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Denesyuk AI, Permyakov SE, Permyakov EA, Johnson MS, Denessiouk K, Uversky VN. Canonical structural-binding modes in the calmodulin-target protein complexes. J Biomol Struct Dyn 2023; 41:7582-7594. [PMID: 36106955 DOI: 10.1080/07391102.2022.2123391] [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: 05/11/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Abstract
Intracellular calcium sensor protein calmodulin (CaM) belongs to the large EF-hand protein superfamily. CaM shows a unique and not fully understood ability to bind to multiple targets, allows them to participate in a variety of regulatory processes. The protein has two approximately symmetrical globular domains (the N- and C-lobes). Analysis of the CaM-binding sites of target proteins showed that they have two hydrophobic 'anchor' amino acids separated by 10 to 17 residues. Consequently, several CaM-binding motifs: {1-10}, {1-11}, {1-13}, {1-14}, {1-16}, {1-17}, differing by the distance between the two anchor residues along the amino acid sequence, have been identified. Despite extensive structural information on the role of target-protein amino acid residues in the formation of complexes with CaM, much less is known about the role of amino acids from CaM contributing to these interactions. In this work, a quantitative analysis of the contact surfaces of CaM and target proteins has been carried out for 35 representative three-dimensional structures. It has been shown that, in addition to the two hydrophobic terminal residues of the target fragment, the interaction also involves residues that are 4 residues earlier in the sequence (binding mode {1-5}). It has also been found that the N- and C-lobes of CaM bind the {1-5} motif located at the ends of the target in a structurally identical manner. Methionine residues at positions 51 (corresponding to 124 in the C-lobe), 71 (144), and 72 (145) of the CaM amino acid sequence are key hydrophobic residues for this interaction. They are located at the N- and C-boundaries of the even EF-hand motifs. The hydrophobic core of CaM ('Ф-quatrefoil') consists of 10 amino acids in the N-lobe (and in the C-lobe): Phe16 (Phe89), Phe19 (Phe92), Ile27 (Ile100), Thr29 (Ala102), Leu32 (Leu105), Ile52 (Ile125), Val55 (Ala128), Ile63 (Val136), Phe65 (Tyr138), and Phe68 (Phe141) and do not intersect with the target-binding methionine residues. CaM belongs to the 'dynamic' group of EF-hand proteins, in which calcium and protein ligand binding causes only global conformational changes but does not alter the conservative 'black' and 'grey' clusters described in our earlier works (PLoS One. 2014; 9(10):e109287). The membership of CaM in the 'dynamic' group is determined by the triggering and protective methionine layer: Met51 (Met124), Met71 (Met144) and Met72 (Met145). HIGHLIGHTSInterchain interactions in the unique 35 CaM complex structures were analyzed.Methionine amino acids of the N- and C-lobes of CaM form triggering and protective layers.Interactions of the target terminal residues with these methionine layers are structurally identical.CaM belonging to the 'dynamic' group is determined by the triggering and protective methionine layer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alexander I Denesyuk
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, InFLAMES Research Flagship Center, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the, Russian Academy of Sciences, Federal Research Center, "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino Moscow Region, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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2
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Dürvanger Z, Juhász T, Liliom K, Harmat V. Structures of calmodulin-melittin complexes show multiple binding modes lacking classical anchoring interactions. J Biol Chem 2023; 299:104596. [PMID: 36906144 PMCID: PMC10140167 DOI: 10.1016/j.jbc.2023.104596] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Calmodulin (CaM) is a Ca2+ sensor protein found in all eukaryotic cells that regulates a large number of target proteins in a Ca2+ concentration-dependent manner. As a transient type hub protein, it recognizes linear motifs of its targets, though for the Ca2+-dependent binding no consensus sequence was identified. Its complex with melittin, a major component of bee venom, is often used as a model system of protein - protein complexes. Yet, the structural aspects of the binding are not well understood, as only diverse, low-resolution data are available concerning the association. We present the crystal structure of melittin in complex with Ca2+-saturated calmodulins from two, evolutionarily distant species, Homo sapiens and Plasmodium falciparum representing three binding modes of the peptide. Results - augmented by molecular dynamics simulations - indicate that multiple binding modes can exist for CaM-melittin complexes, as an intrinsic characteristic of the binding. While the helical structure of melittin remains, swapping of its salt bridges and partial unfolding of its C-terminal segment can occur. In contrast to the classical way of target recognition by CaM, we found that different sets of residues can anchor at the hydrophobic pockets of CaM, which were considered as main recognition sites. Finally, the nanomolar binding affinity of the CaM-melittin complex is created by an ensemble of arrangements of similar stability - tight binding is achieved not by optimized specific interactions but by simultaneously satisfying less optimal interaction patterns in co-existing different conformers.
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Affiliation(s)
- Zsolt Dürvanger
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Tünde Juhász
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Liliom
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Veronika Harmat
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary; ELKH-ELTE Protein Modelling Research Group, Eötvös Loránd Research Network, Budapest, Hungary.
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3
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Sosa-Peinado A, León-Cruz E, Velázquez-López I, Matuz-Mares D, Cano-Sánchez P, González-Andrade M. Theoretical-experimental studies of calmodulin-peptide interactions at different calcium equivalents. J Biomol Struct Dyn 2022; 40:2689-2700. [DOI: 10.1080/07391102.2020.1841679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Erika León-Cruz
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Deyamira Matuz-Mares
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Patricia Cano-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, México
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4
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Arakawa Y, Shiba T, Igawa K, Sasaki S, Tsuji H. 4′-Alkylseleno-4-cyanobiphenyls, nSeCB: synthesis and substituent effects on the phase-transition and liquid crystalline behaviors. CrystEngComm 2022. [DOI: 10.1039/d2ce00551d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A homologous series of 4′-alkylseleno-4-cyanobiphenyls (nSeCB) was synthesized and their phase-transition behaviors were investigated and compared with those of the alkyl, alkoxy, and alkylthio homologs.
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Affiliation(s)
- Yuki Arakawa
- Department of Applied Chemistry and Life Science, Graduate School of Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Takuma Shiba
- Department of Applied Chemistry and Life Science, Graduate School of Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Kazunobu Igawa
- Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan
| | - Shunsuke Sasaki
- Nantes Université, CNRS, Institut des Matériaux de Nantes Jean Rouxel, IMN, F-44000 Nantes, France
| | - Hideto Tsuji
- Department of Applied Chemistry and Life Science, Graduate School of Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
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5
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Young BD, Varney KM, Wilder PT, Costabile BK, Pozharski E, Cook ME, Godoy-Ruiz R, Clarke OB, Mancia F, Weber DJ. Physiologically Relevant Free Ca 2+ Ion Concentrations Regulate STRA6-Calmodulin Complex Formation via the BP2 Region of STRA6. J Mol Biol 2021; 433:167272. [PMID: 34592217 PMCID: PMC8568335 DOI: 10.1016/j.jmb.2021.167272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/13/2021] [Accepted: 09/21/2021] [Indexed: 11/28/2022]
Abstract
The interaction of calmodulin (CaM) with the receptor for retinol uptake, STRA6, involves an α-helix termed BP2 that is located on the intracellular side of this homodimeric transporter (Chen et al., 2016 [1]). In the absence of Ca2+, NMR data showed that a peptide derived from BP2 bound to the C-terminal lobe (C-lobe) of Mg2+-bound CaM (MgCaM). Upon titration of Ca2+ into MgCaM-BP2, NMR chemical shift perturbations (CSPs) were observed for residues in the C-lobe, including those in the EF-hand Ca2+-binding domains, EF3 and EF4 (CaKD = 60 ± 7 nM). As higher concentrations of free Ca2+ were achieved, CSPs occurred for residues in the N-terminal lobe (N-lobe) including those in EF1 and EF2 (CaKD = 1000 ± 160 nM). Thermodynamic and kinetic Ca2+ binding studies showed that BP2 addition increased the Ca2+-binding affinity of CaM and slowed its Ca2+ dissociation rates (koff) in both the C- and N-lobe EF-hand domains, respectively. These data are consistent with BP2 binding to the C-lobe of CaM at low free Ca2+ concentrations (<100 nM) like those found at resting intracellular levels. As free Ca2+ levels approach 1000 nM, which is typical inside a cell upon an intracellular Ca2+-signaling event, BP2 is shown here to interact with both the N- and C-lobes of Ca2+-loaded CaM (CaCaM-BP2). Because this structural rearrangement observed for the CaCaM-BP2 complex occurs as intracellular free Ca2+ concentrations approach those typical of a Ca2+-signaling event (CaKD = 1000 ± 160 nM), this conformational change could be relevant to vitamin A transport by full-length CaCaM-STRA6.
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Affiliation(s)
- Brianna D Young
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA
| | - Kristen M Varney
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Paul T Wilder
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Brianna K Costabile
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edwin Pozharski
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Mary E Cook
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA
| | - Raquel Godoy-Ruiz
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - David J Weber
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Dr., Rockville, MD 20850, USA.
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6
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Wang Z, Feng Y, Song T, Su J, Fu M, Lei H. Study on the interaction of Zea mays L. centrin and melittin. RSC Adv 2021; 11:36098-36104. [PMID: 35492757 PMCID: PMC9043476 DOI: 10.1039/d1ra06627g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/31/2021] [Indexed: 11/21/2022] Open
Abstract
Zea mays L. centrin (Zmcen) is a 20 kDa calcium binding protein also known as caltractin.
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Affiliation(s)
- Zhijun Wang
- Department of Chemistry, Changzhi University, Changzhi 046011, China
| | - Yanlong Feng
- Department of Chemistry, Changzhi University, Changzhi 046011, China
| | - Tiantian Song
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Jie Su
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Mengjie Fu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Haiying Lei
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
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7
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Nelson SED, Weber DK, Rebbeck RT, Cornea RL, Veglia G, Thomas DD. Met125 is essential for maintaining the structural integrity of calmodulin's C-terminal domain. Sci Rep 2020; 10:21320. [PMID: 33288831 PMCID: PMC7721703 DOI: 10.1038/s41598-020-78270-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/17/2020] [Indexed: 11/09/2022] Open
Abstract
We have used NMR and circular dichroism spectroscopy to investigate the structural and dynamic effects of oxidation on calmodulin (CaM), using peroxide and the Met to Gln oximimetic mutations. CaM is a Ca2+-sensitive regulatory protein that interacts with numerous targets. Due to its high methionine content, CaM is highly susceptible to oxidation by reactive oxygen species under conditions of cell stress and age-related muscle degeneration. CaM oxidation alters regulation of a host of CaM's protein targets, emphasizing the importance of understanding the mechanism of CaM oxidation in muscle degeneration and overall physiology. It has been shown that the M125Q CaM mutant can mimic the functional effects of methionine oxidation on CaM's regulation of the calcium release channel, ryanodine receptor (RyR). We report here that the M125Q mutation causes a localized unfolding of the C-terminal lobe of CaM, preventing the formation of a hydrophobic cluster of residues near the EF-hand Ca2+ binding sites. NMR analysis of CaM oxidation by peroxide offers further insights into the susceptibility of CaM's Met residues to oxidation and the resulting structural effects. These results further resolve oxidation-driven structural perturbation of CaM, with implications for RyR regulation and the decay of muscle function in aging.
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Affiliation(s)
- Sarah E D Nelson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
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8
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SAC3B is a target of CML19, the centrin 2 of Arabidopsis thaliana. Biochem J 2020; 477:173-189. [PMID: 31860002 DOI: 10.1042/bcj20190674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 01/15/2023]
Abstract
Arabidopsis centrin 2, also known as calmodulin-like protein 19 (CML19), is a member of the EF-hand superfamily of calcium (Ca2+)-binding proteins. In addition to the notion that CML19 interacts with the nucleotide excision repair protein RAD4, CML19 was suggested to be a component of the transcription export complex 2 (TREX-2) by interacting with SAC3B. However, the molecular determinants of this interaction have remained largely unknown. Herein, we identified a CML19-binding site within the C-terminus of SAC3B and characterized the binding properties of the corresponding 26-residue peptide (SAC3Bp), which exhibits the hydrophobic triad centrin-binding motif in a reversed orientation (I8W4W1). Using a combination of spectroscopic and calorimetric experiments, we shed light on the SAC3Bp-CML19 complex structure in solution. We demonstrated that the peptide interacts not only with Ca2+-saturated CML19, but also with apo-CML19 to form a protein-peptide complex with a 1 : 1 stoichiometry. Both interactions involve hydrophobic and electrostatic contributions and include the burial of Trp residues of SAC3Bp. However, the peptide likely assumes different conformations upon binding to apo-CML19 or Ca2+-CML19. Importantly, the peptide dramatically increases the affinity for Ca2+ of CML19, especially of the C-lobe, suggesting that in vivo the protein would be Ca2+-saturated and bound to SAC3B even at resting Ca2+-levels. Our results, providing direct evidence that Arabidopsis SAC3B is a CML19 target and proposing that CML19 can bind to SAC3B through its C-lobe independent of a Ca2+ stimulus, support a functional role for these proteins in TREX-2 complex and mRNA export.
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9
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Ramirez LM, Shekhtman A, Pande J. Hydrophobic residues of melittin mediate its binding to αA-crystallin. Protein Sci 2019; 29:572-588. [PMID: 31762096 DOI: 10.1002/pro.3792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 01/01/2023]
Abstract
The molecular chaperone αA-crystallin, mainly localized in the human ocular lens, is believed to protect the lens from opacification and cataract, by suppressing the aggregation of the other lens proteins. The present study provides structural and thermodynamic insights into the ability of human αA-crystallin (HAA) to bind to its partially unfolded clients in the lens, using a small peptide, melittin from bee venom, as a model client. We characterized the thermodynamic parameters of the binding process between melittin and HAA through isothermal titration calorimetry (ITC), and found the binding to be endothermic and entropy-driven. We identified the amino acids in melittin important for binding to HAA by saturation-transfer difference (STD) nuclear magnetic resonance (NMR) experiments, and analysis of NMR line broadening upon titration of melittin with HAA. Our results suggest that hydrophobic residues Ile17 and Ile20 on the C-terminal region of melittin are in close contact with HAA in the melittin-HAA complex. Information obtained from NMR experiments was used to generate structural models of the melittin-HAA complex by molecular docking with high-ambiguity driven docking (HADDOCK). Structural models of the melittin-HAA complex reveal important principles underlying the interaction of HAA with its clients.
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Affiliation(s)
- Lisa M Ramirez
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
| | - Jayanti Pande
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
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10
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Trande M, Pedretti M, Bonza MC, Di Matteo A, D'Onofrio M, Dominici P, Astegno A. Cation and peptide binding properties of CML7, a calmodulin-like protein from Arabidopsis thaliana. J Inorg Biochem 2019; 199:110796. [PMID: 31419675 DOI: 10.1016/j.jinorgbio.2019.110796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Plants contain a large family of so-called calmodulin-like proteins (CMLs) which differ from canonical calmodulin in that they show greater variability in sequence, length, and number of EF-hand domains. The presence of this extended CML family has raised questions regarding the role of these proteins: are they functionally redundant or do they play specific functions in physiological plant processes? To answer these questions, comprehensive biochemical and structural information on CML proteins is fundamental. Among the 50 CMLs from Arabidopsis thaliana, herein we described the ability of CML7 to bind metal ions focusing on the Ca2+ and Mg2+ sensing properties, as well as on metal-induced conformational changes. Circular dichroism and nuclear magnetic resonance (NMR) studies indicated that both Ca2+ and Mg2+ stabilize CML7, as reflected in conformational rearrangements in secondary and tertiary structure and in increases in thermal stability of the protein. However, the conformational changes that binding induces differ between the two metal ions, and only Ca2+ binding controls a structural transition that leads to hydrophobic exposure, as suggested by 8-anilino-1-naphthalenesulfonic acid fluorescence. Isothermal titration calorimetry data coupled with NMR experiments revealed the presence of two high affinity Ca2+-binding sites in the C-lobe of CML7 and two weaker sites in the N-lobe. The paired nature of these CML7 EF-hands enables them to bind Ca2+ with positive cooperativity within each globular domain. Our results clearly place CML7 in the category of Ca2+ sensors. Along with this, the protein can bind to a model target peptide (melittin) in a Ca2+-dependent manner.
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Affiliation(s)
- Matteo Trande
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Maria Cristina Bonza
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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11
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Borrell KL, Cancglin C, Stinger BL, DeFrates KG, Caputo GA, Wu C, Vaden TD. An Experimental and Molecular Dynamics Study of Red Fluorescent Protein mCherry in Novel Aqueous Amino Acid Ionic Liquids. J Phys Chem B 2017; 121:4823-4832. [PMID: 28425717 DOI: 10.1021/acs.jpcb.7b03582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The search for biocompatible ionic liquids (ILs) with novel biochemical and biomedical applications has recently gained greater attention. In this report, we characterize the effects of two novel amino acid-based aqueous ILs composed of tetramethylguanidinium (TMG) and amino acids on the structure and stability of a widely used red fluorescent protein (mCherry). Our experimental data shows that while the aspartic acid-based IL (TMGAsp) has effects similar to previously studied conventional ILs (BMIBF4, EMIAc, and TMGAc), the alanine-based IL (TMGAla) has a much stronger destabilization effect on the protein structure. Addition of 0.30 M TMGAla to mCherry decreases the unfolding temperature from 83 to 60 °C. Even at 25 °C, TMGAla results in a blue shift of the mCherry absorbance and fluorescence peaks and an increased Stokes shift. Molecular dynamics simulations show that the chromophore conformation and its interaction with mCherry with TMGAla are changed relative to those with TMGAsp or in the absence of ILs. Protein-ILs contact analysis indicates that the mCherry-Asp interactions are hydrophilic but the (fewer) mCherry-Ala interactions are more hydrophobic and may modulate the TMG interaction with the protein. Hence, the anion hydrophobicity may explain the special TMGAla destabilization of mCherry.
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Affiliation(s)
- Kelsey L Borrell
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Christine Cancglin
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Brittany L Stinger
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Kelsey G DeFrates
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Chun Wu
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Timothy D Vaden
- Department of Chemistry and Biochemistry amd ‡Department of Biomedical and Translational Sciences, Rowan University , 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
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13
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Moroz YS, Binder W, Nygren P, Caputo GA, Korendovych IV. Painting proteins blue: β-(1-azulenyl)-L-alanine as a probe for studying protein-protein interactions. Chem Commun (Camb) 2013; 49:490-2. [PMID: 23207368 PMCID: PMC3547328 DOI: 10.1039/c2cc37550h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We demonstrated that β-(1-azulenyl)-L-alanine, a fluorescent pseudoisosteric analog of tryptophan, exhibits weak environmental dependence and thus allows for using weak intrinsic quenchers, such as methionines, to monitor protein-protein interactions while not perturbing them.
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Affiliation(s)
- Yurii S. Moroz
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Wolfgang Binder
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
- Department of Chemistry, Technical University of Graz, Graz, Austria
| | - Patrik Nygren
- Department of Hematology and Oncology, University of Pennsylvania Medical School, Philadelphia, PA 19014, USA
| | - Gregory A. Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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14
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Lau SY, Procko E, Gaudet R. Distinct properties of Ca2+-calmodulin binding to N- and C-terminal regulatory regions of the TRPV1 channel. J Gen Physiol 2012; 140:541-55. [PMID: 23109716 PMCID: PMC3483115 DOI: 10.1085/jgp.201210810] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Transient receptor potential (TRP) vanilloid 1 (TRPV1) is a molecular pain receptor belonging to the TRP superfamily of nonselective cation channels. As a polymodal receptor, TRPV1 responds to heat and a wide range of chemical stimuli. The influx of calcium after channel activation serves as a negative feedback mechanism leading to TRPV1 desensitization. The cellular calcium sensor calmodulin (CaM) likely participates in the desensitization of TRPV1. Two CaM-binding sites are identified in TRPV1: the N-terminal ankyrin repeat domain (ARD) and a short distal C-terminal (CT) segment. Here, we present the crystal structure of calcium-bound CaM (Ca(2+)-CaM) in complex with the TRPV1-CT segment, determined to 1.95-Å resolution. The two lobes of Ca(2+)-CaM wrap around a helical TRPV1-CT segment in an antiparallel orientation, and two hydrophobic anchors, W787 and L796, contact the C-lobe and N-lobe of Ca(2+)-CaM, respectively. This structure is similar to canonical Ca(2+)-CaM-peptide complexes, although TRPV1 contains no classical CaM recognition sequence motif. Using structural and mutational studies, we established the TRPV1 C terminus as a high affinity Ca(2+)-CaM-binding site in both the isolated TRPV1 C terminus and in full-length TRPV1. Although a ternary complex of CaM, TRPV1-ARD, and TRPV1-CT had previously been postulated, we found no biochemical evidence of such a complex. In electrophysiology studies, mutation of the Ca(2+)-CaM-binding site on TRPV1-ARD abolished desensitization in response to repeated application of capsaicin, whereas mutation of the Ca(2+)-CaM-binding site in TRPV1-CT led to a more subtle phenotype of slowed and reduced TRPV1 desensitization. In summary, our results show that the TRPV1-ARD is an important mediator of TRPV1 desensitization, whereas TRPV1-CT has higher affinity for CaM and is likely involved in separate regulatory mechanisms.
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Affiliation(s)
- Sze-Yi Lau
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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15
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Lu Y, Kwan AH, Jeffries CM, Guss JM, Trewhella J. The motif of human cardiac myosin-binding protein C is required for its Ca2+-dependent interaction with calmodulin. J Biol Chem 2012; 287:31596-607. [PMID: 22801425 DOI: 10.1074/jbc.m112.383299] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The N-terminal modules of cardiac myosin-binding protein C (cMyBP-C) play a regulatory role in mediating interactions between myosin and actin during heart muscle contraction. The so-called "motif," located between the second and third immunoglobulin modules of the cardiac isoform, is believed to modulate contractility via an "on-off" phosphorylation-dependent tether to myosin ΔS2. Here we report a novel Ca(2+)-dependent interaction between the motif and calmodulin (CaM) based on the results of a combined fluorescence, NMR, and light and x-ray scattering study. We show that constructs of cMyBP-C containing the motif bind to Ca(2+)/CaM with a moderate affinity (K(D) ∼10 μM), which is similar to the affinity previously determined for myosin ΔS2. However, unlike the interaction with myosin ΔS2, the Ca(2+)/CaM interaction is unaffected by substitution with a triphosphorylated motif mimic. Further, Ca(2+)/CaM interacts with the highly conserved residues (Glu(319)-Lys(341)) toward the C-terminal end of the motif. Consistent with the Ca(2+) dependence, the binding of CaM to the motif is mediated via the hydrophobic clefts within the N- and C-lobes that are known to become more exposed upon Ca(2+) binding. Overall, Ca(2+)/CaM engages with the motif in an extended clamp configuration as opposed to the collapsed binding mode often observed in other CaM-protein interactions. Our results suggest that CaM may act as a structural conduit that links cMyBP-C with Ca(2+) signaling pathways to help coordinate phosphorylation events and synchronize the multiple interactions between cMyBP-C, myosin, and actin during the heart muscle contraction.
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Affiliation(s)
- Yanling Lu
- School of Molecular Bioscience, Building G08, The University of Sydney, New South Wales 2006, Australia
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16
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Verheyen E, van der Wal S, Deschout H, Braeckmans K, de Smedt S, Barendregt A, Hennink WE, van Nostrum CF. Protein macromonomers containing reduction-sensitive linkers for covalent immobilization and glutathione triggered release from dextran hydrogels. J Control Release 2011; 156:329-36. [DOI: 10.1016/j.jconrel.2011.08.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 08/26/2011] [Accepted: 08/27/2011] [Indexed: 10/17/2022]
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17
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Hearst SM, Walker LR, Shao Q, Lopez M, Raucher D, Vig PJS. The design and delivery of a thermally responsive peptide to inhibit S100B-mediated neurodegeneration. Neuroscience 2011; 197:369-80. [PMID: 21958864 DOI: 10.1016/j.neuroscience.2011.09.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 09/10/2011] [Accepted: 09/12/2011] [Indexed: 11/13/2022]
Abstract
S100B, a glial-secreted protein, is believed to play a major role in neurodegeneration in Alzheimer's disease, Down syndrome, traumatic brain injury, and spinocerebellar ataxia type 1 (SCA1). SCA1 is a trinucleotide repeat disorder in which the expanded polyglutamine mutation in the protein ataxin-1 primarily targets Purkinje cells of the cerebellum. Currently, the exact mechanism of S100B-mediated Purkinje cell damage in SCA1 is not clear. However, here we show that S100B may act via the activation of the receptor for advanced glycation end product (RAGE) signaling pathway, resulting in oxidative stress-mediated injury to mutant ataxin-1-expressing neurons. To combat S100B-mediated neurodegeneration, we have designed a selective thermally responsive S100B inhibitory peptide, Synb1-ELP-TRTK. Our therapeutic polypeptide was developed using three key elements: (1) the elastin-like polypeptide (ELP), a thermally responsive polypeptide, (2) the TRTK12 peptide, a known S100B inhibitory peptide, and (3) a cell-penetrating peptide, Synb1, to enhance intracellular delivery. Binding studies revealed that our peptide, Synb1-ELP-TRTK, interacts with its molecular target S100B and maintains a high S100B binding affinity as comparable with the TRTK12 peptide alone. In addition, in vitro studies revealed that Synb1-ELP-TRTK treatment reduces S100B uptake in SHSY5Y cells. Furthermore, the Synb1-ELP-TRTK peptide decreased S100B-induced oxidative damage to mutant ataxin-1-expressing neurons. To test the delivery capabilities of ELP-based therapeutic peptides to the cerebellum, we treated mice with fluorescently labeled Synb1-ELP and observed that thermal targeting enhanced peptide delivery to the cerebellum. Here, we have laid the framework for thermal-based therapeutic targeting to regions of the brain, particularly the cerebellum. Overall, our data suggest that thermal targeting of ELP-based therapeutic peptides to the cerebellum is a novel treatment strategy for cerebellar neurodegenerative disorders.
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Affiliation(s)
- S M Hearst
- Department of Neurology, University of Mississippi Medical Center, Jackson, MS, USA
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18
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Pavlov N, Gilles P, Didierjean C, Wenger E, Naydenova E, Martinez J, Calmès M. Asymmetric Synthesis of β2-Tryptophan Analogues via Friedel–Crafts Alkylation of Indoles with a Chiral Nitroacrylate. J Org Chem 2011; 76:6116-24. [DOI: 10.1021/jo200733t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nikola Pavlov
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1
et Université Montpellier 2, Bâtiment Chimie (17), Université Montpellier 2, place E. Bataillon,
34095 Montpellier cedex 5, France
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 8
Kliment Ohridski blvd., Sofia 1756, Bulgaria
| | - Pierre Gilles
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1
et Université Montpellier 2, Bâtiment Chimie (17), Université Montpellier 2, place E. Bataillon,
34095 Montpellier cedex 5, France
| | - Claude Didierjean
- Laboratoire de Crystallographie,
Résonance Magnétique et Modélisation, Nancy Université, UMR7036 CNRS-UHP, Boulevard
des Aiguillettes, BPP239, 54506 Vandoeuvre-Lès-Nancy Cedex,
France
| | - Emmanuel Wenger
- Laboratoire de Crystallographie,
Résonance Magnétique et Modélisation, Nancy Université, UMR7036 CNRS-UHP, Boulevard
des Aiguillettes, BPP239, 54506 Vandoeuvre-Lès-Nancy Cedex,
France
| | - Emilia Naydenova
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, 8
Kliment Ohridski blvd., Sofia 1756, Bulgaria
| | - Jean Martinez
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1
et Université Montpellier 2, Bâtiment Chimie (17), Université Montpellier 2, place E. Bataillon,
34095 Montpellier cedex 5, France
| | - Monique Calmès
- Institut des Biomolécules
Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1
et Université Montpellier 2, Bâtiment Chimie (17), Université Montpellier 2, place E. Bataillon,
34095 Montpellier cedex 5, France
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19
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Verheyen E, Delain-Bioton L, van der Wal S, el Morabit N, Barendregt A, Hennink WE, van Nostrum CF. Conjugation of methacrylamide groups to a model protein via a reducible linker for immobilization and subsequent triggered release from hydrogels. Macromol Biosci 2010; 10:1517-26. [PMID: 20824693 DOI: 10.1002/mabi.201000168] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 06/15/2010] [Indexed: 02/03/2023]
Abstract
An efficient strategy is reported to introduce methacrylamide groups on the lysine residues of a model protein (lysozyme) for immobilization and triggered release from a hydrogel network. A novel spacer unit was designed, containing a disulfide bond, such that the release of the protein can be triggered by reduction. The modified proteins were characterized by MALDI-TOF MS, titration of free NH(2) residues and spectral analysis. The modification reaction is well controlled, and the number of introduced functions can be tailored by changing the reaction conditions. Gel electrophoresis experiments showed that the methacrylamide modified protein can be immobilized in a polyacrylamide hydrogel and subsequently released by reduction of the spacer by which the protein was grafted to the polymeric network.
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Affiliation(s)
- Ellen Verheyen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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20
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Using nonfluorescent Förster resonance energy transfer acceptors in protein binding studies. Anal Biochem 2009; 393:196-204. [DOI: 10.1016/j.ab.2009.06.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 06/10/2009] [Accepted: 06/24/2009] [Indexed: 11/18/2022]
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21
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Yamniuk AP, Ishida H, Lippert D, Vogel HJ. Thermodynamic effects of noncoded and coded methionine substitutions in calmodulin. Biophys J 2009; 96:1495-507. [PMID: 19217866 PMCID: PMC2717255 DOI: 10.1016/j.bpj.2008.10.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/28/2008] [Indexed: 11/16/2022] Open
Abstract
The methionine residues in the calcium (Ca2+) regulatory protein calmodulin (CaM) are structurally and functionally important. They are buried within the N- and C-domains of apo-CaM but become solvent-exposed in Ca2+-CaM, where they interact with numerous target proteins. Previous structural studies have shown that methionine substitutions to the noncoded amino acids selenomethionine, ethionine, or norleucine, or mutation to leucine do not impact the main chain structure of CaM. Here we used differential scanning calorimetry to show that these substitutions enhance the stability of both domains, with the largest increase in melting temperature (19-26 degrees C) achieved with leucine or norleucine in the apo-C-domain. Nuclear magnetic resonance spectroscopy experiments also revealed the loss of a slow conformational exchange process in the Leu-substituted apo-C-domain. In addition, isothermal titration calorimetry experiments revealed considerable changes in the enthalpy and entropy of target binding to apo-CaM and Ca2+-CaM, but the free energy of binding was largely unaffected due to enthalpy-entropy compensation. Collectively, these results demonstrate that noncoded and coded methionine substitutions can be accommodated in CaM because of the structural plasticity of the protein. However, adjustments in side-chain packing and dynamics lead to significant differences in protein stability and the thermodynamics of target binding.
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Affiliation(s)
- Aaron P. Yamniuk
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hiroaki Ishida
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Dustin Lippert
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Hans J. Vogel
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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22
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Effects of selenium on the structure and function of recombinant human S-adenosyl-L-methionine dependent arsenic (+3 oxidation state) methyltransferase in E. coli. J Biol Inorg Chem 2009; 14:485-96. [PMID: 19159958 DOI: 10.1007/s00775-008-0464-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2008] [Accepted: 12/26/2008] [Indexed: 10/21/2022]
Abstract
The effects of Se(IV) on the structure and function of recombinant human arsenic (+3 oxidation state) methyltransferase (AS3MT) purified from the cytoplasm of Escherichia coli were studied. The coding region of human AS3MT complementary DNA was amplified from total RNA extracted from HepG2 cell by reverse transcription PCR. Soluble and active human AS3MT was expressed in the E. coli with a Trx fusion tag under a lower induction temperature of 25 degrees C. Spectra (UV-vis, circular dichroism, and fluorescence) were first used to probe the interaction of Se(IV) and recombinant human AS3MT and the structure-function relationship of the enzyme. The recombinant human AS3MT had a secondary structure of 29.0% alpha-helix, 23.9% beta-pleated sheet, 17.9% beta-turn, and 29.2% random coil. When Se(IV) was added, the content of the alpha-helix did not change, but that of the beta-pleated sheet increased remarkably in the conformation of recombinant human AS3MT. Se(IV) inhibited the enzymatic methylation of inorganic As(III) in a concentration-dependent manner. The IC(50) value for Se(IV) was 2.38 muM. Double-reciprocal (1/V vs. 1/[inorganic As(III)]) plots showed Se(IV) to be a noncompetitive inhibitor of the methylation of inorganic As(III) by recombinant human AS3MT with a K (i) value of 2.61 muM. We hypothesized that Se(IV) interacts with the sulfhydryl group of cysteine(s) in the structural residues rather than the cysteines of the active site (Cys156 and Cys206). When Se(IV) was combined with cysteine(s) in the structural residues, the conformation of recombinant human AS3MT changed and the enzymatic activity decreased. Considering the quenching of tryptophan fluorescence, Cys72 and/or Cys226 are deduced to be primary targets for Se(IV).
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23
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Shaw GS, Marlatt NM, Ferguson PL, Barber KR, Bottomley SP. Identification of a dimeric intermediate in the unfolding pathway for the calcium-binding protein S100B. J Mol Biol 2008; 382:1075-88. [PMID: 18706914 DOI: 10.1016/j.jmb.2008.07.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 06/30/2008] [Accepted: 07/31/2008] [Indexed: 11/18/2022]
Abstract
The S100 proteins comprise 25 calcium-signalling members of the EF-hand protein family. Unlike typical EF-hand signalling proteins such as calmodulin and troponin-C, the S100 proteins are dimeric, forming both homo- and heterodimers in vivo. One member of this family, S100B, is a homodimeric protein shown to control the assembly of several cytoskeletal proteins and regulate phosphorylation events in a calcium-sensitive manner. Calcium binding to S100B causes a conformational change involving movement of helix III in the second calcium-binding site (EF2) that exposes a hydrophobic surface enabling interactions with other proteins such as tubulin and Ndr kinase. In several S100 proteins, calcium binding also stabilizes dimerization compared to the calcium-free states. In this work, we have examined the guanidine hydrochloride (GuHCl)-induced unfolding of dimeric calcium-free S100B. A series of tryptophan substitutions near the dimer interface and the EF2 calcium-binding site were studied by fluorescence spectroscopy and showed biphasic unfolding curves. The presence of a plateau near 1.5 M GuHCl showed the presence of an intermediate that had a greater exposed hydrophobic surface area compared to the native dimer based on increased 4,4-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid fluorescence. Furthermore, (1)H-(15)N heteronuclear single quantum coherence analyses as a function of GuHCl showed significant chemical shift changes in regions near the EF1 calcium-binding loop and between the linker and C-terminus of helix IV. Together these observations show that calcium-free S100B unfolds via a dimeric intermediate.
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Affiliation(s)
- Gary S Shaw
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1.
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24
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Zhao X, DeVries JS, McDonald R, Sykes BD. Determination of the 19F NMR chemical shielding tensor and crystal structure of 5-fluoro-dl-tryptophan. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 187:88-96. [PMID: 17475524 DOI: 10.1016/j.jmr.2007.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 03/13/2007] [Accepted: 03/22/2007] [Indexed: 05/15/2023]
Abstract
5-Fluoro-dl-tryptophan (5F-Trp) is a very sensitive probe used to investigate orientation and dynamics of biomacromolecules at the in situ level. In order to establish a (19)F NMR strategy, the crystal structure and (19)F chemical shielding tensor of 5F-Trp are reported. A novel approach was developed to use F-F homonuclear dipole-dipole coupling information to analyze single-crystal NMR data without determining crystal orientations. The measured values for the principal components of the shielding tensor are sigma(11)=0.9, sigma(22)=-63.3, and sigma(33)=-82.9 ppm relative to TFA in D(2)O. The principal axes of the shielding tensors coincide with the indole ring symmetry, which makes it a straightforward and powerful tool to monitor protein alignment in oriented environments. Hartree-Fock (HF) and density functional theory (DFT) calculations of the chemical shielding tensors are also reported.
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Affiliation(s)
- Xingang Zhao
- Department of Biochemistry, University of Alberta, 419 Medical Sciences Building, Edmonton, Alberta, Canada
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25
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Moroder L. Isosteric replacement of sulfur with other chalcogens in peptides and proteins. J Pept Sci 2005; 11:187-214. [PMID: 15782428 DOI: 10.1002/psc.654] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The review addresses the functional and structural properties of the two series of chalcogen analogues of amino acids in peptides and proteins, the methionine and the serine/cysteine series, and discusses the synthesis of the related selenium/tellurium analogues as well as their use in peptide synthesis and protein expression. Advances in synthetic methodologies and recombinant technologies and their combined applications in native and expressed protein ligation allows the isomorphous character of selenium- and tellurium-containing amino acids to be exploited for production of heavy metal mutants of proteins and thus to facilitate the phasing problem in x-ray crystallography. In addition, selenocysteine has been recognized as an ideal tool for the production of selenoenzymes with new catalytic activities. Moreover, the fully isomorphous character of disulfide replacement with diselenide is well suited to increase the robustness of cystine frameworks in cystine-rich peptides and proteins and for the de novo design of even non-native cystine frameworks by exploiting the highly negative redox potential of selenols.
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Affiliation(s)
- Luis Moroder
- Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany.
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26
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Goraya TA, Cooper DMF. Ca2+-calmodulin-dependent phosphodiesterase (PDE1): Current perspectives. Cell Signal 2005; 17:789-97. [PMID: 15763421 DOI: 10.1016/j.cellsig.2004.12.017] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 12/21/2004] [Indexed: 10/25/2022]
Abstract
Ca2+-calmodulin-dependent phosphodiesterases (PDE1), like Ca2+-sensitive adenylyl cyclases (AC), are key enzymes that play a pivotal role in mediating the cross-talk between cAMP and Ca2+ signalling. Our understanding of how ACs respond to Ca2+ has advanced greatly, with significant breakthroughs at both the molecular and functional level. By contrast, little is known of the mechanisms that might underlie the regulation of PDE1 by Ca2+ in the intact cell. In living cells, Ca2+ signals are complex and diverse, exhibiting different spatial and temporal properties. The potential therefore exists for dynamic changes in the subcellular distribution and activation of PDE1 in relation to intracellular Ca2+ dynamics. PDE1s are a large family of multiply-spliced gene products. Therefore, it is possible that a cell-type specific response to elevation in [Ca2+]i can occur, depending on the isoform of PDE1 expressed. In this article, we summarize current knowledge on Ca2+ regulation of PDE1 in the intact cell and discuss approaches that might be undertaken to delineate the responses of this important group of enzymes to changes in [Ca2+]i.
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Affiliation(s)
- Tasmina A Goraya
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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27
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Yamniuk AP, Vogel HJ. Structurally homologous binding of plant calmodulin isoforms to the calmodulin-binding domain of vacuolar calcium-ATPase. J Biol Chem 2004; 279:7698-707. [PMID: 14670974 DOI: 10.1074/jbc.m310763200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The discovery that plants contain multiple calmodulin (CaM) isoforms having variable sequence identity to mammalian CaM has sparked a flurry of new questions regarding the intracellular role of Ca(2+) regulation in plants. To date, the majority of research in this field has focused on the differential enzymatic regulation of various mammalian CaM-dependent enzymes by the different plant CaM isoforms. However, there is comparatively little information on the structural recognition of target enzymes found exclusively in plant cells. Here we have used a variety of spectroscopic techniques, including nuclear magnetic resonance, circular dichroism, and fluorescence spectroscopy, to study the interactions of the most conserved and most divergent CaM isoforms from soybean, SCaM-1, and SCaM-4, respectively, with a synthetic peptide derived from the CaM-binding domain of cauliflower vacuolar calcium-ATPase. Despite their sequence divergence, both SCaM-1 and SCaM-4 interact with the calcium-ATPase peptide in a similar calcium-dependent, stoichiometric manner, adopting an antiparallel binding orientation with an alpha-helical peptide. The single Trp residue is bound in a solvent-inaccessible hydrophobic pocket on the C-terminal domain of either protein. Thermodynamic analysis of these interactions using isothermal titration calorimetry demonstrates that the formation of each calcium-SCaM-calcium-ATPase peptide complex is driven by favorable binding enthalpy and is very similar to the binding of mammalian CaM to the CaM-binding domains of myosin light chain kinases and calmodulin-dependent protein kinase I.
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Affiliation(s)
- Aaron P Yamniuk
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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28
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Reiner DS, Hetsko ML, Meszaros JG, Sun CH, Morrison HG, Brunton LL, Gillin FD. Calcium signaling in excystation of the early diverging eukaryote, Giardia lamblia. J Biol Chem 2003; 278:2533-40. [PMID: 12397071 DOI: 10.1074/jbc.m208033200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Excystation of Giardia lamblia, which initiates infection, is a poorly understood but dramatic differentiation induced by physiological signals from the host. Our data implicate a central role for calcium homeostasis in excystation. Agents that alter cytosolic Ca(2+) levels (1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid-tetra(acetyloxymethyl) ester, a Ca(2+) channel blocker, Ca(2+) ionophores, and thapsigargin) strongly inhibit excystation. Treatment of Giardia with thapsigargin raised intracellular Ca(2+) levels, and peak Ca(2+) responses increased with each stage of excystation, consistent with the kinetics of inhibition. Fluorescent thapsigargin localized to a likely Ca(2+) storage compartment in cysts. The ability to sequester ions in membrane-bounded compartments is a hallmark of the eukaryotic cell. These studies support the existence of a giardial thapsigargin-sensitive Ca(2+) storage compartment resembling the sarcoplasmic/endoplasmic reticulum calcium ATPase pump-leak system and suggest that it is important in regulation of differentiation and appeared early in the evolution of eukaryotic cells. Calmodulin antagonists also blocked excystation. The divergent giardial calmodulin localized to the eight flagellar basal bodies/centrosomes, like protein kinase A. Inhibitor kinetics suggest that protein kinase A signaling triggers excystation, whereas calcium signaling is mainly required later, for parasite activation and emergence. Thus, the basal bodies may be a cellular control center to coordinate the resumption of motility and cytokinesis in excystation.
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Affiliation(s)
- David S Reiner
- Department of Pathology, University of California, San Diego, 92103, USA
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Gribenko AV, Guzmán-Casado M, Lopez MM, Makhatadze GI. Conformational and thermodynamic properties of peptide binding to the human S100P protein. Protein Sci 2002; 11:1367-75. [PMID: 12021435 PMCID: PMC2373636 DOI: 10.1110/ps.0202202] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
S100P is a member of the S100 subfamily of calcium-binding proteins that are believed to be associated with various diseases, and in particular deregulation of S100P expression has been documented for prostate and breast cancer. Previously, we characterized the effects of metal binding on the conformational properties of S100P and proposed that S100P could function as a Ca2+ conformational switch. In this study we used fluorescence and CD spectroscopies and isothermal titration calorimetry to characterize the target-recognition properties of S100P using a model peptide, melittin. Based on these experimental data we show that S100P and melittin can interact in a Ca2+-dependent and -independent manner. Ca2+-independent binding occurs with low affinity (Kd approximately 0.2 mM), has a stoichiometry of four melittin molecules per S100P dimer and is presumably driven by favorable electrostatic interactions between the acidic protein and the basic peptide. In contrast, Ca2+-dependent binding of melittin to S100P occurs with high affinity (Kd approximately 5 microM) has a stoichiometry of two molecules of melittin per S100P dimer, appears to have positive cooperativity, and is driven by hydrophobic interactions. Furthermore, Ca2+-dependent S100P-melittin complex formation is accompanied by significant conformational changes: Melittin, otherwise unstructured in solution, adopts a helical conformation upon interaction with Ca2+-S100P. These results support a model for the Ca2+-dependent conformational switch in S100P for functional target recognition.
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Affiliation(s)
- Alexey V Gribenko
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, USA
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30
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Rodney GG, Moore CP, Williams BY, Zhang JZ, Krol J, Pedersen SE, Hamilton SL. Calcium binding to calmodulin leads to an N-terminal shift in its binding site on the ryanodine Receptor. J Biol Chem 2001; 276:2069-74. [PMID: 11035044 DOI: 10.1074/jbc.m008891200] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The skeletal muscle calcium release channel, ryanodine receptor, is activated by calcium-free calmodulin and inhibited by calcium-bound calmodulin. Previous biochemical studies from our laboratory have shown that calcium-free calmodulin and calcium bound calmodulin protect sites at amino acids 3630 and 3637 from trypsin cleavage (Moore, C. P., Rodney, G., Zhang, J. Z., Santacruz-Toloza, L., Strasburg, G., and Hamilton, S. L. (1999) Biochemistry 38, 8532-8537). We now demonstrate that both calcium-free calmodulin and calcium-bound calmodulin bind with nanomolar affinity to a synthetic peptide matching amino acids 3614-3643 of the ryanodine receptor. Deletion of the last nine amino acids (3635-3643) destroys the ability of the peptide to bind calcium-free calmodulin, but not calcium-bound calmodulin. We propose a novel mechanism for calmodulin's interaction with a target protein. Our data suggest that the binding sites for calcium-free calmodulin and calcium-bound calmodulin are overlapping and, when calcium binds to calmodulin, the calmodulin molecule shifts to a more N-terminal location on the ryanodine receptor converting it from an activator to an inhibitor of the channel. This region of the ryanodine receptor has previously been identified as a site of intersubunit contact, suggesting the possibility that calmodulin regulates ryanodine receptor activity by regulating subunit-subunit interactions.
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Affiliation(s)
- G G Rodney
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
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31
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Gomes AV, Barnes JA, Vogel HJ. Spectroscopic characterization of the interaction between calmodulin-dependent protein kinase I and calmodulin. Arch Biochem Biophys 2000; 379:28-36. [PMID: 10864438 DOI: 10.1006/abbi.2000.1827] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Calmodulin-dependent protein kinase I (CaM kinase I) is a member of the expanding class of protein kinases that are regulated by calmodulin (CaM). Its putative CaM-binding region is believed to occur within a 22-residue sequence (amino acids 299-320). This sequence was chemically synthesized and utilized for CaM interaction studies. Gel band shift assays and densitometry experiments with intact CaM kinase I and the CaM-binding domain peptide (CaMKIp) reveal that they bind in an analogous manner, giving rise to 1:1 complexes. Fluorescence analysis using dansyl-CaM showed that conformational changes in CaM on binding CaM kinase I or CaMKIp were nearly identical, suggesting that the peptide mimicked the CaM-binding ability of the intact protein. In the presence of CaM, the peptide displays an enhancement of its unique Trp fluorescence as well as a marked blue shift of the emission maximum, reflecting a transfer to a more rigid, less polar environment. Quenching studies, using acrylamide, confirmed that the Trp in the peptide on binding CaM is no longer freely exposed to solvent as is the case for the free peptide. Studies with a series of Met mutants of CaM showed that the Trp-containing N-terminal end of CaMKIp was bound to the C-terminal lobe of CaM. Near-UV CD spectra also indicate that the Trp of the peptide and Phe residues of the protein are involved in the binding. These results show that the CaM-binding domain of CaM kinase I binds to CaM in a manner analogous to that of myosin light chain kinase.
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Affiliation(s)
- A V Gomes
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
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