaling molecule, through conformational changes from the "closed" apo conformation to the "open" Ca(2+)-bound conformation. Mg(2+) also binds to CaM and stabilizes its folded structure, but the NMR signals are broadened by slow conformational fluctuations. Using the E104D/E140D mutant, designed to decrease the signal broadening in the presence of Mg(2+) with minimal perturbations of the overall structure, the solution structure of the Mg(2+)-bound form of the CaM C-terminal domain was determined by multidimensional NMR spectroscopy. The Mg(2+)-induced conformational change mainly occurred in EF hand IV, while EF-hand III retained the apo structure. The helix G and helix H sides of the binding sequence undergo conformational changes needed for the Mg(2+) coordination, and thus the helices tilt slightly. The aromatic rings on helix H move to form a new cluster of aromatic rings in the hydrophobic core. Although helix G tilts slightly to the open orientation, the closed conformation is maintained. The fact that the Mg(2+)-induced conformational changes in EF-hand IV and the hydrophobic core are also seen upon Ca(2+) binding suggests that the Ca(2+)-induced conformational changes can be divided into two categories, those specific to Ca(2+) and those common to Ca(2+) and Mg(2+).
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Affiliation(s)
- Wakana Ohashi
- Genomic Sciences Center, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama 230-0045, Japan
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49
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Grabarek Z. Insights into modulation of calcium signaling by magnesium in calmodulin, troponin C and related EF-hand proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:913-21. [PMID: 21262274 DOI: 10.1016/j.bbamcr.2011.01.017] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 10/18/2022]
Abstract
The Ca(2+)-binding helix-loop-helix structural motif called "EF-hand" is a common building block of a large family of proteins that function as intracellular Ca(2+)-receptors. These proteins respond specifically to micromolar concentrations of Ca(2+) in the presence of ~1000-fold excess of the chemically similar divalent cation Mg(2+). The intracellular free Mg(2+) concentration is tightly controlled in a narrow range of 0.5-1.0mM, which at the resting Ca(2+) levels is sufficient to fully or partially saturate the Ca(2+)-binding sites of many EF-hand proteins. Thus, to convey Ca(2+) signals, EF-hand proteins must respond differently to Ca(2+) than to Mg(2+). In this review the structural aspects of Mg(2+) binding to EF-hand proteins are considered and interpreted in light of the recently proposed two-step Ca(2+)-binding mechanism (Grabarek, Z., J. Mol. Biol., 2005, 346, 1351). It is proposed that, due to stereochemical constraints imposed by the two-EF-hand domain structure, the smaller Mg(2+) ion cannot engage the ligands of an EF-hand in the same way as Ca(2+) and defaults to stabilizing the apo-like conformation of the EF-hand. It is proposed that Mg(2+) plays an active role in the Ca(2+)-dependent regulation of cellular processes by stabilizing the "off state" of some EF-hand proteins, thereby facilitating switching off their respective target enzymes at the resting Ca(2+) levels. Therefore, some pathological conditions attributed to Mg(2+) deficiency might be related to excessive activation of underlying Ca(2+)-regulated cellular processes. This article is part of a Special Issue entitled: 11th European Symposium on Calcium.
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Affiliation(s)
- Zenon Grabarek
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA 02472-2829, USA.
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50
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Kapoor N, Gupta R, Menon ST, Folta-Stogniew E, Raleigh DP, Sakmar TP. Nucleobindin 1 is a calcium-regulated guanine nucleotide dissociation inhibitor of G{alpha}i1. J Biol Chem 2010; 285:31647-60. [PMID: 20679342 PMCID: PMC2951237 DOI: 10.1074/jbc.m110.148429] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Indexed: 01/06/2023] Open
Abstract
Nucleobindin 1 (NUCB1) is a widely expressed multidomain calcium-binding protein whose precise physiological and biochemical functions are not well understood. We engineered and heterologously expressed a soluble form of NUCB1 (sNUCB1) and characterized its biophysical and biochemical properties. We show that sNUCB1 exists as a dimer in solution and that each monomer binds two divalent calcium cations. Calcium binding causes conformational changes in sNUCB1 as judged by circular dichroism and fluorescence spectroscopy experiments. Earlier reports suggested that NUCB1 might interact with heterotrimeric G protein α subunits. We show that dimeric calcium-free sNUCB1 binds to expressed Gα(i1) and that calcium binding inhibits the interaction. The binding of sNUCB1 to Gα(i1) inhibits its basal rate of GDP release and slows its rate and extent of GTPγS uptake. Additionally, our tissue culture experiments show that sNUCB1 prevents receptor-mediated Gα(i)-dependent inhibition of adenylyl cyclase. Thus, we conclude that sNUCB1 is a calcium-dependent guanine nucleotide dissociation inhibitor (GDI) for Gα(i1). To our knowledge, sNUCB1 is the first example of a calcium-dependent GDI for heterotrimeric G proteins. We also show that the mechanism of GDI activity of sNUCB1 is unique and does not arise from the consensus GoLoco motif found in RGS proteins. We propose that cytoplasmic NUCB1 might function to regulate heterotrimeric G protein trafficking and G protein-coupled receptor-mediated signal transduction pathways.
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Affiliation(s)
- Neeraj Kapoor
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
| | - Ruchi Gupta
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
| | - Santosh T. Menon
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
| | - Ewa Folta-Stogniew
- the W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, Connecticut 06520, and
| | - Daniel P. Raleigh
- the Department of Chemistry and
- Graduate Program in Biochemistry and Structural Biology and Graduate Program in Biophysics, State University of New York, Stony Brook, New York 11794
| | - Thomas P. Sakmar
- From the Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10065
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