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Eisner D, Neher E, Taschenberger H, Smith G. Physiology of intracellular calcium buffering. Physiol Rev 2023; 103:2767-2845. [PMID: 37326298 DOI: 10.1152/physrev.00042.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/08/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023] Open
Abstract
Calcium signaling underlies much of physiology. Almost all the Ca2+ in the cytoplasm is bound to buffers, with typically only ∼1% being freely ionized at resting levels in most cells. Physiological Ca2+ buffers include small molecules and proteins, and experimentally Ca2+ indicators will also buffer calcium. The chemistry of interactions between Ca2+ and buffers determines the extent and speed of Ca2+ binding. The physiological effects of Ca2+ buffers are determined by the kinetics with which they bind Ca2+ and their mobility within the cell. The degree of buffering depends on factors such as the affinity for Ca2+, the Ca2+ concentration, and whether Ca2+ ions bind cooperatively. Buffering affects both the amplitude and time course of cytoplasmic Ca2+ signals as well as changes of Ca2+ concentration in organelles. It can also facilitate Ca2+ diffusion inside the cell. Ca2+ buffering affects synaptic transmission, muscle contraction, Ca2+ transport across epithelia, and the killing of bacteria. Saturation of buffers leads to synaptic facilitation and tetanic contraction in skeletal muscle and may play a role in inotropy in the heart. This review focuses on the link between buffer chemistry and function and how Ca2+ buffering affects normal physiology and the consequences of changes in disease. As well as summarizing what is known, we point out the many areas where further work is required.
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Affiliation(s)
- David Eisner
- Division of Cardiovascular Sciences, University of Manchester, Manchester, United Kingdom
| | - Erwin Neher
- Membrane Biophysics Laboratory, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Holger Taschenberger
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Godfrey Smith
- School of Cardiovascular and Metabolic Health, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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2
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Elverson K, Freeman S, Manson F, Warwicker J. Computational Investigation of Mechanisms for pH Modulation of Human Chloride Channels. Molecules 2023; 28:5753. [PMID: 37570721 PMCID: PMC10420675 DOI: 10.3390/molecules28155753] [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: 11/29/2022] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Many transmembrane proteins are modulated by intracellular or extracellular pH. Investigation of pH dependence generally proceeds by mutagenesis of a wide set of amino acids, guided by properties such as amino-acid conservation and structure. Prediction of pKas can streamline this process, allowing rapid and effective identification of amino acids of interest with respect to pH dependence. Commencing with the calcium-activated chloride channel bestrophin 1, the carboxylate ligand structure around calcium sites relaxes in the absence of calcium, consistent with a measured lack of pH dependence. By contrast, less relaxation in the absence of calcium in TMEM16A, and maintenance of elevated carboxylate sidechain pKas, is suggested to give rise to pH-dependent chloride channel activity. This hypothesis, modulation of calcium/proton coupling and pH-dependent activity through the extent of structural relaxation, is shown to apply to the well-characterised cytosolic proteins calmodulin (pH-independent) and calbindin D9k (pH-dependent). Further application of destabilised, ionisable charge sites, or electrostatic frustration, is made to other human chloride channels (that are not calcium-activated), ClC-2, GABAA, and GlyR. Experimentally determined sites of pH modulation are readily identified. Structure-based tools for pKa prediction are freely available, allowing users to focus on mutagenesis studies, construct hypothetical proton pathways, and derive hypotheses such as the model for control of pH-dependent calcium activation through structural flexibility. Predicting altered pH dependence for mutations in ion channel disorders can support experimentation and, ultimately, clinical intervention.
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Affiliation(s)
- Kathleen Elverson
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Sally Freeman
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Forbes Manson
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Jim Warwicker
- Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK
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3
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Linse S, Thulin E, Nilsson H, Stigler J. Benefits and constrains of covalency: the role of loop length in protein stability and ligand binding. Sci Rep 2020; 10:20108. [PMID: 33208843 PMCID: PMC7674454 DOI: 10.1038/s41598-020-76598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 10/26/2020] [Indexed: 11/12/2022] Open
Abstract
Protein folding is governed by non-covalent interactions under the benefits and constraints of the covalent linkage of the backbone chain. In the current work we investigate the influence of loop length variation on the free energies of folding and ligand binding in a small globular single-domain protein containing two EF-hand subdomains—calbindin D9k. We introduce a linker extension between the subdomains and vary its length between 1 to 16 glycine residues. We find a close to linear relationship between the linker length and the free energy of folding of the Ca2+-free protein. In contrast, the linker length has only a marginal effect on the Ca2+ affinity and cooperativity. The variant with a single-glycine extension displays slightly increased Ca2+ affinity, suggesting that the slightly extended linker allows optimized packing of the Ca2+-bound state. For the extreme case of disconnected subdomains, Ca2+ binding becomes coupled to folding and assembly. Still, a high affinity between the EF-hands causes the non-covalent pair to retain a relatively high apparent Ca2+ affinity. Our results imply that loop length variation could be an evolutionary option for modulating properties such as protein stability and turnover without compromising the energetics of the specific function of the protein.
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Affiliation(s)
- Sara Linse
- Departments of Biophysical Chemistry, Biochemistry and Structural Biology, Lund University, Lund, Sweden.
| | - Eva Thulin
- Departments of Biophysical Chemistry, Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Hanna Nilsson
- Departments of Biophysical Chemistry, Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Johannes Stigler
- Departments of Biophysical Chemistry, Biochemistry and Structural Biology, Lund University, Lund, Sweden. .,Gene Center, Ludwig-Maximilians-University, 81377, Munich, Germany.
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4
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Orton HW, Otting G. Accurate Electron-Nucleus Distances from Paramagnetic Relaxation Enhancements. J Am Chem Soc 2018; 140:7688-7697. [PMID: 29790335 DOI: 10.1021/jacs.8b03858] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Measurements of paramagnetic relaxation enhancements (PREs) in 1H NMR spectra are an important tool to obtain long-range distance information in proteins, but quantitative interpretation is easily compromised by nonspecific intermolecular PREs. Here we show that PREs generated by lanthanides with anisotropic magnetic susceptibilities offer a route to accurate calibration-free distance measurements. As these lanthanides change 1H chemical shifts due to pseudocontact shifts, the relaxation rates in the paramagnetic and diamagnetic state can be measured with a single sample that simultaneously contains the protein labeled with a paramagnetic and a diamagnetic lanthanide ion. Nonspecific intermolecular PREs are thus automatically subtracted when calculating the PREs as the difference in nuclear relaxation rates between paramagnetic and diamagnetic protein. Although PREs from lanthanides with anisotropic magnetic susceptibilities are complicated by additional cross-correlation effects and residual dipolar couplings (RDCs) in the paramagnetic state, these effects can be controlled by the choice of lanthanide ion and experimental conditions. Using calbindin D9k with erbium, we succeeded in measuring intramolecular PREs with unprecedented accuracy, resulting in distance predictions with a root-mean-square-deviation of <0.9 Å in the range 11-24 Å.
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Affiliation(s)
- Henry W Orton
- Research School of Chemistry , Australian National University , Canberra , Australian Capital Territory 2601 , Australia
| | - Gottfried Otting
- Research School of Chemistry , Australian National University , Canberra , Australian Capital Territory 2601 , Australia
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5
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Charoenphandhu N, Kraidith K, Lertsuwan K, Sripong C, Suntornsaratoon P, Svasti S, Krishnamra N, Wongdee K. Na +/H + exchanger 3 inhibitor diminishes hepcidin-enhanced duodenal calcium transport in hemizygous β-globin knockout thalassemic mice. Mol Cell Biochem 2016; 427:201-208. [PMID: 27995414 DOI: 10.1007/s11010-016-2911-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/03/2016] [Indexed: 12/15/2022]
Abstract
Recent investigation has shown that the liver-derived iron-regulating hormone, hepcidin, can potentiate intestinal calcium absorption in hemizygous β-globin knockout thalassemic (BKO) mice. Since the upregulation of Fe2+ and H+ cotransporter, divalent metal transporter (DMT)-1, has been shown to correlate with thalassemia-induced intestinal calcium absorption impairment, the inhibition of the apical Na+/H+ exchanger (NHE)-3 that is essential for cytoplasmic pH regulation and transepithelial sodium absorption was hypothesized to negatively affect hepcidin action. Herein, the positive effect of hepcidin on the duodenal calcium transport was evaluated using Ussing chamber technique. The results showed that BKO mice had lower absorptive surface area and duodenal calcium transport than wild-type mice. Besides, paracellular transport of zinc in BKO mice was compromised. Hepcidin administration completely restored calcium transport. Since this hepcidin action was totally abolished by inhibitors of the basolateral calcium transporters, Na+/Ca2+ exchanger (NCX1) and plasma membrane Ca2+-ATPase (PMCA1b), the enhanced calcium flux potentially occurred through the transcellular pathway rather than paracellular pathway. Interestingly, the selective NHE3 inhibitor, 100 nM tenapanor, markedly inhibited hepcidin-enhanced calcium transport. Accordingly, hepcidin is one of the promising therapeutic agents for calcium malabsorption in β-thalassemia. It mainly stimulates the transcellular calcium transport across the duodenal epithelium in an NHE3-dependent manner.
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Affiliation(s)
- Narattaphol Charoenphandhu
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Kamonshanok Kraidith
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kornkamon Lertsuwan
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chanakarn Sripong
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Panan Suntornsaratoon
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Saovaros Svasti
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Nateetip Krishnamra
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kannikar Wongdee
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, Thailand. .,Office of Academic Management, Faculty of Allied Health Sciences, Burapha University, Chonburi, Thailand.
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6
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Thammayon N, Wongdee K, Lertsuwan K, Suntornsaratoon P, Thongbunchoo J, Krishnamra N, Charoenphandhu N. Na +/H + exchanger 3 inhibitor diminishes the amino-acid-enhanced transepithelial calcium transport across the rat duodenum. Amino Acids 2016; 49:725-734. [PMID: 27981415 DOI: 10.1007/s00726-016-2374-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/29/2016] [Indexed: 12/22/2022]
Abstract
Na+/H+ exchanger (NHE)-3 is important for intestinal absorption of nutrients and minerals, including calcium. The previous investigations have shown that the intestinal calcium absorption is also dependent on luminal nutrients, but whether aliphatic amino acids and glucose, which are abundant in the luminal fluid during a meal, similarly enhance calcium transport remains elusive. Herein, we used the in vitro Ussing chamber technique to determine epithelial electrical parameters, i.e., potential difference (PD), short-circuit current (Isc), and transepithelial resistance, as well as 45Ca flux in the rat duodenum directly exposed on the mucosal side to glucose or various amino acids. We found that mucosal glucose exposure led to the enhanced calcium transport, PD, and Isc, all of which were insensitive to NHE3 inhibitor (100 nM tenapanor). In the absence of mucosal glucose, several amino acids (12 mM in the mucosal side), i.e., alanine, isoleucine, leucine, proline, and hydroxyproline, markedly increased the duodenal calcium transport. An inhibitor for NHE3 exposure on the mucosal side completely abolished proline- and leucine-enhanced calcium transport, but not transepithelial transport of both amino acids themselves. In conclusion, glucose and certain amino acids in the mucosal side were potent stimulators of the duodenal calcium absorption, but only amino-acid-enhanced calcium transport was NHE3-dependent.
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Affiliation(s)
- Nithipak Thammayon
- Department of Physiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand.,Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Kannikar Wongdee
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Faculty of Allied Health Sciences, Burapha University, Chonburi, 20131, Thailand
| | - Kornkamon Lertsuwan
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.,Department of Biochemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Panan Suntornsaratoon
- Department of Physiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand.,Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Jirawan Thongbunchoo
- Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nateetip Krishnamra
- Department of Physiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand.,Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Narattaphol Charoenphandhu
- Department of Physiology, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand. .,Center of Calcium and Bone Research (COCAB), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand. .,Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand.
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7
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Ferenczi EA, Vierock J, Atsuta-Tsunoda K, Tsunoda SP, Ramakrishnan C, Gorini C, Thompson K, Lee SY, Berndt A, Perry C, Minniberger S, Vogt A, Mattis J, Prakash R, Delp S, Deisseroth K, Hegemann P. Optogenetic approaches addressing extracellular modulation of neural excitability. Sci Rep 2016; 6:23947. [PMID: 27045897 PMCID: PMC4820717 DOI: 10.1038/srep23947] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/10/2016] [Indexed: 12/28/2022] Open
Abstract
The extracellular ionic environment in neural tissue has the capacity to influence, and be influenced by, natural bouts of neural activity. We employed optogenetic approaches to control and investigate these interactions within and between cells, and across spatial scales. We began by developing a temporally precise means to study microdomain-scale interactions between extracellular protons and acid-sensing ion channels (ASICs). By coupling single-component proton-transporting optogenetic tools to ASICs to create two-component optogenetic constructs (TCOs), we found that acidification of the local extracellular membrane surface by a light-activated proton pump recruited a slow inward ASIC current, which required molecular proximity of the two components on the membrane. To elicit more global effects of activity modulation on ‘bystander’ neurons not under direct control, we used densely-expressed depolarizing (ChR2) or hyperpolarizing (eArch3.0, eNpHR3.0) tools to create a slow non-synaptic membrane current in bystander neurons, which matched the current direction seen in the directly modulated neurons. Extracellular protons played contributory role but were insufficient to explain the entire bystander effect, suggesting the recruitment of other mechanisms. Together, these findings present a new approach to the engineering of multicomponent optogenetic tools to manipulate ionic microdomains, and probe the complex neuronal-extracellular space interactions that regulate neural excitability.
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Affiliation(s)
- Emily A Ferenczi
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.,Neurosciences, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Johannes Vierock
- Institute of Biology, Experimental Biophysics, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Kyoko Atsuta-Tsunoda
- Institute of Biology, Experimental Biophysics, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Satoshi P Tsunoda
- Institute of Biology, Experimental Biophysics, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Charu Ramakrishnan
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Christopher Gorini
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Kimberly Thompson
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Soo Yeun Lee
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Andre Berndt
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Chelsey Perry
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Sonja Minniberger
- Institute of Biology, Experimental Biophysics, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Arend Vogt
- Institute of Biology, Experimental Biophysics, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Joanna Mattis
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.,Neurosciences, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Rohit Prakash
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.,Neurosciences, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Scott Delp
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.,HHMI, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.,Department of Psychiatry &Behavioral Science, Stanford University, 401 Quarry Road, Stanford, CA 94305, USA
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Invalidenstraße 42, D-10115 Berlin, Germany
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8
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Herling TW, Arosio P, Müller T, Linse S, Knowles TPJ. A microfluidic platform for quantitative measurements of effective protein charges and single ion binding in solution. Phys Chem Chem Phys 2015; 17:12161-7. [DOI: 10.1039/c5cp00746a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microfluidic electrophoresis enables the comparison of dry sequence and solvated protein charges, and the detection of protein–ion binding.
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Affiliation(s)
| | - Paolo Arosio
- Department of Chemistry
- University of Cambridge
- Cambridge
- UK
| | - Thomas Müller
- Department of Chemistry
- University of Cambridge
- Cambridge
- UK
| | - Sara Linse
- Department of Biochemistry and Structural Biology
- Lund University
- Lund
- Sweden
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9
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Ahmed MH, Byrne JA, McLaughlin J, Ahmed W. Study of Human Serum Albumin Adsorption and Conformational Change on DLC and Silicon Doped DLC Using XPS and FTIR Spectroscopy. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jbnb.2013.42024] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Murphy LA, Ramirez EA, Trinh VT, Herman AM, Anderson VC, Brewster JL. Endoplasmic reticulum stress or mutation of an EF-hand Ca(2+)-binding domain directs the FKBP65 rotamase to an ERAD-based proteolysis. Cell Stress Chaperones 2011; 16:607-19. [PMID: 21761186 PMCID: PMC3220392 DOI: 10.1007/s12192-011-0270-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/12/2011] [Accepted: 05/18/2011] [Indexed: 10/18/2022] Open
Abstract
FKBP65 is an endoplasmic reticulum (ER)-localized chaperone and rotamase, with cargo proteins that include tropoelastin and collagen. In humans, mutations in FKBP65 have recently been shown to cause a form of osteogenesis imperfecta (OI), a brittle bone disease resulting from deficient secretion of mature type I collagen. In this work, we describe the rapid proteolysis of FKBP65 in response to ER stress signals that activate the release of ER Ca(2+) stores. A large-scale screen for stress-induced cellular changes revealed FKBP65 proteins to decrease within 6-12 h of stress activation. Inhibiting IP(3)R-mediated ER Ca(2+) release blocked this response. No other ER-localized chaperone and folding mediators assessed in the study displayed this phenomenon, indicating that this rapid proteolysis of folding mediator is distinctive. Imaging and cellular fractionation confirmed the localization of FKBP65 (72 kDa glycoprotein) to the ER of untreated cells, a rapid decrease in protein levels following ER stress, and the corresponding appearance of a 30-kDa fragment in the cytosol. Inhibition of the proteasome during ER stress revealed an accumulation of FKBP65 in the cytosol, consistent with retrotranslocation and a proteasome-based proteolysis. To assess the role of Ca(2+)-binding EF-hand domains in FKBP65 stability, a recombinant FKBP65-GFP construct was engineered to ablate Ca(2+) binding at each of two EF-hand domains. Cells transfected with the wild-type construct displayed ER localization of the FKBP65-GFP protein and a proteasome-dependent proteolysis in response to ER stress. Recombinant FKBP65-GFP carrying a defect in the EF1 Ca(2+)-binding domain displayed diminished protein in the ER when compared to wild-type FKBP65-GFP. Proteasome inhibition restored mutant protein to levels similar to that of the wild-type FKBP65-GFP. A similar mutation in EF2 did not confer FKBP65 proteolysis. This work supports a model in which stress-induced changes in ER Ca(2+) stores induce the rapid proteolysis of FKBP65, a chaperone and folding mediator of collagen and tropoelastin. The destruction of this protein may identify a cellular strategy for replacement of protein folding machinery following ER stress. The implications for stress-induced changes in the handling of aggregate-prone proteins in the ER-Golgi secretory pathway are discussed. This work was supported by grants from the National Institutes of Health (R15GM065139) and the National Science Foundation (DBI-0452587).
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Affiliation(s)
- Lindsey A. Murphy
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263 USA
| | - Emily A. Ramirez
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263 USA
| | - Van T. Trinh
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263 USA
| | - Alexander M. Herman
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263 USA
| | - Valen C. Anderson
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263 USA
| | - Jay L. Brewster
- Natural Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, CA 90263 USA
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11
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Adsorption and photocatalytic degradation of human serum albumin on TiO2 and Ag–TiO2 films. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2011.05.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Johnson E. NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion. JOURNAL OF BIOMOLECULAR NMR 2011; 50:59-70. [PMID: 21503632 DOI: 10.1007/s10858-011-9504-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 02/09/2011] [Indexed: 05/30/2023]
Abstract
NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca(2+)-free) state of calbindin D(9k). Calculations are performed in an expanding reference frame so as to discriminate between the effects of short- and long-range motions. This approach reveals that the dominant contributions to the order parameters are short-range. Longer-range contributions are limited to specific sites, many of which have been recognized in previous studies of correlated motions. These sites are identified on the basis of an effective reorientational number, n ( eff ). Not only does this parameter identify sites of short- and long-range motion, it also provides a way of evaluating the separability condition that is key to the Lipari-Szabo model-free method. When analyzed in conjunction with the Prompers-Brüschweiler separability index, the n ( eff ) values indicate that longer-range motions play a more prominent role in apo calbindin than they do in ubiquitin.
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Affiliation(s)
- Eric Johnson
- Department of Chemistry and Physical Sciences, College of Mount St. Joseph, Cincinnati, OH 45233, USA.
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13
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Krizaj D, Mercer AJ, Thoreson WB, Barabas P. Intracellular pH modulates inner segment calcium homeostasis in vertebrate photoreceptors. Am J Physiol Cell Physiol 2010; 300:C187-97. [PMID: 20881233 DOI: 10.1152/ajpcell.00264.2010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Neuronal metabolic and electrical activity is associated with shifts in intracellular pH (pH(i)) proton activity and state-dependent changes in activation of signaling pathways in the plasma membrane, cytosol, and intracellular compartments. We investigated interactions between two intracellular messenger ions, protons and calcium (Ca²(+)), in salamander photoreceptor inner segments loaded with Ca²(+) and pH indicator dyes. Resting cytosolic pH in rods and cones in HEPES-based saline was acidified by ∼0.4 pH units with respect to pH of the superfusing saline (pH = 7.6), indicating that dissociated inner segments experience continuous acid loading. Cytosolic alkalinization with ammonium chloride (NH₄Cl) depolarized photoreceptors and stimulated Ca²(+) release from internal stores, yet paradoxically also evoked dose-dependent, reversible decreases in [Ca²(+)](i). Alkalinization-evoked [Ca²(+)](i) decreases were independent of voltage-operated and store-operated Ca²(+) entry, plasma membrane Ca²(+) extrusion, and Ca²(+) sequestration into internal stores. The [Ca²(+)](i)-suppressive effects of alkalinization were antagonized by the fast Ca²(+) buffer BAPTA, suggesting that pH(i) directly regulates Ca²(+) binding to internal anionic sites. In summary, this data suggest that endogenously produced protons continually modulate the membrane potential, release from Ca²(+) stores, and intracellular Ca²(+) buffering in rod and cone inner segments.
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Affiliation(s)
- David Krizaj
- Department of Ophthalmology, Moran Eye Center, University of Utah School of Medicine, Salt Lake City, 84132, USA.
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Lepsík M, Field MJ. Binding of calcium and other metal ions to the EF-hand loops of calmodulin studied by quantum chemical calculations and molecular dynamics simulations. J Phys Chem B 2007; 111:10012-22. [PMID: 17661504 DOI: 10.1021/jp0716583] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Calcium ion binding by the four EF-hand motifs of the protein calmodulin (CaM) is a central event in Ca2+-based cellular signaling. To understand molecular details of this complex process, isolated Ca2+-binding loops can be studied, by use of both experiments and calculations. In this work, we explore the metal specificity of the four Ca2+-binding loops of CaM using density functional theory (DFT) quantum chemical calculations and molecular dynamics simulations. We study CaM complexes with the physiologically important ions of calcium (Ca2+) and magnesium (Mg2+) and also with two other ions, strontium (Sr2+) and lanthanum (La3+). The former is of interest in the area of radioactive waste bioremediation, whereas the latter is often used as a probe of Ca2+-binding sites. We obtain intrinsic metal ion-loop binding energies as well as their components: vacuum, charge-transfer, solvation, entropy, and deformation terms. A detailed analysis of the results reveals that the total binding energy depends on a delicate balance among these energy components. They, in turn, are determined by the cation's charge and size as well as the amino acid composition and flexibility of the loops and the identity of the metal-chelating residues.
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Affiliation(s)
- Martin Lepsík
- Laboratoire de Dynamique Moléculaire, Institut de Biologie Structurale-Jean-Pierre Ebel, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.
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Beuria TK, Shah JH, Santra MK, Kumar V, Panda D. Effects of pH and ionic strength on the assembly and bundling of FtsZ protofilaments: A possible role of electrostatic interactions in the bundling of protofilaments. Int J Biol Macromol 2006; 40:30-9. [PMID: 16815544 DOI: 10.1016/j.ijbiomac.2006.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 05/13/2006] [Accepted: 05/13/2006] [Indexed: 10/24/2022]
Abstract
Assembly, bundling and stability of FtsZ protofilaments are important for the formation and functioning of the cytokinetic Z-ring during bacterial division. We found that the bundling of FtsZ protofilaments decreased strongly with increasing pH from 6.0 to 7.9, while the assembly of FtsZ monomers did not decrease considerably. In addition, the disassembly of FtsZ protofilaments was strongly suppressed at pH 6.0 as compared to the elevated pHs. The far-UV circular dichroism spectra of the native FtsZ and the tryptophan emission spectra of mutated FtsZ (Y371W) did not change by increasing pH from 6 to 7.9 indicating that the structure of FtsZ was not altered significantly. Further, the inhibition of bundling of FtsZ protofilaments predominantly, and the inhibition of assembly to a lesser extent by salt indicated that electrostatic interactions are important for the assembly and bundling of FtsZ protofilaments. These observations are supported by the results of computational docking of Escherichia coli dimer structure. The results suggest that the basic intracellular pH (7.4-7.8) of E. coli may play a role in regulating the assembly dynamics of FtsZ in the Z-ring by reducing protofilament stability and bundling in bacterial cytoplasm.
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Affiliation(s)
- Tushar K Beuria
- School of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Xue WF, Szczepankiewicz O, Bauer MC, Thulin E, Linse S. Intra- versus intermolecular interactions in monellin: contribution of surface charges to protein assembly. J Mol Biol 2006; 358:1244-55. [PMID: 16574151 DOI: 10.1016/j.jmb.2006.02.069] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 02/24/2006] [Accepted: 02/25/2006] [Indexed: 10/24/2022]
Abstract
The relative significance of weak non-covalent interactions in biological context has been much debated. Here, we have addressed the contribution of Coulombic interactions to protein stability and assembly experimentally. The sweet protein monellin, a non-covalently linked heterodimeric protein, was chosen for this study because of its ability to spontaneously reconstitute from separated fragments. The reconstitution of monellin mutants containing large surface charge perturbations was compared to the thermostability of structurally equivalent single-chain monellin containing the same sets of mutations under varying salt concentrations. The affinity between monellin fragments is found to correlate with the thermostability of single chain monellin, indicating the involvement of the same underlying Coulombic interactions. This confirms that there are no principal differences in the interactions involved in folding and binding. Based on comparison with a previous mutational study involving hydrophobic core residues, the relative contribution of Coulombic interactions to stability and affinity is modest. However, the Coulombic perturbations only affect the association rates of reconstitution in contrast to perturbations involving hydrophobic residues, which affect primarily the dissociation rates. These results indicate that Coulombic interactions are likely to be of main importance for the association of protein assembly, relevant for functions of proteins.
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Affiliation(s)
- Wei-Feng Xue
- Department of Biophysical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund SE-22100, Sweden.
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Venkitaramani DV, Fulton DB, Andreotti AH, Johansen KM, Johansen J. Solution structure and backbone dynamics of Calsensin, an invertebrate neuronal calcium-binding protein. Protein Sci 2005; 14:1894-901. [PMID: 15937283 PMCID: PMC2253341 DOI: 10.1110/ps.051412605] [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: 10/25/2022]
Abstract
Calsensin is an EF-hand calcium-binding protein expressed by a subset of peripheral sensory neurons that fasciculate into a single tract in the leech central nervous system. Calsensin is a 9-kD protein with two EF-hand calcium-binding motifs. Using multidimensional NMR spectroscopy we have determined the solution structure and backbone dynamics of calcium-bound Calsensin. Calsensin consists of four helices forming a unicornate-type four-helix bundle. The residues in the third helix undergo slow conformational exchange indicating that the motion of this helix is associated with calciumbinding. The backbone dynamics of the protein as measured by (15)N relaxation rates and heteronuclear NOEs correlate well with the three-dimensional structure. Furthermore, comparison of the structure of Calsensin with other members of the EF-hand calcium-binding protein family provides insight into plausible mechanisms of calcium and target protein binding.
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Affiliation(s)
- Deepa V Venkitaramani
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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Palczewska M, Batta G, Groves P, Linse S, Kuznicki J. Characterization of calretinin I-II as an EF-hand, Ca2+, H+-sensing domain. Protein Sci 2005; 14:1879-87. [PMID: 15937279 PMCID: PMC2253342 DOI: 10.1110/ps.051369805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Calretinin, a neuronal protein with well-defined calcium-binding properties, has a poorly defined function. The pH dependent properties of calretinin (CR), the N-terminal (CR I-II), and C-terminal (CR III-VI) domains were investigated. A drop in pH within the intracellular range (from pH 7.5 to pH 6.5) leads to an increased hydrophobicity of calcium-bound CR and its domains as reported by fluorescence spectroscopy with the hydrophobic probe 2-(p-toluidino)-6-naphthalenesulfonic acid (TNS). The TNS data for the N- and C-terminal domains of CR are additive, providing further support for their independence within the full-length protein. Our work concentrated on CR I-II, which was found to have hydrophobic properties similar to calmodulin at lower pH. The elution of CR I-II from a phenyl-Sepharose column was consistent with the TNS data. The pH-dependent structural changes were further localized to residues 13-28 and 44-51 using nuclear magnetic resonance spectroscopy chemical shift analysis, and there appear to be no large changes in secondary structure. Protonation of His 12 and/or His 27 side chains, coupled with calcium chelation, appears to lead to the organization of a hydrophobic pocket in the N-terminal domain. CR may sense and respond to calcium, proton, and other signals, contributing to conflicting data on the proteins role as a calcium sensor or calcium buffer.
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Affiliation(s)
- Malgorzata Palczewska
- Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
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Dell'Orco D, Xue WF, Thulin E, Linse S. Electrostatic contributions to the kinetics and thermodynamics of protein assembly. Biophys J 2004; 88:1991-2002. [PMID: 15596501 PMCID: PMC1305251 DOI: 10.1529/biophysj.104.049189] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The role of electrostatic interactions in the assembly of a native protein structure was studied using fragment complementation. Contributions of salt, pH, or surface charges to the kinetics and equilibrium of calbindin D(9k) reconstitution was measured in the presence of Ca(2+) using surface plasmon resonance and isothermal titration calorimetry. Whereas surface charge substitutions primarily affect the dissociation rate constant, the association rates are correlated with subdomain net charge in a way expected for Coulomb interactions. The affinity is reduced in all mutants, with the largest effect (260-fold) observed for the double mutant K25E+K29E. At low net charge, detailed charge distribution is important, and charges remote from the partner EF-hand have less influence than close ones. The effects of salt and pH on the reconstitution are smaller than mutational effects. The interaction between the wild-type EF-hands occurs with high affinity (K(A) = 1.3 x 10(10) M(-1); K(D) = 80 pM). The enthalpy of association is overall favorable and there appears to be a very large favorable entropic contribution from the desolvation of hydrophobic surfaces that become buried in the complex. Electrostatic interactions contribute significantly to the affinity between the subdomains, but other factors, such as hydrophobic interactions, dominate.
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Affiliation(s)
- Daniele Dell'Orco
- Department of Biophysical Chemistry, Lund University, S-221 00 Lund, Sweden
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