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Lloyd MD, Gregory KS, Acharya KR. Functional implications of unusual NOS and SONOS covalent linkages found in proteins. Chem Commun (Camb) 2024; 60:9463-9471. [PMID: 39109843 DOI: 10.1039/d4cc03191a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
The tertiary and quaternary structures of many proteins are stabilized by strong covalent forces, of which disulfide bonds are the most well known. A new type of intramolecular and intermolecular covalent bond has been recently reported, consisting of the Lys and Cys side-chains linked by an oxygen atom (NOS). These post-translational modifications are widely distributed amongst proteins, and are formed under oxidative conditions. Similar linkages are observed during antibiotic biosynthesis, where hydroxylamine intermediates are tethered to the sulfur of enzyme active site Cys residues. These linkages open the way to understanding protein structure and function, give new insights into enzyme catalysis and natural product biosynthesis, and offer new strategies for drug design.
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Affiliation(s)
- Matthew D Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - Kyle S Gregory
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.
| | - K Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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2
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Guo J, Keegan RM, Rigden DJ, Erskine PT, Wood SP, Li S, Cooper JB. The X-ray structure of juvenile hormone diol kinase from the silkworm Bombyx mori. Acta Crystallogr F Struct Biol Commun 2021; 77:465-472. [PMID: 34866602 PMCID: PMC8647211 DOI: 10.1107/s2053230x21012012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/10/2021] [Indexed: 11/11/2022] Open
Abstract
Insect juvenile hormones (JHs) are a family of sesquiterpenoid molecules that are secreted into the haemolymph. JHs have multiple roles in insect development, metamorphosis and sexual maturation. A number of pesticides work by chemically mimicking JHs, thus preventing insects from developing and reproducing normally. The haemolymph levels of JH are governed by the rates of its biosynthesis and degradation. One enzyme involved in JH catabolism is JH diol kinase (JHDK), which uses ATP (or GTP) to phosphorylate JH diol to JH diol phosphate, which can be excreted. The X-ray structure of JHDK from the silkworm Bombyx mori has been determined at a resolution of 2.0 Å with an R factor of 19.0% and an Rfree of 24.8%. The structure possesses three EF-hand motifs which are occupied by calcium ions. This is in contrast to the recently reported structure of the JHDK-like-2 protein from B. mori (PDB entry 6kth), which possessed only one calcium ion. Since JHDK is known to be inhibited by calcium ions, it is likely that our structure represents the calcium-inhibited form of the enzyme. The electrostatic surface of the protein suggests a binding site for the triphosphate of ATP close to the N-terminal end of the molecule in a cavity between the N- and C-terminal domains. Superposition with a number of calcium-activated photoproteins suggests that there may be parallels between the binding of JH diol to JHDK and the binding of luciferin to aequorin.
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Affiliation(s)
- Jingxu Guo
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Ronan M. Keegan
- Scientific Computing Department, Science and Technologies Facilities Council, UK Research and Innovation, Didcot, United Kingdom
| | - Daniel J. Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7BE, United Kingdom
| | - Peter T. Erskine
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, United Kingdom
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, United Kingdom
| | - Steve P. Wood
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, United Kingdom
- Institute of Biomedical and Biomolecular Science, School of Biological Sciences, University of Portsmouth, King Henry Building, Portsmouth PO1 2DY, United Kingdom
| | - Sheng Li
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, 320 Yue Yang Road, Shanghai 200031, People’s Republic of China
| | - Jonathan B. Cooper
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, United Kingdom
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, United Kingdom
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3
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Adiga D, Radhakrishnan R, Chakrabarty S, Kumar P, Kabekkodu SP. The Role of Calcium Signaling in Regulation of Epithelial-Mesenchymal Transition. Cells Tissues Organs 2020; 211:134-156. [PMID: 33316804 DOI: 10.1159/000512277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/13/2020] [Indexed: 11/19/2022] Open
Abstract
Despite substantial advances in the field of cancer therapeutics, metastasis is a significant challenge for a favorable clinical outcome. Epithelial to mesenchymal transition (EMT) is a process of acquiring increased motility, invasiveness, and therapeutic resistance by cancer cells for their sustained growth and survival. A plethora of intrinsic mechanisms and extrinsic microenvironmental factors drive the process of cancer metastasis. Calcium (Ca2+) signaling plays a critical role in dictating the adaptive metastatic cell behavior comprising of cell migration, invasion, angiogenesis, and intravasation. By modulating EMT, Ca2+ signaling can regulate the complexity and dynamics of events leading to metastasis. This review summarizes the role of Ca2+ signal remodeling in the regulation of EMT and metastasis in cancer.
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Affiliation(s)
- Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India.,Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India, .,Center for DNA Repair and Genome Stability (CDRGS), Manipal Academy of Higher Education, Manipal, India,
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4
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Xu H, Zhang Y, Zhang L, Wang Z, Guo P, Zhao P. Structural characterization and functional analysis of juvenile hormone diol kinase from the silkworm, Bombyx mori. Int J Biol Macromol 2020; 167:570-577. [PMID: 33249150 DOI: 10.1016/j.ijbiomac.2020.11.138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 10/22/2022]
Abstract
Juvenile hormone diol kinase (JHDK) is an important enzyme involved in the juvenile hormone metabolism pathway, which catalyzes the phosphorylation of juvenile hormone diol to form the polar metabolite JH diol phosphate. Here, we reported the first crystal structure of insect JHDK from Bombyx mori, BmJHDK-L2, determined at a resolution of 1.22 Å. The structure of BmJHDK-L2 mainly comprises of eight α-helical segments linked with loops, forming four helix-loop-helix motifs. In these four helix-loop-helix motifs with only one calcium ion bound in the first motif. Circular dichroism spectra indicated that BmJHDK-L2 has strong thermal stability, which is independent of the divalent cation. The structure of BmJHDK-L2 further allowed us to define an ATP-binding site using computational simulation and binding assays, providing a structural basis for development of inhibitor of JHDK. Moreover, the expression profile of BmJHDK-L2 indicated a predominant role in juvenile hormone metabolism in the Malpighian tubules of silkworm. Collectively, these findings expand our knowledge regarding the structural and biochemical features of insect JHDK proteins.
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Affiliation(s)
- Haiyang Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Yunshi Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Li Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Zhan Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400716, China
| | - Pengchao Guo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
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5
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Zhu L, Wang L, Matsuura A, Zhang M, Lu P, Iimura K, Nagata K, Suzuki M. Purification, crystallization and X-ray analysis of Pf-SCP (sarcoplasmic Ca-binding protein), related to storage and transport of calcium in mantle of Pinctada fucata. Protein Expr Purif 2020; 178:105781. [PMID: 33137413 DOI: 10.1016/j.pep.2020.105781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/18/2020] [Indexed: 10/23/2022]
Abstract
Pf-SCP, a 21 kDa protein with two EF-hand motifs and a phosphorylation site, was identified from mantle tissue and binds to calcium ions and transports calcium components from cell to the shell of Pinctada fucata. To reveal the molecular basis of the calcium binding activity of Pf-SCP, we expressed the recombinant protein of full-length Pf-SCP in Escherichia coli. Recombinant Pf-SCP (rPf-SCP) purified by Ni affinity chromatography and size exclusion chromatography appeared as a single band on SDS-PAGE. The circular dichroism spectroscopy showed that the α-helix content decreased when rPf-SCP interacted with both calcium ions and calcium carbonate. Western blotting and immunostaining verified the Pf-SCP expression in the shell and localization most in the mantle epithelial cells. To further understand the structural and functional regulation of Pf-SCP by calcium ions and calcium carbonate, the crystallization experiments of rPf-SCP in the presence of calcium ions were performed. A crystal of rPf-SCP obtained in the presence of calcium ions diffracted X-rays up to a resolution of 1.8 Å. The space group of the crystal is C2 with unit cell parameters of a = 96.828 Å, b = 55.906 Å, c = 102.14 Å and β = 90.009°, indicating that three molecules of rPf-SCP are contained in an asymmetric unit as estimated at the value of the Matthews coefficient. These results suggest that Pf-SCP may play a role in calcium ions transportation and shell mineralization by concentrating calcium ions inside the mantle epithelial cells and interacting with calcium carbonate molecules.
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Affiliation(s)
- Lingxiao Zhu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Liying Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Akihiro Matsuura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mimin Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Peng Lu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kurin Iimura
- Food Department, Department of Home Economics, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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6
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Ca 2+-binding protein from Entamoeba histolytica (EhCaBP6) is a novel GTPase. Biochem Biophys Res Commun 2020; 527:631-637. [PMID: 32423808 DOI: 10.1016/j.bbrc.2020.04.141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 04/28/2020] [Indexed: 11/23/2022]
Abstract
GTPases are molecular switches, which regulate a variety of cellular processes such as cell polarity, gene transcription, microtubule dynamics, cell-cycle etc. In this paper, we characterize a Ca2+-binding protein from Entamoeba histolytica (EhCaBP6) as a novel GTPase. We locate the active site for GTP hydrolysis within the C-terminal domain of EhCaBP6, although it requires full length protein for its complete range of activity. Using NMR studies, we observe that GTP binding induces conformational change in EhCaBP6. The identification of this novel and unusual Ca2+-dependent GTPase is important to elucidate the unconventional cell cycle of E. histolytica.
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7
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Chataigner L, Guo J, Erskine PT, Coker AR, Wood SP, Gombos Z, Cooper JB. Binding of Gd(3+) to the neuronal signalling protein calexcitin identifies an exchangeable Ca(2+)-binding site. Acta Crystallogr F Struct Biol Commun 2016; 72:276-81. [PMID: 27050260 PMCID: PMC4822983 DOI: 10.1107/s2053230x16003526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/29/2016] [Indexed: 11/11/2022] Open
Abstract
Calexcitin was first identified in the marine snail Hermissenda crassicornis as a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg(2+) and Ca(2+), while EF-3 is likely to bind only Ca(2+). The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of calexcitin is most readily replaced by exogenous metal ions, potentially shedding light on which of the EF-hands play a `sensory' role in neuronal calcium signalling. By co-crystallizing recombinant calexcitin with equimolar Gd(3+) in the presence of trace Ca(2+), EF-1 was shown to become fully occupied by Gd(3+) ions, while the other two sites remain fully occupied by Ca(2+). The structure of the Gd(3+)-calexcitin complex has been refined to an R factor of 21.5% and an Rfree of 30.4% at 2.2 Å resolution. These findings suggest that EF-1 of calexcitin is the Ca(2+)-binding site with the lowest selectivity for Ca(2+), and the implications of this finding for calcium sensing in neuronal signalling pathways are discussed.
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Affiliation(s)
- Lucas Chataigner
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Jingxu Guo
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Peter T. Erskine
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
| | - Alun R. Coker
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Steve P. Wood
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Zoltan Gombos
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Jonathan B. Cooper
- Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
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8
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Ehara H, Makino M, Kodama K, Konoki K, Ito T, Sekine SI, Fukuzawa S, Yokoyama S, Tachibana K. Crystal Structure of Okadaic Acid Binding Protein 2.1: A Sponge Protein Implicated in Cytotoxin Accumulation. Chembiochem 2015; 16:1435-9. [PMID: 25965326 DOI: 10.1002/cbic.201500141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 12/18/2022]
Abstract
Okadaic acid (OA) is a marine polyether cytotoxin that was first isolated from the marine sponge Halichondria okadai. OA is a potent inhibitor of protein serine/threonine phosphatases (PP) 1 and 2A, and the structural basis of phosphatase inhibition has been well investigated. However, the role and mechanism of OA retention in the marine sponge have remained elusive. We have solved the crystal structure of okadaic acid binding protein 2.1 (OABP2.1) isolated from H. okadai; it has strong affinity for OA and limited sequence homology to other proteins. The structure revealed that OABP2.1 consists of two α-helical domains, with the OA molecule deeply buried inside the protein. In addition, the global fold of OABP2.1 was unexpectedly similar to that of aequorin, a jellyfish photoprotein. The presence of structural homologues suggested that, by using similar protein scaffolds, marine invertebrates have developed diverse survival systems adapted to their living environments.
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Affiliation(s)
- Haruhiko Ehara
- Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan).,RIKEN Systems and Structural Biology Center, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan).,RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan)
| | - Marie Makino
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Koichiro Kodama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Keiichi Konoki
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555 (Japan)
| | - Takuhiro Ito
- Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan).,RIKEN Systems and Structural Biology Center, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan).,RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan)
| | - Shun-ichi Sekine
- Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan).,RIKEN Systems and Structural Biology Center, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan).,RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan)
| | - Seketsu Fukuzawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan).
| | - Shigeyuki Yokoyama
- Department of Biophysics and Biochemistry and Laboratory of Structural Biology, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan). .,RIKEN Systems and Structural Biology Center, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan). .,RIKEN Structural Biology Laboratory, 1-7-22, Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan).
| | - Kazuo Tachibana
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan).
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9
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Erskine PT, Fokas A, Muriithi C, Rehman H, Yates LA, Bowyer A, Findlow IS, Hagan R, Werner JM, Miles AJ, Wallace BA, Wells SA, Wood SP, Cooper JB. X-ray, spectroscopic and normal-mode dynamics of calexcitin: structure-function studies of a neuronal calcium-signalling protein. ACTA ACUST UNITED AC 2015; 71:615-31. [PMID: 25760610 DOI: 10.1107/s1399004714026704] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 12/04/2014] [Indexed: 01/28/2023]
Abstract
The protein calexcitin was originally identified in molluscan photoreceptor neurons as a 20 kDa molecule which was up-regulated and phosphorylated following a Pavlovian conditioning protocol. Subsequent studies showed that calexcitin regulates the voltage-dependent potassium channel and the calcium-dependent potassium channel as well as causing the release of calcium ions from the endoplasmic reticulum (ER) by binding to the ryanodine receptor. A crystal structure of calexcitin from the squid Loligo pealei showed that the fold is similar to that of another signalling protein, calmodulin, the N- and C-terminal domains of which are known to separate upon calcium binding, allowing interactions with the target protein. Phosphorylation of calexcitin causes it to translocate to the cell membrane, where its effects on membrane excitability are exerted and, accordingly, L. pealei calexcitin contains two protein kinase C phosphorylation sites (Thr61 and Thr188). Thr-to-Asp mutations which mimic phosphorylation of the protein were introduced and crystal structures of the corresponding single and double mutants were determined, which suggest that the C-terminal phosphorylation site (Thr188) exerts the greatest effects on the protein structure. Extensive NMR studies were also conducted, which demonstrate that the wild-type protein predominantly adopts a more open conformation in solution than the crystallographic studies have indicated and, accordingly, normal-mode dynamic simulations suggest that it has considerably greater capacity for flexible motion than the X-ray studies had suggested. Like calmodulin, calexcitin consists of four EF-hand motifs, although only the first three EF-hands of calexcitin are involved in binding calcium ions; the C-terminal EF-hand lacks the appropriate amino acids. Hence, calexcitin possesses two functional EF-hands in close proximity in its N-terminal domain and one functional calcium site in its C-terminal domain. There is evidence that the protein has two markedly different affinities for calcium ions, the weaker of which is most likely to be associated with binding of calcium ions to the protein during neuronal excitation. In the current study, site-directed mutagenesis has been used to abolish each of the three calcium-binding sites of calexcitin, and these experiments suggest that it is the single calcium-binding site in the C-terminal domain of the protein which is likely to have a sensory role in the neuron.
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Affiliation(s)
- P T Erskine
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - A Fokas
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - C Muriithi
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - H Rehman
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - L A Yates
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - A Bowyer
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - I S Findlow
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - R Hagan
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - J M Werner
- Centre of Biological Sciences, University of Southampton, Southampton SO17 1BJ, England
| | - A J Miles
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, England
| | - S A Wells
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, England
| | - S P Wood
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
| | - J B Cooper
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England
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10
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Pang C, Cao T, Li J, Jia M, Zhang S, Ren S, An H, Zhan Y. Combining fragment homology modeling with molecular dynamics aims at prediction of Ca²⁺ binding sites in CaBPs. J Comput Aided Mol Des 2013; 27:697-705. [PMID: 23934058 DOI: 10.1007/s10822-013-9668-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/31/2013] [Indexed: 11/28/2022]
Abstract
The family of calcium-binding proteins (CaBPs) consists of dozens of members and contributes to all aspects of the cell's function, from homeostasis to learning and memory. However, the Ca²⁺-binding mechanism is still unclear for most of CaBPs. To identify the Ca²⁺-binding sites of CaBPs, this study presented a computational approach which combined the fragment homology modeling with molecular dynamics simulation. For validation, we performed a two-step strategy as follows: first, the approach is used to identify the Ca²⁺-binding sites of CaBPs, which have the EF-hand Ca²⁺-binding site and the detailed binding mechanism. To accomplish this, eighteen crystal structures of CaBPs with 49 Ca²⁺-binding sites are selected to be analyzed including calmodulin. The computational method identified 43 from 49 Ca²⁺-binding sites. Second, we performed the approach to large-conductance Ca²⁺-activated K⁺ (BK) channels which don't have clear Ca²⁺-binding mechanism. The simulated results are consistent with the experimental data. The computational approach may shed some light on the identification of Ca²⁺-binding sites in CaBPs.
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Affiliation(s)
- ChunLi Pang
- Institute of Biophysics, Hebei University of Technology, Tianjin, China
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11
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Cox JA. Divers models of divalent cation interaction to calcium-binding proteins: techniques and anthology. Methods Mol Biol 2013; 963:15-35. [PMID: 23296602 DOI: 10.1007/978-1-62703-230-8_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Intracellular Ca(2+)-binding proteins (CaBPs) are sensors of the calcium signal and several of them even shape the signal. Most of them are equipped with at least two EF-hand motifs designed to bind Ca(2+). Their affinities are very variable, can display cooperative effects, and can be modulated by physiological Mg(2+) concentrations. These binding phenomena are monitored by four major techniques: equilibrium dialysis, fluorimetry with fluorescent Ca(2+) indicators, flow dialysis, and isothermal titration calorimetry. In the last quarter of the twentieth century reports on the ion-binding characteristics of several abundant wild-type CaBPs were published. With the advent of recombinant CaBPs it became possible to determine these properties on previously inaccessible proteins. Here I report on studies by our group carried out in the last decade on eight families of recombinant CaBPs, their mutants, or truncated domains. Moreover this chapter deals with the currently used methods for quantifying the binding of Ca(2+) and Mg(2+) to CaBPs.
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Affiliation(s)
- Jos A Cox
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.
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Zhao X, Pang H, Wang S, Zhou W, Yang K, Bartlam M. Structural basis for prokaryotic calcium-mediated regulation by a Streptomyces coelicolor calcium binding protein. Protein Cell 2010; 1:771-9. [PMID: 21203918 PMCID: PMC4875191 DOI: 10.1007/s13238-010-0085-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 06/10/2010] [Indexed: 01/07/2023] Open
Abstract
The important and diverse regulatory roles of Ca(2+) in eukaryotes are conveyed by the EF-hand containing calmodulin superfamily. However, the calcium-regulatory proteins in prokaryotes are still poorly understood. In this study, we report the three-dimensional structure of the calcium-binding protein from Streptomyces coelicolor, named CabD, which shares low sequence homology with other known helix-loop-helix EF-hand proteins. The CabD structure should provide insights into the biological role of the prokaryotic calcium-binding proteins. The unusual structural features of CabD compared with prokaryotic EF-hand proteins and eukaryotic sarcoplasmic calcium-binding proteins, including the bending conformation of the first C-terminal α-helix, unpaired ligand-binding EF-hands and the lack of the extreme C-terminal loop region, suggest it may have a distinct and significant function in calcium-mediated bacterial physiological processes, and provide a structural basis for potential calcium-mediated regulatory roles in prokaryotes.
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Affiliation(s)
- Xiaoyan Zhao
- Laboratory of Structural Biology, Tsinghua University, Beijing, 100084 China
| | - Hai Pang
- Laboratory of Structural Biology, Tsinghua University, Beijing, 100084 China
| | - Shenglan Wang
- Center for Microbial Metabolism and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Weihong Zhou
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Keqian Yang
- Center for Microbial Metabolism and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Mark Bartlam
- Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin, 300071 China
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Garcia L, Saraiva Garcia CH, Calábria LK, Costa Nunes da Cruz G, Sánchez Puentes A, Báo SN, Fontes W, Ricart CAO, Salmen Espindola F, Valle de Sousa M. Proteomic Analysis of Honey Bee Brain upon Ontogenetic and Behavioral Development. J Proteome Res 2009; 8:1464-73. [DOI: 10.1021/pr800823r] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Liudy Garcia
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Carlos H. Saraiva Garcia
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Luciana Karen Calábria
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Gabriel Costa Nunes da Cruz
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Aniel Sánchez Puentes
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Sonia N. Báo
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Wagner Fontes
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Carlos A. O. Ricart
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Foued Salmen Espindola
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
| | - Marcelo Valle de Sousa
- Mass Spectrometry Group, Physics Department, CEADEN, Havana, Cuba, Brazilian Center for Protein Research, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil, Genetic and Biochemistry Institute, Federal University of Uberlândia, Uberlândia, MG, Brazil, Department for Proteome Analysis, CIGB, Havana, Cuba, and Laboratory of Electron Microscopy, Department of Cell Biology, University of Brasília, Brasília, DF, Brazil
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